TY  - JOUR
AB  - Histone post-translational modifications (PTMs) are crucial to eukaryotic genome regulation, with a range of reported functions and mechanisms of action. Though often studied individually, it has long been recognized that the modifications function by combinatorial synergy or antagonism. Interplay may involve PTMs on the same histone, within the same nucleosome (containing a histone octamer), or between nucleosomes in higher-order chromatin. Given this, the field must distinguish ever greater complexity, and the context in which it is studied, with brevity and precision. The proteoform was introduced to define individual forms of a protein by sequence and PTMs, followed by the nucleoform to describe the particular gathering of histones within an individual nucleosome. There is now a need to define specific forms of these entities in prose while providing space for experimental nuance. To this end, we introduce a nomenclature that can express discrete PTMs, proteoforms, nucleoforms, or situations where defined PTMs exist in an uncertain context. Though specifically designed for the chromatin field, adaptions of the framework could be used to describe—and thus dissect—how proteoforms are configured in functionally distinct complexes across biology.
AU  - Keogh, M.C.*
AU  - Almouzni, G.*
AU  - Andrews, A.J.*
AU  - Armache, K.J.*
AU  - Arrowsmith, C.H.*
AU  - Baek, S.H.*
AU  - Bedford, M.T.*
AU  - Bernstein, E.*
AU  - Côté, J.-A.*
AU  - David, Y.*
AU  - Denu, J.M.*
AU  - Fierz, B.*
AU  - Garcia, B.A.*
AU  - Glass, K.C.*
AU  - Gozani, O.*
AU  - Helin, K.*
AU  - Henikoff, S.*
AU  - Jensen, O.N.*
AU  - Josefowicz, S.Z.*
AU  - Kelleher, N.L.*
AU  - Kutateladze, T.G.*
AU  - Lindner, H.H.*
AU  - Lu, C.*
AU  - Luger, K.*
AU  - Mallick, P.*
AU  - Musselman, C.A.*
AU  - Muir, T.W.*
AU  - Pasa-Tolic, L.*
AU  - Schneider, R.
AU  - Shi, X.*
AU  - Shi, Y.*
AU  - Sidoli, S.*
AU  - Smith, L.M.*
AU  - Tyler, J.K.*
AU  - Wolberger, C.*
AU  - Workman, J.L.*
AU  - Strahl, B.D.*
AU  - Young, N.L.*
C1  - 75705
C2  - 57997
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 3554-3561
TI  - A needed nomenclature for nucleosomes.
JO  - Mol. Cell
VL  - 85
IS  - 19
PB  - Cell Press
PY  - 2025
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - In contrast to the well-understood role of core histones in DNA packaging, the function of the linker histone (H1) remains enigmatic. Challenging the prevailing view that linker histones are a general feature of heterochromatin, here we show a critical requirement for H1 in Polycomb repressive complex 2 (PRC2) function. A CRISPR-Cas9 genetic screen using a fluorescent PRC2 reporter identified an essential role for the poorly characterized gene CRAMP1 in PRC2-mediated repression. CRAMP1 localizes to the promoters of expressed H1 genes and positively regulates their transcription. CRAMP1 ablation simultaneously depletes all linker histones, which results in selective decompaction of H3K27me3-marked loci and derepression of PRC2 target genes without concomitant loss of PRC2 occupancy or enzymatic activity. Strikingly, we find that linker histones preferentially localize to genomic loci marked by H3K27me3 across diverse cell types and organisms. Altogether, these data demonstrate a prominent role for linker histones in epigenetic repression by PRC2.
AU  - Matthews, R.E.*
AU  - Danac, J.M.C.*
AU  - Naden, E.L.*
AU  - Farleigh Smith, L.E.*
AU  - Lestari, S.*
AU  - Gungi, A.*
AU  - Appert, A.*
AU  - Buttress, T.*
AU  - Verma, A.*
AU  - Sinclair, O.*
AU  - Chong, F.
AU  - Suberu, J.*
AU  - Antrobus, R.*
AU  - Bonev, B.
AU  - Dawson, M.A.*
AU  - Reid, A.J.*
AU  - Timms, R.T.*
AU  - Ahringer, J.*
AU  - Tchasovnikarova, I.A.*
C1  - 74933
C2  - 57762
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 2503-2516.e8
TI  - CRAMP1 drives linker histone expression to enable Polycomb repression.
JO  - Mol. Cell
VL  - 85
IS  - 13
PB  - Cell Press
PY  - 2025
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Oligoadenylate synthetase (OAS) proteins are immune sensors for double-stranded RNA and are critical for restricting viruses. OAS2 comprises two OAS domains, only one of which can synthesize 2'-5'-oligoadenylates for RNase L activation. Existing structures of OAS1 provide a model for enzyme activation, but they do not explain how multiple OAS domains discriminate RNA length. Here, we discover that human OAS2 exists in an auto-inhibited state as a zinc-mediated dimer and present a mechanism for RNA length discrimination: the catalytically deficient domain acts as a molecular ruler that prevents autoreactivity to short RNAs. We demonstrate that dimerization and myristoylation localize OAS2 to Golgi membranes and that this is required for OAS2 activation and the restriction of viruses that exploit the endomembrane system for replication, e.g., coronaviruses. Finally, our results highlight the non-redundant role of OAS proteins and emphasize the clinical relevance of OAS2 by identifying a patient with a loss-of-function mutation associated with autoimmune disease.
AU  - Merold, V.*
AU  - Bekere, I.*
AU  - Kretschmer, S.*
AU  - Schnell, A.F.*
AU  - Kmiec, D.*
AU  - Sivarajan, R.*
AU  - Lammens, K.*
AU  - Liu, R.*
AU  - Mergner, J.*
AU  - Teppert, J.*
AU  - Hirschenberger, M.*
AU  - Henrici, A.*
AU  - Hammes, S.*
AU  - Buder, K.*
AU  - Weitz, M.*
AU  - Hackmann, K.*
AU  - Koenig, L.M.*
AU  - Pichlmair, A.
AU  - Schwierz, N.*
AU  - Sparrer, K.M.J.*
AU  - Lee-Kirsch, M.A.*
AU  - de Oliveira Mann, C.C.*
C1  - 74798
C2  - 57597
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 2176-2193.e13
TI  - Structural basis for OAS2 regulation and its antiviral function.
JO  - Mol. Cell
VL  - 85
IS  - 11
PB  - Cell Press
PY  - 2025
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The yeast glucose-induced degradation-deficient (GID) E3 ubiquitin ligase forms a suite of complexes with interchangeable receptors that selectively recruit N-terminal degron motifs of metabolic enzyme substrates. The orthologous higher eukaryotic C-terminal to LisH (CTLH) E3 complex has been proposed to also recognize substrates through an alternative subunit, WDR26, which promotes the formation of supramolecular CTLH E3 assemblies. Here, we discover that human WDR26 binds the metabolic enzyme nicotinamide/nicotinic-acid-mononucleotide-adenylyltransferase 1 (NMNAT1) and mediates its CTLH E3-dependent ubiquitylation independently of canonical GID/CTLH E3-family substrate receptors. The CTLH subunit YPEL5 inhibits NMNAT1 ubiquitylation and cellular turnover by WDR26-CTLH E3, thereby affecting NMNAT1-mediated metabolic activation and cytotoxicity of the prodrug tiazofurin. Cryoelectron microscopy (cryo-EM) structures of NMNAT1- and YPEL5-bound WDR26-CTLH E3 complexes reveal an internal basic degron motif of NMNAT1 essential for targeting by WDR26-CTLH E3 and degron mimicry by YPEL5's N terminus antagonizing substrate binding. Thus, our data provide a mechanistic understanding of how YPEL5-WDR26-CTLH E3 acts as a modulator of NMNAT1-dependent metabolism.
AU  - Gottemukkala, K.V.*
AU  - Chrustowicz, J.*
AU  - Sherpa, D.*
AU  - Sepic, S.*
AU  - Vu, D.T.*
AU  - Karayel, Ö.*
AU  - Papadopoulou, E.C.*
AU  - Gross, A.*
AU  - Schorpp, K.
AU  - von Gronau, S.*
AU  - Hadian, K.
