TY  - JOUR
AB  - The regulatory circuitry of cell-specific transcriptional programs is thought to be influenced by transposable elements (TEs), whereby TEs serve as raw material for the diversification and genome-wide distribution of genetic elements that contain cis-regulatory activity. However, the transcriptional activators of TEs in relevant physiological contexts are largely unknown. Here, we undertook an evolutionary approach to identify regulators of two main families of MERVL, a major regulator of transcription during early mouse development. Using a combination of phyloregulatory, transcriptomic, and loss-of-function approaches, we demonstrate that SRF is a novel regulator of MERVL and embryonic transcription during zygotic genome activation. By resolving the phylogenetic history of two major MERVL families, we delineate the evolutionary acquisition of SRF and DUX binding sites and show that the acquisition of the SRF site precedes that of DUX. SRF contributes to embryonic transcription through the regulation of MERVLs, which in turn serve as promoters for host genes. Our work identifies new transcriptional regulators and TEs that shape the gene expression programs in early embryos and highlights the process of TE domestication via the sequential acquisition of transcription factor binding sites and coevolution with the host.
AU  - Hermant, C.
AU  - Mourra-Díaz, D.M.
AU  - Oomen, M.E.
AU  - Altamirano-Pacheco, L.
AU  - Pal, M.
AU  - Nakatani, T.
AU  - Torres-Padilla, M.E.
C1  - 73549
C2  - 56865
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 490-509
TI  - The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation.
JO  - Genes Dev.
VL  - 39
IS  - 7-8
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2025
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Cell diversification is at the base of increasing multicellular organism complexity in phylogeny achieved during ontogeny. However, there are also functions common to all cells, such as cell division, cell migration, translation, endocytosis, exocytosis, etc. Here we revisit the organelles involved in such common functions, reviewing recent evidence of unexpected differences of proteins at these organelles. For instance, centrosomes or mitochondria differ significantly in their protein composition in different, sometimes closely related, cell types. This has relevance for development and disease. Particularly striking is the high amount and diversity of RNA-binding proteins at these and other organelles, which brings us to review the evidence for RNA at different organelles and suborganelles. We include a discussion about (sub)organelles involved in translation, such as the nucleolus and ribosomes, for which unexpected cell type-specific diversity has also been reported. We propose here that the heterogeneity of these organelles and compartments represents a novel mechanism for regulating cell diversity. One reason is that protein functions can be multiplied by their different contributions in distinct organelles, as also exemplified by proteins with moonlighting function. The specialized organelles still perform pan-cellular functions but in a cell type-specific mode, as discussed here for centrosomes, mitochondria, vesicles, and other organelles. These can serve as regulatory hubs for the storage and transport of specific and functionally important regulators. In this way, they can control cell differentiation, plasticity, and survival. We further include examples highlighting the relevance for disease and propose to examine organelles in many more cell types for their possible differences with functional relevance.
AU  - Schieweck, R.*
AU  - Götz, M.
C1  - 70248
C2  - 55465
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 98-114
TI  - Pan-cellular organelles and suborganelles-from common functions to cellular diversity?
JO  - Genes Dev.
VL  - 38
IS  - 3-4
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2024
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - The majority of our genome is composed of repeated DNA sequences that assemble into heterochromatin, a highly compacted structure that constrains their mutational potential. How heterochromatin forms during development and how its structure is maintained are not fully understood. Here, we show that mouse heterochromatin phase-separates after fertilization, during the earliest stages of mammalian embryogenesis. Using high-resolution quantitative imaging and molecular biology approaches, we show that pericentromeric heterochromatin displays properties consistent with a liquid-like state at the two-cell stage, which change at the four-cell stage, when chromocenters mature and heterochromatin becomes silent. Disrupting the condensates results in altered transcript levels of pericentromeric heterochromatin, suggesting a functional role for phase separation in heterochromatin function. Thus, our work shows that mouse heterochromatin forms membrane-less compartments with biophysical properties that change during development and provides new insights into the self-organization of chromatin domains during mammalian embryogenesis.
AU  - Guthmann, M.
AU  - Qian, C.*
AU  - Gialdini, I.*
AU  - Nakatani, T.
AU  - Ettinger, A.
AU  - Schauer, T.
AU  - Kukhtevich, I.
AU  - Schneider, R.
AU  - Lamb, D.C.*
AU  - Burton, A.
AU  - Torres-Padilla, M.E.
C1  - 67688
C2  - 53995
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 336-350
TI  - A change in biophysical properties accompanies heterochromatin formation in mouse embryos.
JO  - Genes Dev.
VL  - 37
IS  - 7-8
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2023
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Fertilization in mammals is accompanied by an intense period of chromatin remodeling and major changes in nuclear organization. How the earliest events in embryogenesis, including zygotic genome activation (ZGA) during maternal-to-zygotic transition, influence such remodeling remains unknown. Here, we have investigated the establishment of nuclear architecture, focusing on the remodeling of lamina-associated domains (LADs) during this transition. We report that LADs reorganize gradually in two-cell embryos and that blocking ZGA leads to major changes in nuclear organization, including altered chromatin and genomic features of LADs and redistribution of H3K4me3 toward the nuclear lamina. Our data indicate that the rearrangement of LADs is an integral component of the maternal-to-zygotic transition and that transcription contributes to shaping nuclear organization at the beginning of mammalian development.
