TY - JOUR AU - Chen, X.W.* AU - Don, A.S.* AU - Fedorova, M.* AU - Harayama, T.* AU - Krahmer, N. AU - Nagata, S.* AU - Narayan, P.* AU - Nicholas, D.* AU - Nowinski, S.M.* AU - Saheki, Y.* AU - Semenkovich, C.F.* AU - Zhao, X.* AU - Zou, Y.* C1 - 73311 C2 - 57005 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 169-174 TI - Time for lipid cell biology. JO - Nat. Cell Biol. VL - 27 IS - 2 PB - Nature Portfolio PY - 2025 SN - 1465-7392 ER - TY - JOUR AB - The regulatory mechanisms that drive oncogene expression in gliomas remain poorly understood. A study now identifies a role for widespread rearrangements of the enhancer connectome. Such rearrangements are linked to known genetic risk variants, revealing how genetic predisposition contributes to malignancy. AU - Fratton, A. AU - Bonev, B. C1 - 75707 C2 - 58160 SP - 1603-1604 TI - Deciphering glioma susceptibility. JO - Nat. Cell Biol. VL - 27 IS - 10 PY - 2025 SN - 1465-7392 ER - TY - JOUR AB - Recent machine-learning (ML)-based advances in single-cell data science have enabled the stratification of human tissue donors at single-cell resolution, promising to provide valuable diagnostic and prognostic insights. However, such insights are susceptible to biases. Here we discuss various biases that emerge along the pipeline of ML-based single-cell analysis, ranging from societal biases affecting whose samples are collected, to clinical and cohort biases that influence the generalizability of single-cell datasets, biases stemming from single-cell sequencing, ML biases specific to (weakly supervised or unsupervised) ML models trained on human single-cell samples and biases during the interpretation of results from ML models. We end by providing methods for single-cell data scientists to assess and mitigate biases, and call for efforts to address the root causes of biases. AU - Willem, T. AU - Shitov, V.A. AU - Luecken, M. AU - Kilbertus, N. AU - Bauer, S. AU - Piraud, M. AU - Buyx, A.* AU - Theis, F.J. C1 - 73433 C2 - 57061 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 384–392 TI - Biases in machine-learning models of human single-cell data. JO - Nat. Cell Biol. VL - 27 PB - Nature Portfolio PY - 2025 SN - 1465-7392 ER - TY - JOUR AB - Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show that fasting induces an intestine-specific, reversible and large-scale spatial reorganization of chromatin in Caenorhabditis elegans. This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, acting through the regulation of RNA Pol I, but not Pol II nor Pol III, and is accompanied by remodelling of the nucleolus. By uncoupling the 3D genome configuration from the animal's nutritional status, we find that the expression of metabolic and stress-related genes increases when the spatial reorganization of chromatin occurs, showing that the 3D genome might support the transcriptional response in fasted animals. Our work documents a large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients. AU - Al-Refaie, N. AU - Padovani, F. AU - Hornung, J. AU - Pudelko, L AU - Binando, F. AU - Del Carmen Fabregat, A.* AU - Zhao, Q.* AU - Towbin, B.D.* AU - Cenik, E.S.* AU - Stroustrup, N.* AU - Padeken, J.* AU - Schmoller, K.M. AU - Cabianca, D.S. C1 - 71779 C2 - 56182 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis. JO - Nat. Cell Biol. PB - Nature Portfolio PY - 2024 SN - 1465-7392 ER - TY - JOUR AB - Ferroptosis, an intricately regulated form of cell death characterized by uncontrolled lipid peroxidation, has garnered substantial interest since this term was first coined in 2012. Recent years have witnessed remarkable progress in elucidating the detailed molecular mechanisms that govern ferroptosis induction and defence, with particular emphasis on the roles of heterogeneity and plasticity. In this Review, we discuss the molecular ecosystem of ferroptosis, with implications that may inform and enable safe and effective therapeutic strategies across a broad spectrum of diseases. AU - Dai, E.* AU - Chen, X.* AU - Linkermann, A.* AU - Jiang, X.* AU - Kang, R.* AU - Kagan, V.E.* AU - Bayir, H.* AU - Yang, W.S.* AU - Garcia-Saez, A.J.* AU - Ioannou, M.S.