AU  - Murray, P.J.*
AU  - Mann, M.*
AU  - Schulman, B.A.*
AU  - Alpi, A.F.*
C1  - 70700
C2  - 55719
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 1948-1963.e11
TI  - Non-canonical substrate recognition by the human WDR26-CTLH E3 ligase regulates prodrug metabolism.
JO  - Mol. Cell
VL  - 84
IS  - 10
PB  - Cell Press
PY  - 2024
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Selenium-dependent glutathione peroxidase 4 (GPX4) is the guardian of ferroptosis, preventing unrestrained (phospho)lipid peroxidation by reducing phospholipid hydroperoxides (PLOOH). However, the contribution of other phospholipid peroxidases in ferroptosis protection remains unclear. We show that cells lacking GPX4 still exhibit substantial PLOOH-reducing capacity, suggesting a contribution of alternative PLOOH peroxidases. By scrutinizing potential candidates, we found that although overexpression of peroxiredoxin 6 (PRDX6), a thiol-specific antioxidant enzyme with reported PLOOH-reducing activity, failed to prevent ferroptosis, its genetic loss sensitizes cancer cells to ferroptosis. Mechanistically, we uncover that PRDX6, beyond its known peroxidase activity, acts as a selenium-acceptor protein, facilitating intracellular selenium utilization and efficient selenium incorporation into selenoproteins, including GPX4. Its physiological significance was demonstrated by reduced GPX4 expression in Prdx6-deficient mouse brains and increased sensitivity to ferroptosis in PRDX6-deficient tumor xenografts in mice. Our study highlights PRDX6 as a critical player in directing cellular selenium utilization and dictating ferroptosis sensitivity.
AU  - Ito, J.
AU  - Nakamura, T.
AU  - Toyama, T.*
AU  - Chen, D.
AU  - Berndt, C.*
AU  - Poschmann, G.*
AU  - Mourao, A.
AU  - Doll, S.
AU  - Suzuki, M.*
AU  - Zhang, W.
AU  - Zheng, J.
AU  - Trümbach, D.
AU  - Yamada, N.
AU  - Ono, K.
AU  - Yazaki, M.*
AU  - Kawai, Y.*
AU  - Arisawa, M.*
AU  - Ohsaki, Y.*
AU  - Shirakawa, H.*
AU  - Wahida, A.
AU  - Proneth, B.
AU  - Saito, Y.*
AU  - Nakagawa, K.*
AU  - Mishima, E.
AU  - Conrad, M.
C1  - 72381
C2  - 56605
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 4629-4644.e9
TI  - PRDX6 dictates ferroptosis sensitivity by directing cellular selenium utilization.
JO  - Mol. Cell
VL  - 84
IS  - 23
PB  - Cell Press
PY  - 2024
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Two recent studies in Molecular Cell1 and Nature2 show that evicted RNA polymerases reassociate rapidly with post-replicative chromatin and proceed into an unusual transcription cycle, bypassing regular controls and creating a temporary window for altered gene expression.
AU  - Werner, M.
AU  - Hamperl, S.
C1  - 69813
C2  - 55261
SP  - 186-188
TI  - A quick restart: RNA polymerase jumping onto post-replicative chromatin.
JO  - Mol. Cell
VL  - 84
IS  - 2
PY  - 2024
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the multidomain RNA-binding protein FUBP1 as a key splicing factor that binds to a hitherto unknown cis-regulatory motif. By collecting NMR, structural, and in vivo interaction data, we demonstrate that FUBP1 stabilizes U2AF2 and SF1, key components at the 3' splice site, through multivalent binding interfaces located within its disordered regions. Transcriptional profiling and kinetic modeling reveal that FUBP1 is required for efficient splicing of long introns, which is impaired in cancer patients harboring FUBP1 mutations. Notably, FUBP1 interacts with numerous U1 snRNP-associated proteins, suggesting a unique role for FUBP1 in splice site bridging for long introns. We propose a compelling model for 3' splice site recognition of long introns, which represent 80% of all human introns.
AU  - Ebersberger, S.*
AU  - Hipp, C.
AU  - Mulorz, M.M.*
AU  - Buchbender, A.*
AU  - Hubrich, D.*
AU  - Kang, H.-S.
AU  - Martinez Lumbreras, S.
AU  - Kristofori, P.*
AU  - Sutandy, F.X.R.*
AU  - Llacsahuanga Allcca, L.*
AU  - Schönfeld, J.*
AU  - Bakisoglu, C.*
AU  - Busch, A.*
AU  - Hänel, H.*
AU  - Tretow, K.*
AU  - Welzel, M.*
AU  - Di Liddo, A.*
AU  - Möckel, M.M.*
AU  - Zarnack, K.*
AU  - Ebersberger, I.*
AU  - Legewie, S.*
AU  - Luck, K.*
AU  - Sattler, M.
AU  - König, J.*
C1  - 68057
C2  - 54535
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 2653-2672.e15
TI  - FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns.
JO  - Mol. Cell
VL  - 83
IS  - 15
PB  - Cell Press
PY  - 2023
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - In this issue of Molecular Cell, Crozier et al.,1 Foy et al.,2 Manohar et al.,3 and Wilson et al.4 show how excessive cell growth caused by a temporary G1 arrest leads to permanent cell cycle exit at different stages of the cell cycle.
AU  - Khurana, A.
AU  - Chadha, Y.
AU  - Schmoller, K.M.
C1  - 68765
C2  - 54975
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 3946-3947
TI  - Too big not to fail: Different paths lead to senescence of enlarged cells.
JO  - Mol. Cell
VL  - 83
IS  - 22
PB  - Cell Press
PY  - 2023
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - In the eukaryotic cytosol, the Hsp70 and the Hsp90 chaperone machines work in tandem with the maturation of a diverse array of client proteins. The transfer of nonnative clients between these systems is essential to the chaperoning process, but how it is regulated is still not clear. We discovered that NudC is an essential transfer factor with an unprecedented mode of action: NudC interacts with Hsp40 in Hsp40-Hsp70-client complexes and displaces Hsp70. Then, the interaction of NudC with Hsp90 allows the direct transfer of Hsp40-bound clients to Hsp90 for further processing. Consistent with this mechanism, NudC increases client activation in vitro as well as in cells and is essential for cellular viability. Together, our results show the complexity of the cooperation between the major chaperone machineries in the eukaryotic cytosol.
AU  - Biebl, M.M.*
AU  - Delhommel, F.
AU  - Faust, O.*
AU  - Zak, K.M.
AU  - Agam, G.*
AU  - Guo, X.*
AU  - Mühlhofer, M.*
AU  - Dahiya, V.*
AU  - Hillebrand, D.*
AU  - Popowicz, G.M.
AU  - Kampmann, M.*
AU  - Lamb, D.C.*
AU  - Rosenzweig, R.*
AU  - Sattler, M.
AU  - Buchner, J.*
C1  - 64217
C2  - 51797
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 555-569.e7
TI  - NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems.
JO  - Mol. Cell
VL  - 82
IS  - 3
PB  - Cell Press
PY  - 2022
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Ferroptosis is a unique type of non-apoptotic cell death resulting from the unrestrained occurrence of peroxidized phospholipids, which are subject to iron-mediated production of lethal oxygen radicals. This cell death modality has been detected across many organisms, including in mammals, where it can be used as a defense mechanism against pathogens or even harnessed by T cells to sensitize tumor cells toward effective killing. Conversely, ferroptosis is considered one of the main cell death mechanisms promoting degenerative diseases. Emerging evidence suggests that ferroptosis represents a vulnerability in certain cancers. Here, we critically review recent advances linking ferroptosis vulnerabilities of dedifferentiating and persister cancer cells to the dependency of these cells on iron, a potential Achilles heel for small-molecule intervention. We provide a perspective on the mechanisms reliant on iron that contribute to the persister cancer cell state and how this dependency may be exploited for therapeutic benefits.
AU  - Rodriguez, R.*
AU  - Schreiber, S.L.*
AU  - Conrad, M.
C1  - 64026
C2  - 51661
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 728-740
TI  - Persister cancer cells: Iron addiction and vulnerability to ferroptosis.
JO  - Mol. Cell
VL  - 82
IS  - 4
PB  - Cell Press
PY  - 2022
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.