AU  - Pal, M.
AU  - Altamirano-Pacheco, L.
AU  - Schauer, T.
AU  - Torres-Padilla, M.E.
C1  - 68735
C2  - 54944
SP  - 901-912
TI  - Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity.
JO  - Genes Dev.
VL  - 37
IS  - 19-20
PY  - 2023
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Imprinted gene clusters are confined genomic regions containing genes with parent-of-origin-dependent transcriptional activity. In this issue of Genes & Development, Loftus and colleagues (pp. 829-843) made use of an insightful combination of descriptive approaches, genetic manipulations, and epigenome-editing approaches to show that differences in nuclear topology precede the onset of imprinted expression at the Peg13-Kcnk9 locus. Furthermore, the investigators provide data in line with a model suggesting that parent-of-origin-specific topological differences could be responsible for parent-of-origin-specific enhancer activity and thus imprinted expression.
AU  - Stricker, S.H.
C1  - 68668
C2  - 54873
SP  - 779-780
TI  - Folding makes an imprint.
JO  - Genes Dev.
VL  - 37
IS  - 17-18
PY  - 2023
SN  - 0890-9369
ER  - 

TY  - JOUR
AU  - Torres-Padilla, M.E.
C1  - 67622
C2  - 53929
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 56-57
TI  - Totipotency, development, and chromatin.
JO  - Genes Dev.
VL  - 37
IS  - 1-2
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2023
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Senescence is a stress-responsive tumor suppressor mechanism associated with expression of the senescence-associated secretory phenotype (SASP). Through the SASP, senescent cells trigger their own immune-mediated elimination, which if evaded leads to tumorigenesis. Senescent parenchymal cells are separated from circulating immunocytes by the endothelium, which is targeted by microenvironmental signaling. Here we show that SASP induces endothelial cell NF-κB activity and that SASP-induced endothelial expression of the canonical NF-κB component Rela underpins senescence surveillance. Using human liver sinusoidal endothelial cells (LSECs), we show that SASP-induced endothelial NF-κB activity regulates a conserved transcriptional program supporting immunocyte recruitment. Furthermore, oncogenic hepatocyte senescence drives murine LSEC NF-κB activity in vivo. Critically, we show two distinct endothelial pathways in senescence surveillance. First, endothelial-specific loss of Rela prevents development of Stat1-expressing CD4+ T lymphocytes. Second, the SASP up-regulates ICOSLG on LSECs, with the ICOS-ICOSLG axis contributing to senescence cell clearance. Our results show that the endothelium is a nonautonomous SASP target and an organizing center for immune-mediated senescence surveillance.
AU  - Yin, K.
AU  - Patten, D.*
AU  - Gough, S.C.*
AU  - de Barros Gonçalves, S.*
AU  - Chan, A.*
AU  - Olan, I.*
AU  - Cassidy, L.*
AU  - Poblocka, M.*
AU  - Zhu, H.*
AU  - Lun, A.*
AU  - Schuijs, M.J.*
AU  - Young, A.*
AU  - Martinez Jimenez, C.P.
AU  - Halim, T.Y.F.*
AU  - Shetty, S.*
AU  - Narita, M.*
AU  - Hoare, M.*
C1  - 65480
C2  - 52204
SP  - 533-549
TI  - Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance.
JO  - Genes Dev.
VL  - 36
IS  - 9-10
PY  - 2022
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - The establishment of cell fates involves alterations of transcription factor repertoires and repurposing of transcription factors by post-translational modifications. In embryonic stem cells (ESCs), the chromatin organizers SATB2 and SATB1 balance pluripotency and differentiation by activating and repressing pluripotency genes, respectively. Here, we show that conditional Satb2 gene inactivation weakens ESC pluripotency, and we identify SUMO2 modification of SATB2 by the E3 ligase ZFP451 as a potential driver of ESC differentiation. Mutations of two SUMO-acceptor lysines of Satb2 (Satb2 K→ R ) or knockout of Zfp451 impair the ability of ESCs to silence pluripotency genes and activate differentiation-associated genes in response to retinoic acid (RA) treatment. Notably, the forced expression of a SUMO2-SATB2 fusion protein in either Satb2 K→ R or Zfp451 -/- ESCs rescues, in part, their impaired differentiation potential and enhances the down-regulation of Nanog The differentiation defect of Satb2 K→ R ESCs correlates with altered higher-order chromatin interactions relative to Satb2 wt ESCs. Upon RA treatment of Satb2 wt ESCs, SATB2 interacts with ZFP451 and the LSD1/CoREST complex and gains binding at differentiation genes, which is not observed in RA-treated Satb2 K→ R cells. Thus, SATB2 SUMOylation may contribute to the rewiring of transcriptional networks and the chromatin interactome of ESCs in the transition of pluripotency to differentiation.
AU  - Antonio Urrutia, G.*
AU  - Ramachandran, H.*
AU  - Cauchy, P.*
AU  - Boo, K.*
AU  - Ramamoorthy, S.*
AU  - Boller, S.*
AU  - Dogan, E.*
AU  - Clapes, T.*
AU  - Trompouki, E.*
AU  - Torres-Padilla, M.E.