* AU - Janowitz, T.* AU - Ran, Q.* AU - Gu, W.* AU - Gan, B.* AU - Krysko, D.V.* AU - Zhu, X.* AU - Wang, J.* AU - Krautwald, S.* AU - Toyokuni, S.* AU - Xie, Y.* AU - Greten, F.R.* AU - Yi, Q.* AU - Schick, J. AU - Liu, J.* AU - Gabrilovich, D.I.* AU - Zeh, H.J.* AU - Zhang, D.D.* AU - Yang, M.* AU - Iovanna, J.L.* AU - Kopf, M.* AU - Adolph, T.E.* AU - Chi, J.T.* AU - Li, C.* AU - Ichijo, H.* AU - Karin, M.* AU - Sankaran, V.G.* AU - Zou, W.* AU - Galluzzi, L.* AU - Bush, A.I.* AU - Li, B.* AU - Melino, G.* AU - Baehrecke, E.H.* AU - Lotze, M.T.* AU - Klionsky, D.J.* AU - Stockwell, B.R.* AU - Kroemer, G.* AU - Tang, D.* C1 - 70099 C2 - 55419 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - A guideline on the molecular ecosystem regulating ferroptosis. JO - Nat. Cell Biol. PB - Nature Portfolio PY - 2024 SN - 1465-7392 ER - TY - JOUR AB - Correction to: Nature Cell Biologyhttps://doi.org/10.1038/ncb3225, published online 17 August 2015 In the version of the article initially published, the 4EBP1 DN panel in Fig. 7a and the Torin 1 panel (fluorescence) in Supplementary Fig. 7a were duplicated due to an error in figure preparation. Supplementary Fig. 7a is correct. The corrected images for Fig. 7a stemming from an existing experimental replicate are shown below in Fig. 1. The errors are in presentation only and do not affect the conclusions of the study. The authors apologize for this error. (Figure presented.) Corrected Fig. 7a. AU - Herranz, N.* AU - Gallage, S.* AU - Mellone, M.* AU - Wuestefeld, T.* AU - Klotz, S.* AU - Hanley, C.J.* AU - Raguz, S.* AU - Acosta, J.C.* AU - Innes, A.J.* AU - Banito, A.* AU - Georgilis, A.* AU - Montoya, A.* AU - Wolter, K.* AU - Dharmalingam, G.* AU - Faull, P.* AU - Carroll, T.* AU - Martínez-Barbera, J.P.* AU - Cutillas, P.* AU - Reisinger, F. AU - Heikenwälder, M. AU - Miller, R.A.* AU - Withers, D.* AU - Zender, L.* AU - Thomas, G.J.* AU - Gil, J.* C1 - 70733 C2 - 55672 TI - Author Correction: mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype. JO - Nat. Cell Biol. VL - 26 IS - 6 PY - 2024 SN - 1465-7392 ER - TY - JOUR AB - Dynamic epigenomic reprogramming occurs during mammalian oocyte maturation and early development. However, the underlying transcription circuitry remains poorly characterized. By mapping cis-regulatory elements using H3K27ac, we identified putative enhancers in mouse oocytes and early embryos distinct from those in adult tissues, enabling global transitions of regulatory landscapes around fertilization and implantation. Gene deserts harbour prevalent putative enhancers in fully grown oocytes linked to oocyte-specific genes and repeat activation. Embryo-specific enhancers are primed before zygotic genome activation and are restricted by oocyte-inherited H3K27me3. Putative enhancers in oocytes often manifest H3K4me3, bidirectional transcription, Pol II binding and can drive transcription in STARR-seq and a reporter assay. Finally, motif analysis of these elements identified crucial regulators of oogenesis, TCF3 and TCF12, the deficiency of which impairs activation of key oocyte genes and folliculogenesis. These data reveal distinctive regulatory landscapes and their interacting transcription factors that underpin the development of mammalian oocytes and early embryos. AU - Liu, B.* AU - He, Y.* AU - Wu, X.* AU - Lin, Z.* AU - Ma, J.* AU - Qiu, Y.* AU - Xiang, Y.* AU - Kong, F.* AU - Lai, F.* AU - Pal, M. AU - Wang, P.* AU - Ming, J.* AU - Zhang, B.* AU - Wang, Q.* AU - Wu, J.* AU - Xia, W.* AU - Shen, W.* AU - Na, J.* AU - Torres-Padilla, M.E. AU - Li, J.* AU - Xie, W.