AU  - Gjaltema, R.A.F.*
AU  - Schwämmle, T.*
AU  - Kautz, P.*
AU  - Robson, M.*
AU  - Schöpflin, R.*
AU  - Ravid Lustig, L.*
AU  - Brandenburg, L.O.*
AU  - Dunkel, I.*
AU  - Vechiatto, C.*
AU  - Ntini, E.*
AU  - Mutzel, V.*
AU  - Schmiedel, V.*
AU  - Marsico, A.
AU  - Mundlos, S.*
AU  - Schulz, E.G.*
C1  - 63891
C2  - 51737
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 190-208.e17
TI  - Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus.
JO  - Mol. Cell
VL  - 82
IS  - 1
PB  - Cell Press
PY  - 2021
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - DNA replication initiates at genomic locations known as origins of replication, which, in S. cerevisiae, share a common DNA consensus motif. Despite being virtually nucleosome-free, origins of replication are greatly influenced by the surrounding chromatin state. Here, we show that histone H3 lysine 37 mono-methylation (H3K37me1) is catalyzed by Set1p and Set2p and that it regulates replication origin licensing. H3K37me1 is uniformly distributed throughout most of the genome, but it is scarce at replication origins, where it increases according to the timing of their firing. We find that H3K37me1 hinders Mcm2 interaction with chromatin, maintaining low levels of MCM outside of conventional replication origins. Lack of H3K37me1 results in defective DNA replication from canonical origins while promoting replication events at inefficient and non-canonical sites. Collectively, our results indicate that H3K37me1 ensures correct execution of the DNA replication program by protecting the genome from inappropriate origin licensing and spurious DNA replication.
AU  - Santos-Rosa, H.*
AU  - Millán-Zambrano, G.*
AU  - Han, N.*
AU  - Leonardi, T.*
AU  - Klimontova, M.*
AU  - Nasiscionyte, S.
AU  - Pandolfini, L.*
AU  - Tzelepis, K.*
AU  - Bartke, T.
AU  - Kouzarides, T.*
C1  - 62035
C2  - 50580
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 2793-2807.e8
TI  - Methylation of histone H3 at lysine 37 by Set1 and Set2 prevents spurious DNA replication.
JO  - Mol. Cell
VL  - 81
IS  - 13
PB  - Cell Press
PY  - 2021
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Mitochondria contain a specific translation machinery for the synthesis of mitochondria-encoded respiratory chain components. Mitochondrial tRNAs (mt-tRNAs) are also generated from the mitochondrial DNA and, similar to their cytoplasmic counterparts, are post-transcriptionally modified. Here, we find that the RNA methyltransferase METTL8 is a mitochondrial protein that facilitates 3-methyl-cytidine (m3C) methylation at position C32 of the mt-tRNASer(UCN) and mt-tRNAThr. METTL8 knockout cells show a reduction in respiratory chain activity, whereas overexpression increases activity. In pancreatic cancer, METTL8 levels are high, which correlates with lower patient survival and an enhanced respiratory chain activity. Mitochondrial ribosome profiling uncovered mitoribosome stalling on mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons. Further analysis of the respiratory chain complexes using mass spectrometry revealed reduced incorporation of the mitochondrially encoded proteins ND6 and ND1 into complex I. The well-balanced translation of mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons through METTL8-mediated m3C32 methylation might, therefore, facilitate the optimal composition and function of the mitochondrial respiratory chain.
AU  - Schöller, E.*
AU  - Marks, J.*
AU  - Marchand, V.*
AU  - Bruckmann, A.*
AU  - Powell, C.A.*
AU  - Reichold, M.*
AU  - Mutti, C.D.*
AU  - Dettmer, K.*
AU  - Feederle, R.
AU  - Hüttelmaier, S.*
AU  - Helm, M.*
AU  - Oefner, P.*
AU  - Minczuk, M.*
AU  - Motorin, Y.*
AU  - Hafner, M.*
AU  - Meister, G.*
C1  - 63657
C2  - 51504
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 4810-4825.e12
TI  - Balancing of mitochondrial translation through METTL8-mediated m3C modification of mitochondrial tRNAs.
JO  - Mol. Cell
VL  - 81
IS  - 23
PB  - Cell Press
PY  - 2021
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - A number of regulatory factors are recruited to chromatin by specialized RNAs. Whether RNA has a more general role in regulating the interaction of proteins with chromatin has not been determined. We used proteomics methods to measure the global impact of nascent RNA on chromatin in embryonic stem cells. Surprisingly, we found that nascent RNA primarily antagonized the interaction of chromatin modifiers and transcriptional regulators with chromatin. Transcriptional inhibition and RNA degradation induced recruitment of a set of transcriptional regulators, chromatin modifiers, nucleosome remodelers, and regulators of higher-order structure. RNA directly bound to factors, including BAF, NuRD, EHMT1, and INO80 and inhibited their interaction with nucleosomes. The transcriptional elongation factor P-TEFb directly bound pre-mRNA, and its recruitment to chromatin upon Pol II inhibition was regulated by the 7SK ribonucleoprotein complex. We postulate that by antagonizing the interaction of regulatory proteins with chromatin, nascent RNA links transcriptional output with chromatin composition.
AU  - Skalska, L.*
AU  - Begley, V.*
AU  - Beltran, M.*
AU  - Lukauskas, S.
AU  - Khandelwal, G.*
AU  - Faull, P.*
AU  - Bhamra, A.*
AU  - Tavares, M.*
AU  - Wellman, R.*
AU  - Tvardovskiy, A.
AU  - Foster, B.
AU  - Ruiz de Los Mozos, I.*
AU  - Herrero, J.*
AU  - Surinova, S.*
AU  - Snijders, A.P.*
AU  - Bartke, T.
AU  - Jenner, R.G.*
C1  - 62463
C2  - 50831
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 2944-2959.e10
TI  - Nascent RNA antagonizes the interaction of a set of regulatory proteins with chromatin.
JO  - Mol. Cell
VL  - 81
IS  - 14
PB  - Cell Press
PY  - 2021
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 "sub-scales" with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that transcriptional control uncouples Whi5 synthesis from cell size, and we identify histones as the major class of sub-scaling transcripts besides WHI5 by screening for similar genes. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to newborn cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each newborn cell regardless of cell size. Disrupting both Whi5 synthesis and chromatin-based partitioning weakens G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.
AU  - Swaffer, M.P.*
AU  - Kim, J.*
AU  - Chandler-Brown, D.*
AU  - Langhinrichs, M.*
AU  - Marinov, G.K.*
AU  - Greenleaf, W.J.*
AU  - Kundaje, A.*
AU  - Schmoller, K.M.
AU  - Skotheim, J.M.*
C1  - 63416
C2  - 51427
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 4861-4875.e7
TI  - Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size.
JO  - Mol. Cell
VL  - 81
IS  - 23
PB  - Cell Press
PY  - 2021
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Transcriptional memory of gene expression enables adaptation to repeated stimuli across many organisms. However, the regulation and heritability of transcriptional memory in single cells and through divisions remains poorly understood. Here, we combined microfluidics with single-cell live imaging to monitor Saccharomyces cerevisiae galactokinase 1 (GAL1) expression over multiple generations. By applying pedigree analysis, we dissected and quantified the maintenance and inheritance of transcriptional reinduction memory in individual cells through multiple divisions. We systematically screened for loss- and gain-of-memory knockouts to identify memory regulators in thousands of single cells. We identified new loss-of-memory mutants, which affect memory inheritance into progeny. We also unveiled a gain-of-memory mutant, elp6 Delta, and suggest that this new phenotype can be mediated through decreased histone occupancy at the GAL1 promoter. Our work uncovers principles of maintenance and inheritance of gene expression states and their regulators at the single-cell level.
AU  - Bheda, P.
AU  - Aguilar-Gomez, D.
AU  - Becker, N.B.*
AU  - Becker, J.*
AU  - Stavrou, E.*
AU  - Kukhtevich, I.
AU  - Höfer, T.*
AU  - Maerkl, S.*
AU  - Charvin, G.*
AU  - Marr, C.
AU  - Kirmizis, A.*
AU  - Schneider, R.
C1  - 59197
C2  - 48724
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 915-925
TI  - Single-cell tracing dissects regulation of maintenance and inheritance of transcriptional reinduction memory.