AU  - Palvimo, J.J.*
AU  - Pichler, A.*
AU  - Grosschedl, R.*
C1  - 62515
C2  - 50898
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 1142-1160
TI  - ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation.
JO  - Genes Dev.
VL  - 35
IS  - 15-16
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2021
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Transposable elements (TEs) are genetic elements capable of changing position within the genome. Although their mobilization can constitute a threat to genome integrity, nearly half of modern mammalian genomes are composed of remnants of TE insertions. The first critical step for a successful transposition cycle is the generation of a full-length transcript. TEs have evolved cis-regulatory elements enabling them to recruit host-encoded factors driving their own, selfish transcription. TEs are generally transcriptionally silenced in somatic cells, and the mechanisms underlying their repression have been extensively studied. However, during germline formation, preimplantation development, and tumorigenesis, specific TE families are highly expressed. Understanding the molecular players at stake in these contexts is of utmost importance to establish the mechanisms regulating TEs, as well as the importance of their transcription to the biology of the host. Here, we review the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific TE families or subfamilies. We discuss the diversity of TE regulatory elements within mammalian genomes and highlight the importance of TE mobilization in the dispersal of transcription factor-binding sites over the course of evolution.
AU  - Hermant, C.
AU  - Torres-Padilla, M.E.
C1  - 60951
C2  - 49756
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 22-39
TI  - TFs for TEs: The transcription factor repertoire of mammalian transposable elements.
JO  - Genes Dev.
VL  - 35
IS  - 1-2
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2021
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Covalent chemical modifications of cellular RNAs directly impact all biological processes. However, our mechanistic understanding of the enzymes catalyzing these modifications, their substrates and biological functions, remains vague. Amongst RNA modifications N6-methyladenosine (m6A) is widespread and found in messenger (mRNA), ribosomal (rRNA), and noncoding RNAs. Here, we undertook a systematic screen to uncover new RNA methyltransferases. We demonstrate that the methyltransferase-like 5 (METTL5) protein catalyzes m6A in 18S rRNA at position A1832 We report that absence of Mettl5 in mouse embryonic stem cells (mESCs) results in a decrease in global translation rate, spontaneous loss of pluripotency, and compromised differentiation potential. METTL5-deficient mice are born at non-Mendelian rates and develop morphological and behavioral abnormalities. Importantly, mice lacking METTL5 recapitulate symptoms of patients with DNA variants in METTL5, thereby providing a new mouse disease model. Overall, our biochemical, molecular, and in vivo characterization highlights the importance of m6A in rRNA in stemness, differentiation, development, and diseases.
AU  - Ignatova, V.V.
AU  - Stolz, P.*
AU  - Kaiser, S.*
AU  - Gustafsson, T.H.*
AU  - Lastres, P.R.*
AU  - Sanz-Moreno, A.
AU  - Cho, Y.-L.
AU  - Amarie, O.V.*
AU  - Aguilar-Pimentel, J.A.
AU  - Klein-Rodewald, T.
AU  - Calzada-Wack, J.
AU  - Becker, L.
AU  - Marschall, S.
AU  - Kraiger, M.
AU  - Garrett, L.
AU  - Seisenberger, C.
AU  - Hölter, S.M.
AU  - Borland, K.*
AU  - Van De Logt, E.*
AU  - Jansen, P.W.T.C.*
AU  - Baltissen, M.P.*
AU  - Valenta, M.
AU  - Vermeulen, M.*
AU  - Wurst, W.
AU  - Gailus-Durner, V.
AU  - Fuchs, H.
AU  - Hrabě de Angelis, M.
AU  - Rando, O.J.*
AU  - Kellner, S.M.*
AU  - Bultmann, S.*
AU  - Schneider, R.
C1  - 58742
C2  - 48277
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 715-729
TI  - The rRNA m6A methyltransferase METTL5 is involved in pluripotency and developmental programs.
JO  - Genes Dev.
VL  - 34
IS  - 9-10
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2020
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - MDM2 and MDMX, negative regulators of the tumor suppressor p53, can work separately and as a heteromeric complex to restrain p53's functions. MDM2 also has pro-oncogenic roles in cells, tissues, and animals that are independent of p53. There is less information available about p53-independent roles of MDMX or the MDM2-MDMX complex. We found that MDM2 and MDMX facilitate ferroptosis in cells with or without p53. Using small molecules, RNA interference reagents, and mutant forms of MDMX, we found that MDM2 and MDMX, likely working in part as a complex, normally facilitate ferroptotic death. We observed that MDM2 and MDMX alter the lipid profile of cells to favor ferroptosis. Inhibition of MDM2 or MDMX leads to increased levels of FSP1 protein and a consequent increase in the levels of coenzyme Q(10), an endogenous lipophilic antioxidant. This suggests that MDM2 and MDMX normally prevent cells from mounting an adequate defense against lipid peroxidation and thereby promote ferroptosis. Moreover, we found that PPAR alpha activity is essential for MDM2 and MDMX to promote ferroptosis, suggesting that the MDM2-MDMX complex regulates lipids through altering PPAR alpha activity. These findings reveal the complexity of cellular responses to MDM2 and MDMX and suggest that MDM2-MDMX inhibition might be useful for preventing degenerative diseases involving ferroptosis. Furthermore, they suggest that MDM2/MDMX amplification may predict sensitivity of some cancers to ferroptosis inducers.