* C1 - 70807 C2 - 55751 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 962-974 TI - Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators. JO - Nat. Cell Biol. VL - 26 IS - 6 PB - Nature Portfolio PY - 2024 SN - 1465-7392 ER - TY - JOUR AB - Ferroptosis is a distinct lipid peroxidation-dependent form of necrotic cell death. This process has been increasingly contemplated as a new target for cancer therapy because of an intrinsic or acquired ferroptosis vulnerability in difficult-to-treat cancers and tumour microenvironments. Here we review recent advances in our understanding of the molecular mechanisms that underlie ferroptosis and highlight available tools for the modulation of ferroptosis sensitivity in cancer cells and communication with immune cells within the tumour microenvironment. We further discuss how these new insights into ferroptosis-activating pathways can become new armouries in the fight against cancer. AU - Nakamura, T. AU - Conrad, M. C1 - 70822 C2 - 55705 CY - Heidelberger Platz 3, Berlin, 14197, Germany TI - Exploiting ferroptosis vulnerabilities in cancer. JO - Nat. Cell Biol. PB - Nature Portfolio PY - 2024 SN - 1465-7392 ER - TY - JOUR AB - Brown adipose tissue (BAT) is a central thermogenic organ that enhances energy expenditure and cardiometabolic health. However, regulators that specifically increase the number of thermogenic adipocytes are still an unmet need. Here, we show that the cAMP-binding protein EPAC1 is a central regulator of adaptive BAT growth. In vivo, selective pharmacological activation of EPAC1 increases BAT mass and browning of white fat, leading to higher energy expenditure and reduced diet-induced obesity. Mechanistically, EPAC1 coordinates a network of regulators for proliferation specifically in thermogenic adipocytes, but not in white adipocytes. We pinpoint the effects of EPAC1 to PDGFRα-positive preadipocytes, and the loss of EPAC1 in these cells impedes BAT growth and worsens diet-induced obesity. Importantly, EPAC1 activation enhances the proliferation and differentiation of human brown adipocytes and human brown fat organoids. Notably, a coding variant of RAPGEF3 (encoding EPAC1) that is positively correlated with body mass index abolishes noradrenaline-induced proliferation of brown adipocytes. Thus, EPAC1 might be an attractive target to enhance thermogenic adipocyte number and energy expenditure to combat metabolic diseases. AU - Reverte-Salisa, L.* AU - Siddig, S.* AU - Hildebrand, S.* AU - Yao, X.* AU - Zurkovic, J.* AU - Jaeckstein, M.Y.* AU - Heeren, J.* AU - Lezoualc’h, F.* AU - Krahmer, N. AU - Pfeifer, A.* C1 - 69729 C2 - 55196 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 113–123 TI - EPAC1 enhances brown fat growth and beige adipogenesis. JO - Nat. Cell Biol. VL - 26 PB - Nature Portfolio PY - 2024 SN - 1465-7392 ER - TY - JOUR AB - Metabolic demands fluctuate rhythmically and rely on coordination between the circadian clock and nutrient-sensing signalling pathways, yet mechanisms of their interaction remain not fully understood. Surprisingly, we find that class 3 phosphatidylinositol-3-kinase (PI3K), known best for its essential role as a lipid kinase in endocytosis and lysosomal degradation by autophagy, has an overlooked nuclear function in gene transcription as a coactivator of the heterodimeric transcription factor and circadian driver Bmal1–Clock. Canonical pro-catabolic functions of class 3 PI3K in trafficking rely on the indispensable complex between the lipid kinase Vps34 and regulatory subunit Vps15. We demonstrate that although both subunits of class 3 PI3K interact with RNA polymerase II and co-localize with active transcription sites, exclusive loss of Vps15 in cells blunts the transcriptional activity of Bmal1–Clock. Thus, we establish non-redundancy between nuclear Vps34 and Vps15, reflected by the persistent nuclear pool of Vps15 in Vps34-depleted cells and the ability of Vps15 to coactivate Bmal1–Clock independently of its complex with Vps34. In physiology we find that Vps15 is required for metabolic rhythmicity in liver and, unexpectedly, it promotes pro-anabolic de novo purine nucleotide synthesis. We show that Vps15 activates the transcription of Ppat, a key enzyme for the production of inosine monophosphate, a central metabolic intermediate for purine synthesis. Finally, we demonstrate that in fasting, which represses clock transcriptional activity, Vps15 levels are decreased on the promoters of Bmal1 targets, Nr1d1 and Ppat. Our findings open avenues for establishing the complexity for nuclear class 3 PI3K signalling for temporal regulation of energy homeostasis. AU - Alkhoury, C.* AU - Henneman, N.F.* AU - Petrenko, V.