JO  - Mol. Cell
VL  - 78
IS  - 5
PB  - Cell Press
PY  - 2020
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Mutations in the methyl-DNA-binding repressor protein MeCP2 cause the devastating neurodevelopmental disorder Rett syndrome. It has been challenging to understand how MeCP2 regulates transcription because MeCP2 binds broadly across the genome and MeCP2 mutations are associated with widespread small-magnitude changes in neuronal gene expression. We demonstrate here that MeCP2 represses nascent RNA transcription of highly methylated long genes in the brain through its interaction with the NCoR co-repressor complex. By measuring the rates of transcriptional initiation and elongation directly in the brain, we find that MeCP2 has no measurable effect on transcriptional elongation, but instead represses the rate at which Pol II initiates transcription of highly methylated long genes. These findings suggest a new model of MeCP2 function in which MeCP2 binds broadly across highly methylated regions of DNA, but acts at transcription start sites to attenuate transcriptional initiation.
AU  - Boxer, L.D.*
AU  - Renthal, W.*
AU  - Greben, A.W.*
AU  - Whitwam, T.*
AU  - Silberfeld, A.*
AU  - Stroud, H.*
AU  - Li, E.*
AU  - Yang, M.G.*
AU  - Kinde, B.*
AU  - Griffith, E.C.*
AU  - Bonev, B.
AU  - Greenberg, M.E.*
C1  - 57858
C2  - 47982
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 294-309.e9
TI  - MeCP2 represses the rate of transcriptional initiation of highly methylated long genes.
JO  - Mol. Cell
VL  - 77
IS  - 2
PB  - Cell Press
PY  - 2020
SN  - 1097-2765
ER  - 

TY  - JOUR
AU  - Minina, E.A.*
AU  - Staal, J.*
AU  - Alvarez, V.E.*
AU  - Berges, J.A.*
AU  - Berman-Frank, I.*
AU  - Beyaert, R.*
AU  - Bidle, K.D.*
AU  - Bornancin, F.*
AU  - Casanova, M.*
AU  - Cazzulo, J.J.*
AU  - Choi, C.J.*
AU  - Coll, N.S.*
AU  - Dixit, V.M.*
AU  - Dolinar, M.*
AU  - Fasel, N.*
AU  - Funk, C.*
AU  - Gallois, P.*
AU  - Gevaert, K.*
AU  - Gutierrez-Beltran, E.*
AU  - Hailfinger, S.*
AU  - Klemenčič, M.*
AU  - Koonin, E.V.*
AU  - Krappmann, D.
AU  - Linusson, A.*
AU  - Machado, M.F.M.*
AU  - Madeo, F.*
AU  - Megeney, L.A.*
AU  - Moschou, P.N.*
AU  - Mottram, J.C.*
AU  - Nyström, T.*
AU  - Osiewacz, H.D.*
AU  - Overall, C.M.*
AU  - Pandey, K.C.*
AU  - Ruland, J.*
AU  - Salvesen, G.S.*
AU  - Shi, Y.*
AU  - Smertenko, A.*
AU  - Stael, S.*
AU  - Ståhlberg, J.*
AU  - Suárez, M.F.*
AU  - Thome, M.*
AU  - Tuominen, H.*
AU  - van Breusegem, F.*
AU  - van der Hoorn, R.A.L.*
AU  - Vardi, A.*
AU  - Zhivotovsky, B.*
AU  - Lam, E.*
AU  - Bozhkov, P.V.*
C1  - 58525
C2  - 48136
SP  - 927-929
TI  - Classification and nomenclature of metacaspases and paracaspases: No more confusion with caspases.
JO  - Mol. Cell
VL  - 77
IS  - 5
PY  - 2020
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Repair of covalent DNA-protein crosslinks (DPCs) by DNA-dependent proteases has emerged as an essential genome maintenance mechanism required for cellular viability and tumor suppression. However, how proteolysis is restricted to the crosslinked protein while leaving surrounding chromatin proteins unharmed has remained unknown. Using defined DPC model substrates, we show that the DPC protease SPRTN displays strict DNA structure-specific activity. Strikingly, SPRTN cleaves DPCs at or in direct proximity to disruptions within double-stranded DNA. In contrast, proteins crosslinked to intact double- or single-stranded DNA are not cleaved by SPRTN. NMR spectroscopy data suggest that specificity is not merely affinity-driven but achieved through a flexible bipartite strategy based on two DNA binding interfaces recognizing distinct structural features. This couples DNA context to activation of the enzyme, tightly confining SPRTN's action to biologically relevant scenarios.
AU  - Reinking, H.K.*
AU  - Kang, H.-S.
AU  - Götz, M.J.*
AU  - Li, H.Y.*
AU  - Kieser, A.*
AU  - Zhao, S.*
AU  - Acampora, A.C.*
AU  - Weickert, P.*
AU  - Fessler, E.*
AU  - Jae, L.T.*
AU  - Sattler, M.
AU  - Stingele, J.*
C1  - 60050
C2  - 49194
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 102-113.e6
TI  - DNA structure-specific cleavage of DNA-protein crosslinks by the SPRTN protease.
JO  - Mol. Cell
VL  - 80
IS  - 1
PB  - Cell Press
PY  - 2020
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes, but strikingly, it also revealed putative internal start sites in a number of Escherichia coli genes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at internal in-frame and out-of-frame start sites, can be functionally important and contribute to the "alternative" bacterial proteome. The internal start sites may also play regulatory roles in gene expression.
AU  - Meydan, S.*
AU  - Marks, J.*
AU  - Klepacki, D.*
AU  - Sharma, V.
AU  - Baranov, P.V.*
AU  - Firth, A.E.*
AU  - Margus, T.*
AU  - Kefi, A.*
AU  - Vázquez-Laslop, N.*
AU  - Mankin, A.S.*
C1  - 55737
C2  - 46540
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 481-493.e6
TI  - Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome.
JO  - Mol. Cell
VL  - 74
IS  - 3
PB  - Cell Press
PY  - 2019
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.
AU  - Modic, M.
AU  - Grosch, M.
AU  - Rot, G.*
AU  - Schirge, S.
AU  - Lepko, T.
AU  - Yamazaki, T.*
AU  - Lee, F.C.Y.*
AU  - Rusha, E.
AU  - Shaposhnikov, D.
AU  - Palo, M.*
AU  - Merl-Pham, J.
AU  - Cacchiarelli, D.*
AU  - Rogelj, B.*
AU  - Hauck, S.M.
AU  - von Mering, C.*
AU  - Meissner, A.*
AU  - Lickert, H.
AU  - Hirose, T.*
AU  - Ule, J.*
AU  - Drukker, M.
C1  - 55973
C2  - 46660
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 951-965.e13
TI  - Cross-regulation between TDP-43 and paraspeckles promotes pluripotency-differentiation transition.
JO  - Mol. Cell
VL  - 74
IS  - 5
PB  - Cell Press
PY  - 2019
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The glucocorticoid receptor (GR) is a potent metabolic regulator and a major drug target. While GR is known to play integral roles in circadian biology, its rhythmic genomic actions have never been characterized. Here we mapped GR's chromatin occupancy in mouse livers throughout the day and night cycle. We show how GR partitions metabolic processes by time-dependent target gene regulation and controls circulating glucose and triglycerides differentially during feeding and fasting. Highlighting the dominant role GR plays in synchronizing circadian amplitudes, we find that the majority of oscillating genes are bound by and depend on GR. This rhythmic pattern is altered by high-fat diet in a ligand-independent manner. We find that the remodeling of oscillatory gene expression and postprandial GR binding results from a concomitant increase of STAT5 co-occupancy in obese mice. Altogether, our findings highlight GR's fundamental role in the rhythmic orchestration of hepatic metabolism.
AU  - Quagliarini, F.
AU  - Mir, A.A.
AU  - Balazs, K.
AU  - Wierer, M.*
AU  - Dyar, K.A.
AU  - Jouffe, C.
AU  - Makris, K.
AU  - Hawe, J.
AU  - Heinig, M.
AU  - Filipp, F.V.
AU  - Barish, G.D.*
AU  - Uhlenhaut, N.H.