AU  - Venkatesh, D.*
AU  - O'Brien, N.A.*
AU  - Zandkarimi, F.*
AU  - Tong, D.R.*
AU  - Stokes, M.E.*
AU  - Dunn, D.E.*
AU  - Kengmana, E.S.*
AU  - Aron, A.T.*
AU  - Klein, A.M.*
AU  - Csuka, J.M.*
AU  - Moon, S.H.*
AU  - Conrad, M.
AU  - Chang, C.J.*
AU  - Lo, D.C.*
AU  - D'Alessandro, A.*
AU  - Prives, C.*
AU  - Stockwell, B.R.*
C1  - 58836
C2  - 48384
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 526-543
TI  - MDM2 and MDMX promote ferroptosis by PPARα-mediated lipid remodeling.
JO  - Genes Dev.
VL  - 34
IS  - 7-8
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2020
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Plants have evolved complex photoreceptor-controlled mechanisms to sense and respond to seasonal changes in day length. This ability allows plants to optimally time the transition from vegetative growth to flowering. UV-B is an important part intrinsic to sunlight; however, whether and how it affects photoperiodic flowering has remained elusive. Here, we report that, in the presence of UV-B, genetic mutation of REPRESSOR OF UV-B PHOTOMOR-PHOGENESIS 2 (RUP2) renders the facultative long day plant Arabidopsis thaliana a day-neutral plant and that this phenotype is dependent on the UV RESISTANCE LOCUS 8 (UVR8) UV-B photoreceptor. We provide evidence that the floral repression activity of RUP2 involves direct interaction with CONSTANS, repression of this key activator of flowering, and suppression of FLOWERING LOCUS T transcription. RUP2 therefore functions as an essential repressor of UVR8-mediated induction of flowering under noninductive short day conditions and thus provides a crucial mechanism of photoperiodic flowering control.
AU  - Arongaus, A.B.*
AU  - Chen, S.*
AU  - Pireyre, M.*
AU  - Glöckner, N.*
AU  - Galvão, V.C.*
AU  - Albert, A.
AU  - Winkler, J.B.
AU  - Fankhauser, C.*
AU  - Zeiser, K.*
AU  - Ulm, R.*
C1  - 54406
C2  - 45518
CY  - 1 Bungtown Rd, Cold Spring Harbor, Ny 11724 Usa
SP  - 1332-1343
TI  - Arabidopsis RUP2 represses UVR8-mediated flowering in noninductive photoperiods.
JO  - Genes Dev.
VL  - 32
IS  - 19-20
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2018
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Lipid peroxidation is the process by which oxygen combines with lipids to generate lipid hydroperoxides via intermediate formation of peroxyl radicals. Vitamin E and coenzyme Q react with peroxyl radicals to yield peroxides, and then these oxidized lipid species can be detoxified by glutathione and glutathione peroxidase 4 (GPX4) and other components of the cellular antioxidant defense network. Ferroptosis is a form of regulated nonapoptotic cell death involving overwhelming iron-dependent lipid peroxidation. Here, we review the functions and regulation of lipid peroxidation, ferroptosis, and the antioxidant network in diverse species, including humans, other mammals and vertebrates, plants, invertebrates, yeast, bacteria, and archaea. We also discuss the potential evolutionary roles of lipid peroxidation and ferroptosis.
AU  - Conrad, M.
AU  - Kagan, V.E.*
AU  - Bayir, H.*
AU  - Pagnussat, G.C.*
AU  - Head, B.*
AU  - Traber, M.G.*
AU  - Stockwell, B.R.*
C1  - 53580
C2  - 44908
SP  - 602-619
TI  - Regulation of lipid peroxidation and ferroptosis in diverse species.
JO  - Genes Dev.
VL  - 32
IS  - 9-10
PY  - 2018
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - In mammals, epigenetic reprogramming, the acquisition and loss of totipotency, and the first cell fate decision all occur within a 3-d window after fertilization from the one-cell zygote to the formation of the blastocyst. These processes are poorly understood in molecular detail, yet this is an essential prerequisite to uncover principles of stem cells, chromatin biology, and thus regenerative medicine. A unique feature of preimplantation development is the drastic genome-wide changes occurring to nuclear architecture. From studying somatic and in vitro cultured embryonic stem cells (ESCs) it is becoming increasingly established that the three-dimensional (3D) positions of genomic loci relative to each other and to specific compartments of the nucleus can act on the regulation of gene expression, potentially driving cell fate. However, the functionality, mechanisms, and molecular characteristics of the changes in nuclear organization during preimplantation development are only now beginning to be unraveled. Here, we discuss the peculiarities of nuclear compartments and chromatin organization during mammalian preimplantation development in the context of the transition from totipotency to pluripotency.
AU  - Borsos, M.
AU  - Torres-Padilla, M.E.