* AU - Shibayama, Y.* AU - Segaloni, A.* AU - Gadault, A.* AU - Nemazanyy, I.* AU - Le Guillou, E.* AU - Wolide, A.D. AU - Antoniadou, K.* AU - Tong, X.* AU - Tamaru, T.* AU - Ozawa, T.* AU - Girard, M.* AU - Hnia, K.* AU - Lutter, D. AU - Dibner, C.* AU - Panasyuk, G.* C1 - 68425 C2 - 54620 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 975-988 TI - Class 3 PI3K coactivates the circadian clock to promote rhythmic de novo purine synthesis. JO - Nat. Cell Biol. VL - 25 IS - 7 PB - Nature Portfolio PY - 2023 SN - 1465-7392 ER - TY - JOUR AB - Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3. AU - Gaggioli, V.* AU - Lo, C.S.Y.* AU - Reveron-Gomez, N.* AU - Jasencakova, Z.* AU - Domenech, H.* AU - Nguyen, H.* AU - Sidoli, S.* AU - Tvardovskiy, A. AU - Uruci, S.* AU - Slotman, J.A.* AU - Chai, Y.* AU - Gonçalves, J.G.S.C.S.* AU - Manolika, E.M.* AU - Jensen, O.N.* AU - Wheeler, D.* AU - Sridharan, S.* AU - Chakrabarty, S.* AU - Demmers, J.* AU - Kanaar, R.* AU - Groth, A.* AU - Taneja, N.* C1 - 68428 C2 - 54621 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 1017-1032 TI - Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability. JO - Nat. Cell Biol. VL - 25 IS - 7 PB - Nature Portfolio PY - 2023 SN - 1465-7392 ER - TY - JOUR AB - Impaired proinsulin-to-insulin processing in pancreatic β-cells is a key defective step in both type 1 diabetes and type 2 diabetes (T2D) (refs. 1,2), but the mechanisms involved remain to be defined. Altered metabolism of sphingolipids (SLs) has been linked to development of obesity, type 1 diabetes and T2D (refs. 3–8); nonetheless, the role of specific SL species in β-cell function and demise is unclear. Here we define the lipid signature of T2D-associated β-cell failure, including an imbalance of specific very-long-chain SLs and long-chain SLs. β-cell-specific ablation of CerS2, the enzyme necessary for generation of very-long-chain SLs, selectively reduces insulin content, impairs insulin secretion and disturbs systemic glucose tolerance in multiple complementary models. In contrast, ablation of long-chain-SL-synthesizing enzymes has no effect on insulin content. By quantitatively defining the SL–protein interactome, we reveal that CerS2 ablation affects SL binding to several endoplasmic reticulum–Golgi transport proteins, including Tmed2, which we define as an endogenous regulator of the essential proinsulin processing enzyme Pcsk1. Our study uncovers roles for specific SL subtypes and SL-binding proteins in β-cell function and T2D-associated β-cell failure. AU - Griess, K.* AU - Rieck, M.* AU - Müller, N.* AU - Karsai, G.* AU - Hartwig, S.* AU - Pelligra, A.* AU - Hardt, R.* AU - Schlegel, C.* AU - Kuboth, J.* AU - Uhlemeyer, C.* AU - Trenkamp, S.* AU - Jeruschke, K.* AU - Weiss, J.* AU - Peifer-Weiss, L.* AU - Xu, W. AU - Cames, S.* AU - Yi, X.* AU - Cnop, M.* AU - Beller, M.* AU - Stark, H.* AU - Kondadi, A.K.* AU - Reichert, A.S.* AU - Markgraf, D.* AU - Wammers, M.* AU - Häussinger, D.* AU - Kuss, O.* AU - Lerch, S.* AU - Eizirik, D.L.* AU - Lickert, H. AU - Lammert, E.* AU - Roden, M.* AU - Winter, D.* AU - Al-Hasani, H.* AU - Höglinger, D.* AU - Hornemann, T.* AU - Brüning, J.C.* AU - Belgardt, B.F.* C1 - 67090 C2 - 53464 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 20–29 TI - Sphingolipid subtypes differentially control proinsulin processing and systemic glucose homeostasis. JO - Nat. Cell Biol. VL - 25 IS - 1 PB - Nature Portfolio PY - 2023 SN - 1465-7392 ER - TY - JOUR AB - The increasing availability of large-scale single-cell atlases has enabled the detailed description of cell states. In parallel, advances in deep learning allow rapid analysis of newly generated query datasets by mapping them into reference atlases. However, existing data transformations learned to map query data are not easily explainable using biologically known concepts such as genes or pathways. Here we propose expiMap, a biologically informed deep-learning architecture that enables single-cell reference mapping. ExpiMap learns to map cells into biologically understandable components representing known ‘gene programs’. The activity of each cell for a gene program is learned while simultaneously refining them and learning de novo programs. We show that expiMap compares favourably to existing methods while bringing an additional layer of interpretability to integrative single-cell analysis. Furthermore, we demonstrate its applicability to analyse single-cell perturbation responses in different tissues and species and resolve responses of patients who have coronavirus disease 2019 to different treatments across cell types. AU - Lotfollahi, M. AU - Rybakov, S. AU - Hrovatin, K. AU - Hediyeh-Zadeh, S. AU - Talavera Lopez, C.N. AU - Misharin, A.V.