C1  - 57120
C2  - 47663
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 531-545.e5
TI  - Cistromic reprogramming of the diurnal glucocorticoid hormone response by high-fat diet.
JO  - Mol. Cell
VL  - 76
IS  - 4
PB  - Cell Press
PY  - 2019
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The Hsp90 chaperone machinery in eukaryotes comprises a number of distinct accessory factors. Cns1 is one of the few essential co-chaperones in yeast, but its structure and function remained unknown. Here, we report the X-ray structure of the Cns1 fold and NMR studies on the partly disordered, essential segment of the protein. We demonstrate that Cns1 is important for maintaining translation elongation, specifically chaperoning the elongation factor eEF2. In this context, Cns1 interacts with the novel co-factor Hgh1 and forms a quaternary complex together with eEF2 and Hsp90. The in vivo folding and solubility of eEF2 depend on the presence of these proteins. Chaperoning of eEF2 by Cns1 is essential for yeast viability and requires a defined subset of the Hsp90 machinery as well as the identified eEF2 recruiting factor Hgh1.
AU  - Schopf, F.H.*
AU  - Huber, E.M.*
AU  - Dodt, C.*
AU  - Lopez, A.
AU  - Biebl, M.M.*
AU  - Rutz, D.A.*
AU  - Mühlhofer, M.*
AU  - Richter, G.*
AU  - Madl, T.*
AU  - Sattler, M.
AU  - Groll, M.*
AU  - Buchner, J.*
C1  - 55695
C2  - 46520
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 73-87.e8
TI  - The co-chaperone Cnsl and the recruiter protein Hgh1 Link Hsp90 to translation elongation via chaperoning elongation factor 2.
JO  - Mol. Cell
VL  - 74
IS  - 1
PB  - Cell Press
PY  - 2019
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The RING E3 ubiquitin ligase UHRF1 controls DNA methylation through its ability to target the maintenance DNA methyltransferase DNMT1 to newly replicated chromatin. DNMT1 recruitment relies on ubiquitylation of histone H3 by UHRF1; however, how UHRF1 deposits ubiquitin onto the histone is unknown. Here, we demonstrate that the ubiquitin-like domain (UBL) of UHRF1 is essential for RING-mediated H3 ubiquitylation. Using chemical crosslinking and mass spectrometry, biochemical assays, and recombinant chromatin substrates, we show that the UBL participates in structural rearrangements of UHRF1 upon binding to chromatin and the E2 ubiquitin conjugating enzyme UbcH5a/UBE2D1. Similar to ubiquitin, the UBL exerts its effects through a hydrophobic patch that contacts a regulatory surface on the "backside'' of the E2 to stabilize the E2-E3-chromatin complex. Our analysis of the enzymatic mechanism of UHRF1 uncovers an unexpected function of the UBL domain and defines a new role for this domain in DNMT1-dependent inheritance of DNA methylation.
AU  - Foster, B.
AU  - Stolz, P.*
AU  - Mulholland, C.B.*
AU  - Montoya, A.*
AU  - Kramer, H.*
AU  - Bultmann, S.*
AU  - Bartke, T.
C1  - 54666
C2  - 45753
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 739-752
TI  - Critical role of the UBL domain in stimulating the E3 ubiquitin ligase activity of UHRF1 toward chromatin.
JO  - Mol. Cell
VL  - 72
IS  - 4
PB  - Cell Press
PY  - 2018
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is composed of a repetition of YSPTSPS heptads and functions as a loading platform for protein complexes that regulate transcription, splicing, and maturation of RNAs. Here, we studied mammalian CTD mutants to analyze the function of tyrosine1 residues in the transcription cycle. Mutation of 3/4 of the tyrosine residues (YFFF mutant) resulted in a massive read-through transcription phenotype in the antisense direction of promoters as well as in the 3' direction several hundred kilobases downstream of genes. The YFFF mutant shows reduced Pol II at promoter-proximal pause sites, a loss of interaction with the Mediator and Integrator complexes, and impaired recruitment of these complexes to chromatin. Consistent with these observations, Pol II loading at enhancers and maturation of snRNAs are altered in the YFFF context genome-wide. We conclude that tyrosine1 residues of the CTD control termination of transcription by Pol II.
AU  - Shah, N.
AU  - Maqbool, M.A.*
AU  - Yahia, Y.*
AU  - El Aabidine, A.Z.*
AU  - Esnault, C.*
AU  - Forné, I.*
AU  - Decker, T.-M.
AU  - Martin, D.*
AU  - Schüller, R.
AU  - Krebs, S.*
AU  - Blum, H.*
AU  - Imhof, A.*
AU  - Eick, D.
AU  - Andrau, J.C.*
C1  - 52676
C2  - 44109
CY  - Cambridge
SP  - 48-61.e6
TI  - Tyrosine-1 of RNA polymerase II CTD controls global termination of gene transcription in mammals.
JO  - Mol. Cell
VL  - 69
IS  - 1
PB  - Cell Press
PY  - 2018
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The post-translational modification of key residues at the C-terminal domain of RNA polymerase II (RNAP2-CTD) coordinates transcription, splicing, and RNA processing by modulating its capacity to act as a landing platform for a variety of protein complexes. Here, we identify a new modification at the CTD, the deimination of arginine and its conversion to citrulline by peptidyl arginine deiminase 2 (PADI2), an enzyme that has been associated with several diseases, including cancer. We show that, among PADI family members, only PADI2 citrullinates R1810 (Cit1810) at repeat 31 of the CTD. Depletion of PADI2 or loss of R1810 results in accumulation of RNAP2 at transcription start sites, reduced gene expression, and inhibition of cell proliferation. Cit1810 is needed for interaction with the P-TEFb (positive transcription elongation factor b) kinase complex and for its recruitment to chromatin. In this way, CTD-Cit1810 favors RNAP2 pause release and efficient transcription in breast cancer cells.
AU  - Sharma, P.*
AU  - Lioutas, A.*
AU  - Fernandez-Fuentes, N.*
AU  - Quilez, J.*
AU  - Carbonell-Caballero, J.*
AU  - Wright, R.H.G.*
AU  - Di Vona, C.*
AU  - Le Dily, F.*
AU  - Schüller, R.
AU  - Eick, D.
AU  - Oliva, B.*
AU  - Beato, M.*
C1  - 54793
C2  - 45911
CY  - 50 Hampshire St, Floor 5, Cambridge, Ma 02139 Usa
SP  - 84-96
TI  - Arginine citrullination at the C-terminal domain controls RNA polymerase II transcription.
JO  - Mol. Cell
VL  - 73
IS  - 1
PB  - Cell Press
PY  - 2018
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The mitochondrial calcium uniporter complex is essential for calcium (Ca(2+)) uptake into mitochondria of all mammalian tissues, where it regulates bioenergetics, cell death, and Ca(2+) signal transduction. Despite its involvement in several human diseases, we currently lack pharmacological agents for targeting uniporter activity. Here we introduce a high-throughput assay that selects for human MCU-specific small-molecule modulators in primary drug screens. Using isolated yeast mitochondria, reconstituted with human MCU, its essential regulator EMRE, and aequorin, and exploiting a D-lactate- and mannitol/sucrose-based bioenergetic shunt that greatly minimizes false-positive hits, we identify mitoxantrone out of more than 600 clinically approved drugs as a direct selective inhibitor of human MCU. We validate mitoxantrone in orthogonal mammalian cell-based assays, demonstrating that our screening approach is an effective and robust tool for MCU-specific drug discovery and, more generally, for the identification of compounds that target mitochondrial functions.
AU  - Arduino, D.M.
AU  - Wettmarshausen, J.
AU  - Vais, H.*
AU  - Navas-Navarro, P.*
AU  - Cheng, Y.
AU  - Leimpek, A.
AU  - Ma, Z.*
AU  - Delrio-Lorenzo, A.*
AU  - Giordano, A.
AU  - Garcia-Perez, C.
AU  - Médard, G.*
AU  - Kuster, B.*
AU  - García-Sancho, J.*
AU  - Mokranjac, D.*
AU  - Foskett, J.K.*
AU  - Alonso, M.T.*
AU  - Perocchi, F.
C1  - 51732
C2  - 43461
CY  - Cambridge
SP  - 711-723.e7
TI  - Systematic identification of MCU modulators by orthogonal Iiterspecies chemical screening.