C1  - 48134
C2  - 39927
CY  - Cold Spring Harbor
SP  - 611-621
TI  - Building up the nucleus: Nuclear organization in the establishment of totipotency and pluripotency during mammalian development.
JO  - Genes Dev.
VL  - 30
IS  - 6
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2016
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Extensive chromatin remodeling after fertilization is thought to take place to allow a new developmental program to start. This includes dynamic changes in histone methylation and, in particular, the remodeling of constitutive heterochromatic marks such as histone H4 Lys20 trimethylation (H4K20me3). While the essential function of H4K20me1 in preimplantation mouse embryos is well established, the role of the additional H4K20 methylation states through the action of the SUV4-20 methyltransferases has not been addressed. Here we show that Suv4-20h1/h2 are mostly absent in mouse embryos before implantation, underscoring a rapid decrease of H4K20me3 from the two-cell stage onward. We addressed the functional significance of this remodeling by introducing Suv4-20h1 and Suv4-20h2 in early embryos. Ectopic expression of Suv4-20h2 leads to sustained levels of H4K20me3, developmental arrest, and defects in S-phase progression. The developmental phenotype can be partially overcome through inhibition of the ATR pathway, suggesting that the main function for the remodeling of H4K20me3 after fertilization is to allow the timely and coordinated progression of replication. This is in contrast to the replication program in somatic cells, where H4K20me3 has been shown to promote replication origin licensing, and anticipates a different regulation of replication during this early developmental time window.
AU  - Eid, A.*
AU  - Rodriguez-Terrones, D.
AU  - Burton, A.
AU  - Torres-Padilla, M.E.
C1  - 50159
C2  - 42041
CY  - Cold Spring Harbor
SP  - 2513-2526
TI  - SUV4-20 activity in the preimplantation mouse embryo controls timely replication.
JO  - Genes Dev.
VL  - 30
IS  - 22
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2016
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - In order to understand whether early epigenetic mechanisms instruct the long-term behavior of neural stem cells (NSCs) and their progeny, we examined Uhrf1 (ubiquitin-like PHD ring finger-1; also known as Np95), as it is highly expressed in NSCs of the developing brain and rapidly down-regulated upon differentiation. Conditional deletion of Uhrf1 in the developing cerebral cortex resulted in rather normal proliferation and neurogenesis but severe postnatal neurodegeneration. During development, deletion of Uhrf1 lead to global DNA hypomethylation with a strong activation of the intracisternal A particle (IAP) family of endogenous retroviral elements, accompanied by an increase in 5-hydroxymethylcytosine. Down-regulation of Tet enzymes rescued the IAP activation in Uhrf1 conditional knockout (cKO) cells, suggesting an antagonistic interplay between Uhrf1 and Tet on IAP regulation. As IAP up-regulation persists into postnatal stages in the Uhrf1 cKO mice, our data show the lack of means to repress IAPs in differentiating neurons that normally never express Uhrf1. The high load of viral proteins and other transcriptional deregulation ultimately led to postnatal neurodegeneration. Taken together, these data show that early developmental NSC factors can have long-term effects in neuronal differentiation and survival. Moreover, they highlight how specific the consequences of widespread changes in DNA methylation are for certain classes of retroviral elements.
AU  - Ramesh, V.
AU  - Bayam, E.
AU  - Cernilogar, F.M.*
AU  - Bonapace, I.M.*
AU  - Schulze, M.*
AU  - Riemenschneider, M.J.*
AU  - Schotta, G.*
AU  - Götz, M.
C1  - 49854
C2  - 40992
CY  - Cold Spring Harbor
SP  - 2199-2212
TI  - Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration.
JO  - Genes Dev.
VL  - 30
IS  - 19
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2016
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - The Drosophila protein brain tumor (Brat) forms a complex with Pumilio (Pum) and Nanos (Nos) to repress hunchback (hb) mRNA translation at the posterior pole during early embryonic development. It is currently thought that complex formation is initiated by Pum, which directly binds the hb mRNA and subsequently recruits Nos and Brat. Here we report that, in addition to Pum, Brat also directly interacts with the hb mRNA. We identify Brat-binding sites distinct from the Pum consensus motif and show that RNA binding and translational repression by Brat do not require Pum, suggesting so far unrecognized Pum-independent Brat functions. Using various biochemical and biophysical methods, we also demonstrate that the NHL (NCL-1, HT2A, and LIN-41) domain of Brat, a domain previously believed to mediate protein-protein interactions, is a novel, sequence-specific ssRNA-binding domain. The Brat-NHL domain folds into a six-bladed beta propeller, and we identify its positively charged top surface as the RNA-binding site. Brat belongs to the functional diverse TRIM (tripartite motif)-NHL protein family. Using structural homology modeling, we predict that the NHL domains of all TRIM-NHL proteins have the potential to bind RNA, indicating that Brat is part of a conserved family of RNA-binding proteins.
AU  - Loedige, I.*
AU  - Stotz, M.*
AU  - Qamar, S.*
AU  - Kramer, K.*
AU  - Hennig, J.
AU  - Schubert, T.*
AU  - Loeffler, P.*
AU  - Längst, G.*
AU  - Merkl, R.*
AU  - Urlaub, H.*
AU  - Meister, G.*
C1  - 31297
C2  - 34305
CY  - Cold Spring Harbor
SP  - 749-764
TI  - The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation.