* AU - Theis, F.J. C1 - 67409 C2 - 54162 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 337-350 TI - Biologically informed deep learning to query gene programs in single-cell atlases. JO - Nat. Cell Biol. VL - 25 IS - 2 PB - Nature Portfolio PY - 2023 SN - 1465-7392 ER - TY - JOUR AB - The selenoprotein glutathione peroxidase 4 (GPX4) is the guardian of ferroptosis, a form of cell death earmarked by unrestrained lipid peroxidation. A new study shows that the metabolic enzyme creatinine kinase B (CKB) phosphorylates GPX4, which may influence the susceptibility of cancer cells to ferroptosis. AU - Mishima, E. AU - Conrad, M. C1 - 67760 C2 - 54238 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 633-634 TI - Nonmetabolic role for CKB in ferroptosis. JO - Nat. Cell Biol. VL - 25 IS - 5 PB - Nature Portfolio PY - 2023 SN - 1465-7392 ER - TY - JOUR AB - Gene expression is regulated by multiple epigenetic mechanisms, which are coordinated in development and disease. However, current multiomics methods are frequently limited to one or two modalities at a time, making it challenging to obtain a comprehensive gene regulatory signature. Here, we describe a method—3D genome, RNA, accessibility and methylation sequencing (3DRAM-seq)—that simultaneously interrogates spatial genome organization, chromatin accessibility and DNA methylation genome-wide and at high resolution. We combine 3DRAM-seq with immunoFACS and RNA sequencing in cortical organoids to map the cell-type-specific regulatory landscape of human neural development across multiple epigenetic layers. Finally, we apply a massively parallel reporter assay to profile cell-type-specific enhancer activity in organoids and to functionally assess the role of key transcription factors for human enhancer activation and function. More broadly, 3DRAM-seq can be used to profile the multimodal epigenetic landscape in rare cell types and different tissues. AU - Noack, F. AU - Vangelisti, S. AU - Ditzer, N.* AU - Chong, F. AU - Albert, M.* AU - Bonev, B. C1 - 68866 C2 - 53682 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 1873-1883 TI - Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids. JO - Nat. Cell Biol. VL - 12 IS - 12 PB - Nature Portfolio PY - 2023 SN - 1465-7392 ER - TY - JOUR AB - Despite their fundamental role in assessing (patho)physiological cell states, conventional gene reporters can follow gene expression but leave scars on the proteins or substantially alter the mature messenger RNA. Multi-time-point measurements of non-coding RNAs are currently impossible without modifying their nucleotide sequence, which can alter their native function, half-life and localization. Thus, we developed the intron-encoded scarless programmable extranuclear cistronic transcript (INSPECT) as a minimally invasive transcriptional reporter embedded within an intron of a gene of interest. Post-transcriptional excision of INSPECT results in the mature endogenous RNA without sequence alterations and an additional engineered transcript that leaves the nucleus by hijacking the nuclear export machinery for subsequent translation into a reporter or effector protein. We showcase its use in monitoring interleukin-2 (IL2) after T cell activation and tracking the transcriptional dynamics of the long non-coding RNA (lncRNA) NEAT1 during CRISPR interference-mediated perturbation. INSPECT is a method for monitoring gene transcription without altering the mature lncRNA or messenger RNA of the target of interest. AU - Truong, D.J.J. AU - Armbrust, N. AU - Geilenkeuser, J. AU - Lederer, E.