JO  - Mol. Cell
VL  - 67
IS  - 4
PB  - Cell Press
PY  - 2017
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron-transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function.
AU  - Floyd, B.J.*
AU  - Wilkerson, E.M.*
AU  - Veling, M.T.*
AU  - Minogue, C.E.*
AU  - Xia, C.*
AU  - Beebe, E.T.*
AU  - Wrobel, R.L.*
AU  - Cho, H.*
AU  - Kremer, L.S.
AU  - Alston, C.L.*
AU  - Gromek, K.A.*
AU  - Dolan, B.K.*
AU  - Ulbrich, A.*
AU  - Stefely, J.A.*
AU  - Bohl, S.L.*
AU  - Werner, K.M.*
AU  - Jochem, A.*
AU  - Westphall, M.S.*
AU  - Rensvold, J.W.*
AU  - Taylor, R.W.*
AU  - Prokisch, H.
AU  - Kim, J.P.*
AU  - Coon, J.J.*
AU  - Pagliarini, D.J.*
C1  - 49236
C2  - 33701
CY  - Cambridge
SP  - 621-632
TI  - Mitochondrial protein interaction mapping identifies regulators of respiratory chain function.
JO  - Mol. Cell
VL  - 63
IS  - 4
PB  - Cell Press
PY  - 2016
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) consists of heptad repeats with the consensus motif Y1-S2-P3-T4-S5-P6-S7. Dynamic phosphorylation of the CTD coordinates Pol II progression through the transcription cycle. Here, we use genetic and mass spectrometric approaches to directly detect and map phosphosites along the entire CTD. We confirm phosphorylation of CTD residues Y1, S2, T4, S5, and S7 in mammalian and yeast cells. Although specific phosphorylation signatures dominate, adjacent CTD repeats can be differently phosphorylated, leading to a high variation of coexisting phosphosites in mono- and di-heptad CTD repeats. Inhibition of CDK9 kinase specifically reduces S2 phosphorylation levels within the CTD.
AU  - Schüller, R.
AU  - Forne, I.*
AU  - Straub, T.*
AU  - Schreieck, A.*
AU  - Texier, Y.
AU  - Shah, N.
AU  - Decker, T.-M.
AU  - Cramer, P.*
AU  - Imhof, A.*
AU  - Eick, D.
C1  - 47730
C2  - 39547
CY  - Cambridge
SP  - 305-314
TI  - Heptad-specific phosphorylation of RNA polymerase II CTD.
JO  - Mol. Cell
VL  - 61
IS  - 2
PB  - Cell Press
PY  - 2016
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Proteolysis by aspartyl intramembrane proteases such as presenilin and signal peptide peptidase (SPP) underlies many cellular processes in health and disease. Saccharomyces cerevisiae encodes a homolog that we named yeast presenilin fold 1 (Ypf1), which we verify to be an SPP-type protease that localizes to the endoplasmic reticulum (ER). Our work shows that Ypf1 functionally interacts with the ER-associated degradation (ERAD) factors Dfm1 and Doa10 to regulate the abundance of nutrient transporters by degradation. We demonstrate how this noncanonical branch of the ERAD pathway, which we termed "ERAD regulatory" (ERAD-R), responds to ligand-mediated sensing as a trigger. More generally, we show that Ypf1-mediated posttranslational regulation of plasma membrane transporters is indispensible for early sensing and adaptation to nutrient depletion. The combination of systematic analysis alongside mechanistic details uncovers a broad role of intramembrane proteolysis in regulating secretome dynamics.
AU  - Avci, D.*
AU  - Fuchs, S.*
AU  - Schrul, B.*
AU  - Fukumori, A.*
AU  - Breker, M.*
AU  - Frumkin, I.*
AU  - Chen, C.Y.*
AU  - Biniossek, M.L.*
AU  - Kremmer, E.
AU  - Schilling, O.*
AU  - Steiner, H.*
AU  - Schuldiner, M.*
AU  - Lemberg, M.K.*
C1  - 42887
C2  - 35736
SP  - 630-640
TI  - The yeast ER-intramembrane protease Ypf1 refines nutrient sensing by regulating transporter abundance.
JO  - Mol. Cell
VL  - 56
IS  - 5
PY  - 2014
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Hsp90 is the most abundant molecular chaperone in the eukaryotic cell. One of the most stringent clients is the glucocorticoid receptor (GR), whose in vivo function strictly depends on the interaction with the Hsp90 machinery. However, the molecular mechanism of this interaction has been elusive. Here we have reconstituted the interaction of Hsp90 with hormone-bound GR using purified components. Our biochemical and structural analyses define the binding site for GR on Hsp90 and reveal that binding of GR modulates the conformational cycle of Hsp90. FRET experiments demonstrate that a partially closed form of the Hsp90 dimer is the preferred conformation for interaction. Consistent with this, the conformational cycle of Hsp90 is decelerated, and its ATPase activity decreases. Hsp90 cochaperones differentially affect formation of the Hsp90-GR complex, serving as control elements for cycle progression and revealing an intricate interplay of client and cochaperones as molecular modulators of the Hsp90 machine.
AU  - Lorenz, O.R.*
AU  - Freiburger, L.
AU  - Rutz, D.A.*
AU  - Krause, M.*
AU  - Zierer, B.K.*
AU  - Alvira, S.*
AU  - Cuéllar, J.*
AU  - Valpuesta, J.M.*
AU  - Madl, T.
AU  - Sattler, M.
AU  - Buchner, J.*
C1  - 30851
C2  - 33954
CY  - Cambridge
SP  - 941-953
TI  - Modulation of the Hsp90 chaperone cycle by a stringent client protein.
JO  - Mol. Cell
VL  - 53
IS  - 6
PB  - Cell Press
PY  - 2014
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - The HIV Nef protein recruits the polycomb protein Eed and mimics an integrin receptor signal for reasons that are not entirely clear. Here we demonstrate that Nef and Eed complex with the integrin effector paxillin to recruit and activate TNF alpha converting enzyme (TACE alias ADAM 17) and its close relative ADAM10. The activated proteases cleaved proTNF alpha and were shuttled into extracellular vesicles (EVs). Peripheral blood mononuclear cells that ingested these EVs released TNF alpha. Analyzing the mechanism, we found that Pak2, an established host cell effector of Nef, phosphorylated paxillin on Ser272/274 to induce TACE-paxillin association and shuttling into EVs via lipid rafts. Conversely, Pak1 phosphorylated paxillin on Ser258, which inhibited TACE association and lipid raft transfer. Interestingly, melanoma cells used an identical mechanism to shuttle predominantly ADAM10 into EVs. We conclude that HIV-1 and cancer cells exploit a paxillin/integrin-controlled mechanism to release TACE/ADAM10-containing vesicles, ensuring better proliferation/growth conditions in their microenvironment.
AU  - Lee, J.H.*
AU  - Wittki, S.*
AU  - Brau, T.*
AU  - Dreyer, F.S.*
AU  - Kratzel, K.*
AU  - Dindorf, J.*
AU  - Johnston, I.C.D.*
AU  - Gross, S.*
AU  - Kremmer, E.
AU  - Zeidler, R.*
AU  - Schlotzer-Schrehardt, U.*
AU  - Lichtenheld, M.*
AU  - Saksela, K.*
AU  - Harrer, T.*
AU  - Schuler, G.*
AU  - Federico, M.*
AU  - Baur, A.S.*
C1  - 23649
C2  - 31263
SP  - 668-679
TI  - HIV Nef, paxillin, and Pak1/2 regulate activation and secretion of TACE/ADAM10 proteases.
JO  - Mol. Cell
VL  - 49
IS  - 4
PB  - Cell Press
PY  - 2013
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Parkin, a RING-between-RING-type E3 ubiquitin ligase associated with Parkinson's disease, has a wide neuroprotective activity, preventing cell death in various stress paradigms. We identified a stress-protective pathway regulated by parkin that links NF-kappa B signaling and mitochondrial integrity via linear ubiquitination. Under cellular stress, parkin is recruited to the linear ubiquitin assembly complex and increases linear ubiquitination of NF-kappa B essential modulator (NEMO), which is essential for canonical NF-kappa B signaling. As a result, the mitochondrial guanosine triphosphatase OPA1 is transcriptionally upregulated via NF-kappa B-responsive promoter elements for maintenance of mitochondrial integrity and protection from stress-induced cell death. Parkin-induced stress protection is lost in the absence of either NEMO or OPA1, but not in cells defective for the mitophagy pathway. Notably, in parkin-deficient cells linear ubiquitination of NEMO, activation of NF-kappa B, and upregulation of OPA1 are significantly reduced in response to TNF-alpha stimulation, supporting the physiological relevance of parkin in regulating this antiapoptotic pathway.