JO  - Genes Dev.
VL  - 28
IS  - 7
PB  - Cold Spring Harbor Lab Press, Publications Dept
PY  - 2014
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as "transcription factories,'' but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9-mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments.
AU  - Ghamari, A.*
AU  - van de Corput, M.P.C.*
AU  - Thongjuea, S.*
AU  - van Cappellen, W.A.*
AU  - van Ijcken, W.*
AU  - van Haren, J.*
AU  - Soler, E.*
AU  - Eick, D.
AU  - Lenhard, B.*
AU  - Grosveld, F.G.*
C1  - 24557
C2  - 31575
SP  - 767-777
TI  - In vivo live imaging of RNA polymerase II transcription factories in primary cells.
JO  - Genes Dev.
VL  - 27
IS  - 7
PB  - Cold Spring Harbor Lab. Press
PY  - 2013
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Macroautophagy (autophagy) is a regulated catabolic pathway to degrade cellular organelles and macromolecules. The role of autophagy in cancer is complex and may differ depending on tumor type or context. Here we show that pancreatic cancers have a distinct dependence on autophagy. Pancreatic cancer primary tumors and cell lines show elevated autophagy under basal conditions. Genetic or pharmacologic inhibition of autophagy leads to increased reactive oxygen species, elevated DNA damage, and a metabolic defect leading to decreased mitochondrial oxidative phosphorylation. Together, these ultimately result in significant growth suppression of pancreatic cancer cells in vitro. Most importantly, inhibition of autophagy by genetic means or chloroquine treatment leads to robust tumor regression and prolonged survival in pancreatic cancer xenografts and genetic mouse models. These results suggest that, unlike in other cancers where autophagy inhibition may synergize with chemotherapy or targeted agents by preventing the up-regulation of autophagy as a reactive survival mechanism, autophagy is actually required for tumorigenic growth of pancreatic cancers de novo, and drugs that inactivate this process may have a unique clinical utility in treating pancreatic cancers and other malignancies with a similar dependence on autophagy. As chloroquine and its derivatives are potent inhibitors of autophagy and have been used safely in human patients for decades for a variety of purposes, these results are immediately translatable to the treatment of pancreatic cancer patients, and provide a much needed, novel vantage point of attack.
AU  - Yang, S.*
AU  - Wang, X.*
AU  - Contino, G.*
AU  - Liesa, M.*
AU  - Sahin, E.*
AU  - Ying, H.*
AU  - Bause, A.*
AU  - Li, Y.*
AU  - Stommel, J.M.*
AU  - Dell'antonio, G.*
AU  - Mautner, J.
AU  - Tonon, G.*
AU  - Haigis, M.*
AU  - Shirihai, O.S.*
AU  - Doglioni, C.*
AU  - Bardeesy, N.*
AU  - Kimmelman, A.C.*
C1  - 6351
C2  - 29048
SP  - 717-729
TI  - Pancreatic cancers require autophagy for tumor growth.
JO  - Genes Dev.
VL  - 25
IS  - 7
PB  - Cold Spring Harbor Laboratory Press
PY  - 2011
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - During early mouse development, the anterior visceral endoderm (AVE) secretes inhibitor and activator signals that are essential for establishing the anterior-posterior (AP) axis of the embryo and for restricting mesoderm formation to the posterior epiblast in the primitive streak (PS) region. Here we show that AVE cells have an additional morphogenetic function. These cells express the transmembrane protein FLRT3. Genetic ablation of FLRT3 did not affect the signaling functions of the AVE according to the normal expression pattern of Nodal and Wnt and the establishment of a proper AP patterning in the epiblast. However, FLRT3(-/-) embryos showed a highly disorganized basement membrane (BM) in the AVE region. Subsequently, adjacent anterior epiblast cells displayed an epithelial-to-mesenchymal transition (EMT)-like process characterized by the loss of cell polarity, cell ingression, and the up-regulation of the EMT and the mesodermal marker genes Eomes, Brachyury/T, and FGF8. These results suggest that the AVE acts as a morphogenetic boundary to prevent EMT and mesoderm induction in the anterior epiblast by maintaining the integrity of the BM. We propose that this novel function cooperates with the signaling activities of the AVE to restrict EMT and mesoderm induction to the posterior epiblast.
AU  - Egea, J.*
AU  - Erlacher, C.*
AU  - Montanez, E.*
AU  - Burtscher, I.
AU  - Yamagishi, S.*
AU  - Hess, M.*
AU  - Hampel, F.*
AU  - Sánchez, R.*
AU  - Rodriguez-Manzaneque, M.T.*
AU  - Bösl, M.R.*
AU  - Fässler, R.*
AU  - Lickert, H.
AU  - Klein, R.*
C1  - 2601
C2  - 25918
SP  - 3349-3362
TI  - Genetic ablation of FLRT3 reveals a novel morphogenetic function for the anterior visceral endoderm in suppressing mesoderm differentiation.
JO  - Genes Dev.
VL  - 22
IS  - 23
PB  - Cold Spring Harbor Laboratory Press
PY  - 2008
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Experiments in Xenopus have illustrated the importance of extracellular morphogens for embryonic gene regulation in vertebrates. Much less is known about how induction leads to the correct positioning of boundaries; for example, between germ layers. Here we report that the neuroectoderm/mesoderm boundary is controlled by the chromatin remodeling ATPase CHD4/Mi-2beta. Gain and loss of CHD4 function experiments shifted this boundary along the animal-vegetal axis at gastrulation, leading to excess mesoderm formation at the expense of neuroectoderm, or vice versa. This phenotype results from specific alterations in gene transcription, notably of the neural-promoting gene Sip1 and the mesodermal regulatory gene Xbra. We show that CHD4 suppresses Sip1 transcription by direct binding to the 5' end of the Sip1 gene body. Furthermore, we demonstrate that CHD4 and Sip1 expression levels determine the "ON" threshold for Nodal-dependent but not for eFGF-dependent induction of Xbra transcription. The CHD4/Sip1 epistasis thus constitutes a regulatory module, which balances mesoderm and neuroectoderm formation.
AU  - Linder, B.*
AU  - Mentele, E.*
AU  - Mansperger, K.*
AU  - Straub, T.*
AU  - Kremmer, E.
AU  - Rupp, R.A.*
C1  - 3163
C2  - 24808
SP  - 973-983
TI  - CHD4/Mi-2 beta activity is required for the positioning of the mesoderm/neuroectoderm boundary in Xenopus
JO  - Genes Dev.
VL  - 21
IS  - 8
PB  - Cold Spring Harbor Laboratory Press
PY  - 2007
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Glucocorticoid receptor (GR)-mediated transrepression of the transcription factors AP-1 and NF-kappaB, responsible for most of the anti-inflammatory effects of glucocorticoids, is initiated by the tethering of GR to the promoters of target genes. We report that this tethering is mediated by a nuclear isoform of the focal adhesion LIM domain protein Trip6. Trip6 functions as a coactivator for both AP-1 and NF-kappaB. As shown by chromatin immunoprecipitation, Trip6 is recruited to the promoters of target genes together with AP-1 or NF-kappaB. In the presence of glucocorticoids, GR joins the Trip6 complex. Reducing the level of Trip6 by RNA interference or abolishing its interaction with GR by dominant-negative mutation eliminates transrepression. We propose that GR tethering to the target promoter through Trip6 forms the basis of transrepression, and that Trip6 exerts its nuclear functions by acting as a molecular platform, enabling target promoters to integrate activating or repressing signals.
AU  - Kassel, O.*
AU  - Schneider, S.*
AU  - Heilbock, C.*
AU  - Litfin, M.*
AU  - Göttlicher, M.
AU  - Herrlich, P.*
C1  - 4633
C2  - 22233
SP  - 2518-2528
TI  - A nuclear isoform of the focal adhesion LIM-domain protein Trip6 integrates activating and repressing signals at AP-1- and NK-kB-regulated promoters.
JO  - Genes Dev.
VL  - 18
PY  - 2004
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - The vestibular system of the inner ear is responsible for the perception of motion and gravity. Key elements of this organ are otoconia, tiny biomineral particles in the utricle and the saccule. In response to gravity or linear acceleration, otoconia deflect the stereocilia of the hair cells, thus transducing kinetic movements into sensorineural action potentials. Here, we present an allelic series of mutations at the otoconia-deficient head tilt (het) locus, affecting the gene for NADPH oxidase 3 (Nox3). This series of mutations identifies for the first time a protein with a clear enzymatic function as indispensable for otoconia morphogenesis.
AU  - Paffenholz, R.*
AU  - Heinzmann, U.
C1  - 1753
C2  - 22719
SP  - 1-6
TI  - Vestibular defects in head-tilt mice result from mutations in Nox3, encoding an NADPH oxidase.
JO  - Genes Dev.
VL  - 18
IS  - 5
PY  - 2004
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Chemical mutagenesis in the mouse is a powerful approach for phenotype-driven genetics, but questions remain about the efficiency with which new mutations ascertained by their phenotype can be localized and identified, and that knowledge applied to a specific biological problem. During a global screen for dominant phenotypes in about 30,000 animals, a novel class of pigmentation mutants were identified by dark skin (Dsk). We determined the genetic map location, homozygous phenotype, and histology of 10 new Dsk and 2 new dark coat (Dcc) mutations, and identified mutations in Agouti (Met1Leu, Dcc4), Sox18 (Leu220ter, Dcc1), Keratin 2e (Thr500Pro, Dsk2), and Egfr (Leu863Gln, Dsk5). Cutaneous effects of most Dsk mutations are limited to melanocytes, except for the Keratin 2e and Egfr mutations, in which hyperkeratosis and epidermal thickening precede epidermal melanocytosis by 3-6 wk. The Dsk2 mutation is likely to impair intermediate filament assembly, leading to cytolysis of suprabasal keratinocytes and secondary hyperkeratosis and melanocytosis. The Dsk5 mutation causes increased tyrosine kinase activity and a decrease in steady-state receptor levels in vivo. The Dsk mutations represent genes or map locations not implicated previously in pigmentation, and delineate a developmental pathway in which mutations can be classified on the basis of body region, microscopic site, and timing of pigment accumulation.