AU  - Müller-Rischart, A.K.*
AU  - Pilsl, A.*
AU  - Beaudette, P.*
AU  - Patra, M.*
AU  - Hadian, K.
AU  - Funke, M.*
AU  - Peis, R.
AU  - Deinlein, A.*
AU  - Schweimer, C.*
AU  - Kuhn, P.-H.*
AU  - Lichtenthaler, S.F.*
AU  - Motori, E.*
AU  - Hrelia, S.*
AU  - Wurst, W.
AU  - Trümbach, D.
AU  - Langer, T.*
AU  - Krappmann, D.
AU  - Dittmar, G.*
AU  - Tatzelt, J.*
AU  - Winklhofer, K.F.*
C1  - 23929
C2  - 31301
SP  - 908-921
TI  - The E3 ligase Parkin maintains mitochondrial integrity by increasing linear ubiquitination of NEMO.
JO  - Mol. Cell
VL  - 49
IS  - 5
PB  - Cell Press
PY  - 2013
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Centromere clustering during interphase is a phenomenon known to occur in many different organisms and cell types, yet neither the factors involved nor their physiological relevance is well understood. Using Drosophila tissue culture cells and flies, we identified a network of proteins, including the nucleoplasmin-like protein (NLP), the insulator protein CTCF, and the nucleolus protein Modulo, to be essential for the positioning of centromeres. Artificial targeting further demonstrated that NLP and CTCF are sufficient for clustering, while Modulo serves as the anchor to the nucleolus. Centromere clustering was found to depend on centric chromatin rather than specific DNA sequences. Moreover, unclustering of centromeres results in the spatial destabilization of pericentric heterochromatin organization, leading to partial defects in the silencing of repetitive elements, defects during chromosome segregation, and genome instability.
AU  - Padeken, J.*
AU  - Mendiburo, M.J.*
AU  - Chlamydas, S.*
AU  - Schwarz, H.J.*
AU  - Kremmer, E.
AU  - Heun, P.*
C1  - 24688
C2  - 31638
SP  - 236-249
TI  - The nucleoplasmin homolog NLP mediates centromere clustering and anchoring to the nucleolus.
JO  - Mol. Cell
VL  - 50
IS  - 2
PB  - Cell Press
PY  - 2013
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Nucleotide-binding and oligomerization domain (NOD)-like receptors constitute a first line of defense against invading bacteria. X-linked Inhibitor of Apoptosis (XIAP) is implicated in the control of bacterial infections, and mutations in XIAP are causally linked to immunodeficiency in X-linked demonferative syndrome type-2 (XLP-2). Here, we demonstrate that the RING domain of XIAP is essential for NOD2 signaling and that XIAP contributes to exacerbation of inflammation-induced hepatitis in experimental mice. We find that XIAP ubiquitylates RIPK2 and recruits the linear ubiquitin chain assembly complex (LUBAC) to NOD2. We further show that LUBAC activity is required for efficient NF-kappa B activation and secretion of proinflammatory cytokines after NOD2 stimulation. Remarkably, XLP-2-derived XIAP variants have impaired ubiquitin ligase activity, fail to ubiquitylate RIPK2, and cannot facilitate NOD2 signaling. We conclude that XIAP and LUBAC constitute essential ubiquitin ligases in NOD2-mediated inflammatory signaling and propose that deregulation of NOD2 signaling contributes to XLP-2 pathogenesis.
AU  - Damgaard, R.B.*
AU  - Nachbur, U.*
AU  - Yabal, M.*
AU  - Wong, W.W.L.*
AU  - Fiil, B.K.*
AU  - Kastirr, M.*
AU  - Rieser, E.*
AU  - Rickard, J.A.*
AU  - Bankovacki, A.*
AU  - Peschel, C.*
AU  - Ruland, J.
AU  - Bekker-Jensen, S.*
AU  - Mailand, N.*
AU  - Kaufmann, T.*
AU  - Strasser, A.*
AU  - Walczak, H.*
AU  - Silke, J.*
AU  - Jost, P.J.*
AU  - Gyrd-Hansen, M.*
C1  - 8236
C2  - 30032
SP  - 746-758
TI  - The ubiquitin ligase XIAP recruits LUBAC for NOD2 signaling in inflammation and innate immunity.
JO  - Mol. Cell
VL  - 46
IS  - 6
PB  - Cell Press
PY  - 2012
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Packaging of DNA into nucleosomes and the formation of higher-order chromatin structures determine DNA accessibility and activity of genome domains. We identified an RNA-dependent mechanism maintaining the open chromatin structure within euchromatic regions in Drosophila cells. The mechanism of reversible chromatin opening, reconstituted in vitro, depends on the Drosophila decondensation factor 31 (Df31) that specifically binds to RNA and localizes to euchromatic regions. Df31 is capable to tether a heterogeneous pool of short, single-stranded RNAs to chromatin. This class of chromatin-associated RNA (caRNA) is stably linked to chromatin and is largely composed of snoRNAs, which are preferentially bound by Df31. We suggest that the Df31-mediated linkage of snoRNAs and chromatin, forms a RNA-chromatin network resulting in the establishment of open chromatin domains. Analysis of caRNAs in human cells also reveals a strong enrichment of snoRNAs, implying a conserved role for these molecules in higher-order structures of chromatin.
AU  - Schubert, T.*
AU  - Pusch, M.C.*
AU  - Diermeier, S.*
AU  - Benes, V.*
AU  - Kremmer, E.
AU  - Imhof, A.*
AU  - Längst, G.*
C1  - 11442
C2  - 30671
SP  - 434-444
TI  - Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin.
JO  - Mol. Cell
VL  - 48
IS  - 3
PB  - Cell Press
PY  - 2012
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - One of the earliest steps in metazoan pre-mRNA splicing involves binding of U2 snRNP auxiliary factor (U2AF) 65 KDa subunit to the polypyrimidine (Py) tract and of the 35 KDa subunit to the invariant AG dinucleotide at the intron 3' end. Here we use in vitro and in vivo depletion, as well as reconstitution assays using purified components, to identify hnRNP A1 as an RNA binding protein that allows U2AF to discriminate between pyrimidine-rich RNA sequences followed or not by a 3' splice site AG. Biochemical and NMR data indicate that hnRNP A1 forms a ternary complex with the U2AF heterodimer on AG-containing/uridine-rich RNAs, while it displaces U2AF from non-AG-containing/uridine-rich RNAs, an activity that requires the glycine-rich domain of hnRNP A1. Consistent with the functional relevance of this activity for splicing, proofreading assays reveal a role for hnRNP A1 in U2AF-mediated recruitment of U2 snRNP to the pre-mRNA.
AU  - Tavanez, J.P.*
AU  - Madl, T.
AU  - Kooshapur, H.
AU  - Sattler, M.
AU  - Valcárcel, J.*
C1  - 7251
C2  - 29611
SP  - 314-329
TI  - hnRNP A1 proofreads 3' splice site recognition by U2AF.
JO  - Mol. Cell
VL  - 45
IS  - 3
PB  - Elsevier
PY  - 2012
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Specific regulatory nascent chains establish direct interactions with the ribosomal tunnel, leading to translational stalling. Despite a wealth of biochemical data, structural insight into the mechanism of translational stalling in eukaryotes is still lacking. Here we use cryo-electron microscopy to visualize eukaryotic ribosomes stalled during the translation of two diverse regulatory peptides: the fungal arginine attenuator peptide (AAP) and the human cytomegalovirus (hCMV) gp48 upstream open reading frame 2 (uORF2). The C terminus of the AAP appears to be compacted adjacent to the peptidyl transferase center (PTC). Both nascent chains interact with ribosomal proteins L4 and L17 at tunnel constriction in a distinct fashion. Significant changes at the PTC were observed: the eukaryotic-specific loop of ribosomal protein L10e establishes direct contact with the CCA end of the peptidyl-tRNA (P-tRNA), which may be critical for silencing of the PTC during translational stalling. Our findings provide direct structural insight into two distinct eukaryotic stalling processes.