AU  - Fitch, K.R.*
AU  - McGowan, K.A.*
AU  - vvan Raamsdonk, C.D.*
AU  - Fuchs, H.
AU  - Lee, D.*
AU  - Puech, A.*
AU  - Herault, Y.*
AU  - Threadgill, D.W.*
AU  - Hrabě de Angelis, M.
AU  - Barsh, G.S.*
C1  - 22268
C2  - 21038
SP  - 214-228
TI  - Genetics of dark skin in mice.
JO  - Genes Dev.
VL  - 17
PY  - 2003
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - During embryonic development in vertebrates, the endoderm becomes patterned along the anteroposterior axis to produce distinct derivatives. How this regulation is controlled is not well understood. We report that the zebrafish hairy/enhancer of split [E(spl)]-related gene her5 plays a critical role in this process. At gastrulation, following endoderm induction and further cell interaction processes including a local release of Notch/Delta signaling, her5 expression is progressively excluded from the presumptive anterior- and posteriormost mesendodermal territories to become restricted to an adjacent subpopulation of dorsal endodermal precursors. Ectopic misexpressions of wild-type and mutant forms of her5 reveal that her5 functions primarily within the endodermal/endmost mesendodermal germ layer to inhibit cell participation to the endmost-fated mesendoderm. In this process, her5 acts as an active transcriptional repressor. These features are strikingly reminiscent of the function of Drosophila Hairy/E(spl) factors in cell fate decisions. Our results provide the first model for vertebrate endoderm patterning where an early regulatory step at gastrulation, mediated by her5 controls cell contribution jointly to the anterior- and posteriormost mesendodermal regions.
AU  - Bally-Cuif, L.
AU  - Goutel, C.*
AU  - Wassef, M.*
AU  - Wurst, W.
AU  - Rosa, F.*
C1  - 21741
C2  - 19925
SP  - 1664-1677
TI  - Coregulation of anterior and posterior mesendodermal development by a hairy-related transcriptional repressor.
JO  - Genes Dev.
VL  - 14
IS  - 13
PY  - 2000
SN  - 0890-9369
ER  - 

TY  - JOUR
AB  - Proximal–distal outgrowth of the vertebrate limb bud is regulated by the apical ectodermal ridge (AER), which forms at an invariant position along the dorsal–ventral (D/V) axis of the embryo. We have studied the genetic and cellular events that regulate AER formation in the mouse. In contrast to implications from previous studies in chick, we identified two distinct lineage boundaries in mouse ectoderm prior to limb bud outgrowth using a Cre/loxP-based fate-mapping approach and a novel retroviral cell-labeling technique. One border is transient and at the limit of expression of the ventral gene En1, which corresponds to the D/V midline of the AER, and the second border corresponds to the dorsal AER margin. Labeling of AER precursors using an inducible Cre showed that not all cells that initially express AER genes form the AER, indicating that signaling is required to maintain an AER phenotype. Misexpression of En1 at moderate levels specifically in the dorsal AER of transgenic mice was found to produce dorsally shifted AER fragments, whereas high levels of En1 abolished AER formation. In both cases, the dorsal gene Wnt7a was repressed in cells adjacent to the En1-expressing cells, demonstrating that signaling regulated by EN1 occurs across the D/V border. Finally, fate mapping of AER domains in these mutants showed that En1 plays a part in positioning and maintaining the two lineage borders.Proximal–distal outgrowth of the vertebrate limb bud is regulated by the apical ectodermal ridge (AER), which forms at an invariant position along the dorsal–ventral (D/V) axis of the embryo. We have studied the genetic and cellular events that regulate AER formation in the mouse. In contrast to implications from previous studies in chick, we identified two distinct lineage boundaries in mouse ectoderm prior to limb bud outgrowth using a Cre/loxP-based fate-mapping approach and a novel retroviral cell-labeling technique. One border is transient and at the limit of expression of the ventral gene En1, which corresponds to the D/V midline of the AER, and the second border corresponds to the dorsal AER margin. Labeling of AER precursors using an inducible Cre showed that not all cells that initially express AER genes form the AER, indicating that signaling is required to maintain an AER phenotype. Misexpression of En1 at moderate levels specifically in the dorsal AER of transgenic mice was found to produce dorsally shifted AER fragments, whereas high levels of En1 abolished AER formation. In both cases, the dorsal gene Wnt7a was repressed in cells adjacent to the En1-expressing cells, demonstrating that signaling regulated by EN1 occurs across the D/V border. Finally, fate mapping of AER domains in these mutants showed that En1 plays a part in positioning and maintaining the two lineage borders.
AU  - Kimmel, R.A.*
AU  - Turnbull, D.H.*
AU  - Blanquet, V.*
AU  - Wurst, W.
AU  - Loomis, C.A.*
AU  - Joyner, A.L.*
C1  - 3822
C2  - 22819
SP  - 1377-1389
TI  - Two lineage boundaries coordinate vertebrate apical ectodermal ridge formation.
JO  - Genes Dev.
VL  - 14
PY  - 2000
SN  - 0890-9369
ER  -