AU  - Bhushan, S.*
AU  - Meyer, H.
AU  - Starosta, A.L.*
AU  - Becker, T.*
AU  - Mielke, T.*
AU  - Berninghausen, O.*
AU  - Sattler, M.
AU  - Wilson, D.N.*
AU  - Beckmann, R.*
C1  - 4381
C2  - 27933
SP  - 138-146
TI  - Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide.
JO  - Mol. Cell
VL  - 40
IS  - 1
PB  - Elsevier
PY  - 2010
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Posttranslational modifications of the carboxyterminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) specify a molecular recognition code that is deciphered by proteins involved in RNA biogenesis. The CTD is comprised of a repeating heptapeptide (Y1S2P3T4S5P6S7). Recently, phosphorylation of serine 7 was shown to be important for cotranscriptional processing of two snRNAs in mammalian cells. Here we report that Kin28/Cdk7, a subunit of the evolutionarily conserved TFIIH complex, is a Ser7 kinase. The ability of Kin28/Cdk7 to phosphorylate Ser7 is particularly surprising because this kinase functions at promoters of protein-coding genes, rather than being restricted to promoter-distal regions of snRNA genes. Kin28/Cdk7 is also known to phosphorylate Ser5 residues of the CTD at gene promoters. Taken together, our results implicate the TFIIH kinase in placing bivalent Ser5 and Ser7 marks early in gene transcription. These bivalent CTD marks, in concert with cues within nascent transcripts, specify the cotranscriptional engagement of the relevant RNA processing machinery.
AU  - Akhtar, M.S.*
AU  - Heidemann, M.
AU  - Tietjen, J.R.*
AU  - Zhang, D.W.*
AU  - Chapman, R.D.
AU  - Eick, D.
AU  - Ansari, A.Z.*
C1  - 2090
C2  - 26263
SP  - 387-393
TI  - TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II..
JO  - Mol. Cell
VL  - 34
IS  - 3
PB  - Cell Press
PY  - 2009
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Histone modifications play an important role in transcription. We previously studied histone H2B ubiquitylation on lysine 123 and subsequent deubiquitylation by SAGA-associated Ubp8. Unlike other histone modifications, both the addition and removal of ubiquitin are required for optimal transcription. Here we report that deubiquitylation of H2B is important for recruitment of a complex containing the kinase Ctk1, resulting in phosphorylation of the RNA polymerase II (Pol II) C-terminal domain (CTD), and for subsequent recruitment of the Set2 methyltransferase. We find that Ctk1 interacts with histones H2A and H2B, and that persistent H2B ubiquitylation disrupts these interactions. We further show that Ubp8 enters the GAL1 coding region through an interaction with Pol II. These findings reveal a mechanism by which H2B ubiquitylation acts as a barrier to Ctk1 association with active genes, while subsequent deubiquitylation by Ubp8 triggers Ctk1 recruitment at the appropriate point in activation.
AU  - Wyce, A.*
AU  - Xiao, T. *
AU  - Whelan, K.A.*
AU  - Kosman, C.*
AU  - Walter, W.*
AU  - Eick, D.
AU  - Hughes, T.R*
AU  - Krogan, N.J.*
AU  - Strahl, B.D.*
AU  - Berger, S.L.
C1  - 4016
C2  - 24653
SP  - 275-288
TI  - H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.
JO  - Mol. Cell
VL  - 27
IS  - 2
PB  - Cell Press
PY  - 2007
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - T cell receptor (TCR) signaling to IKB kinase (IKK)/NFKB is controlled by PKC theta-dependent activation of the Carma1, Bcl10, and Malt1 (CBM) complex. Antigen-induced phosphorylation of BcI10 has been reported, but its physiological function is unknown. Here we show that the putative downstream kinase IKK beta is required for initial CBM complex formation. Further, upon engagement of IKK beta/Malt1/Bcl10 with Carma1, IKK beta phosphorylates Bcl10 in the C terminus and thereby interferes with Bcl10/Malt1 association and Bcl10-mediated IKK gamma ubiquitination. Mutation of the IKK beta phosphorylation sites on Bcl10 enhances expression of NF-kappa B target genes IL-2 and TNF alpha after activation of primary T cells. Thus, our data provide evidence that IKK beta serves a dual role upstream of its classical substrates, the I kappa B proteins. While being essential for triggering initial CBM complex formation, IKK beta-dependent phosphorylation of Bcl10 exhibits a negative regulatory role in T cell activation.
AU  - Wegener, E.
AU  - Oeckinghaus, A.*
AU  - Papadopoulou, N.
AU  - Lavitas, L.*
AU  - Schmidt-Supprian, M.*
AU  - Ferch, U.*
AU  - Mak, T.W.*
AU  - Ruland, J.*
AU  - Heissmeyer, V.
AU  - Krappmann, D.
C1  - 5086
C2  - 23657
SP  - 13-23
TI  - Essential role for I kappa B kinase beta in remodeling Carma1-Bcl10-Malt1 complexes upon T cell activation
JO  - Mol. Cell
VL  - 23
IS  - 1
PY  - 2006
SN  - 1097-2765
ER  - 

TY  - JOUR
AB  - Base excision repair (BER) plays an essential role in protecting cells from mutagenic base damage caused by oxidative stress, hydrolysis, and environmental factors. POLQ is a DNA polymerase, which appears to be involved in translesion DNA synthesis (TLS) past base damage. We disrupted POLQ, and its homologs HEL308 and POLN in chicken DT40 cells, and also created polq/hel308 and polq/poln double mutants. We found that POLQ-deficient mutants exhibit hypersensitivity to oxidative base damage induced by H2O2, but not to UV or cisplatin. Surprisingly, this phenotype was synergistically increased by concomitant deletion of the major BER polymerase, POLβ. Moreover, extracts from a polq null mutant cell line show reduced BER activity, and POLQ, like POLβ, accumulated rapidly at sites of base damage. Accordingly, POLQ and POLβ share an overlapping function in the repair of oxidative base damage. Taken together, these results suggest a role for vertebrate POLQ in BER. © 2006 Elsevier Inc. All rights reserved.
AU  - Yoshimura, M.*
AU  - Kohzaki, M.*
AU  - Nakamura, J.*
AU  - Asagoshi, K.*
AU  - Sonoda, E.*
AU  - Hou, E.*
AU  - Prasad, R.*
AU  - Wilson, S.H.*
AU  - Tano, K.*
AU  - Yasui, A.*
AU  - Lan, L.*
AU  - Seki, M.*
AU  - Wood, R.D.*
AU  - Arakawa, H.
AU  - Buerstedde, J.M.
AU  - Hochegger, H.*
AU  - Okada, T.*
AU  - Hiraoka, M.*
AU  - Takeda, S.*
C1  - 2441
C2  - 24145
SP  - 115-125
TI  - Vertebrate POLQ and POLß cooperate in base excision repair of oxidative DNA damage.
JO  - Mol. Cell
VL  - 24
IS  - 1
PY  - 2006
SN  - 1097-2765
ER  - 

TY  - JOUR
AU  - Bourbon, H.-M.*
AU  - Meisterernst, M.
C1  - 3425
C2  - 22386
SP  - 553-557
TI  - A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II.
JO  - Mol. Cell
VL  - 14
PY  - 2004
SN  - 1097-2765
ER  - 

TY  - JOUR
AU  - Kliche, S.*
AU  - Nagel, W.*
AU  - Kremmer, E.
AU  - Atzler, C.*
AU  - Ege, A.*
AU  - Knorr, Th.*
AU  - Koszinowski, U.*
AU  - Kolanus, W.*
AU  - Haas, J.*
C1  - 22185
C2  - 20889
SP  - 833-843
TI  - Signaling by Human Herpesvirus 8 kaposin A through Direct Membrane Recruitment of cytohesin-1.
JO  - Mol. Cell
VL  - 7
PY  - 2001
SN  - 1097-2765
ER  -