-M. AU - Santl, T. AU - Beyer, M. AU - Ittermann, S. AU - Steinmaßl, E. AU - Dyka, M. AU - Raffl, G. AU - Phlairaharn, T. AU - Greisle, T. AU - Živanić, M. AU - Grosch, M. AU - Drukker, M. AU - Westmeyer, G.G. C1 - 66597 C2 - 53198 SP - 1666-1676 TI - Intron-encoded cistronic transcripts for minimally invasive monitoring of coding and non-coding RNAs. JO - Nat. Cell Biol. VL - 24 IS - 11 PY - 2022 SN - 1465-7392 ER - TY - JOUR AB - A Correction to this paper has been published: https://doi.org/10.1038/s41556-021-00667-0. AU - Böttcher, A. AU - Büttner, M. AU - Tritschler, S. AU - Sterr, M. AU - Aliluev, A. AU - Oppenländer, L. AU - Burtscher, I. AU - Sass, S. AU - Irmler, M. AU - Beckers, J. AU - Ziegenhain, C.* AU - Enard, W.* AU - Schamberger, A.C. AU - Verhamme, F.M. AU - Eickelberg, O. AU - Theis, F.J. AU - Lickert, H. C1 - 61842 C2 - 50486 SP - 566-576 TI - Author Correction: Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates. JO - Nat. Cell Biol. VL - 23 IS - 5 PY - 2021 SN - 1465-7392 ER - TY - JOUR AB - A detailed understanding of intestinal stem cell (ISC) self-renewal and differentiation is required to treat chronic intestinal diseases. However, the different models of ISC lineage hierarchy1–6 and segregation7–12 are subject to debate. Here, we have discovered non-canonical Wnt/planar cell polarity (PCP)-activated ISCs that are primed towards the enteroendocrine or Paneth cell lineage. Strikingly, integration of time-resolved lineage labelling with single-cell gene expression analysis revealed that both lineages are directly recruited from ISCs via unipotent transition states, challenging the existence of formerly predicted bi- or multipotent secretory progenitors7–12. Transitory cells that mature into Paneth cells are quiescent and express both stem cell and secretory lineage genes, indicating that these cells are the previously described Lgr5+ label-retaining cells7. Finally, Wnt/PCP-activated Lgr5+ ISCs are molecularly indistinguishable from Wnt/β-catenin-activated Lgr5+ ISCs, suggesting that lineage priming and cell-cycle exit is triggered at the post-transcriptional level by polarity cues and a switch from canonical to non-canonical Wnt/PCP signalling. Taken together, we redefine the mechanisms underlying ISC lineage hierarchy and identify the Wnt/PCP pathway as a new niche signal preceding lateral inhibition in ISC lineage priming and segregation. AU - Böttcher, A. AU - Büttner, M. AU - Tritschler, S. AU - Sterr, M. AU - Aliluev, A. AU - Oppenländer, L. AU - Burtscher, I. AU - Sass, S. AU - Irmler, M. AU - Beckers, J. AU - Ziegenhain, C.* AU - Enard, W.* AU - Schamberger, A.C. AU - Verhamme, F.M. AU - Eickelberg, O. AU - Theis, F.J. AU - Lickert, H. C1 - 60923 C2 - 49691 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 23-31 TI - Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates. JO - Nat. Cell Biol. VL - 23 IS - 1 PB - Nature Research PY - 2021 SN - 1465-7392 ER - TY - JOUR AB - Lineage-specific gene expression programs in multicellular organisms are controlled by balanced ON and OFF signals, amongst which heterochromatin regulates expression by restricting activation cues. A study now provides insights into mammalian heterochromatin organisation, function and interplay with lineage-specific transcription factors. AU - Burton, A. AU - Torres-Padilla, M.E. C1 - 62755 C2 - 51034 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 814-816 TI - Deconfining heterochromatin for expression. JO - Nat. Cell Biol. VL - 23 IS - 8 PB - Nature Portfolio PY - 2021 SN - 1465-7392 ER - TY - JOUR AB - Formerly regarded as 'junk' DNA, transposable elements are now thought to be players in genome evolution. A new study reveals remarkable conservation of a retrotransposon insertion acting as an alternative promoter to drive the expression of a cell cycle regulator isoform in early embryos, potentially controlling the timing of pre-implantation development. AU - Canat, A. AU - Torres-Padilla, M.E. C1 - 63807 C2 - 51629 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 1221-1223 TI - Retrotransposing a promoter for development. JO - Nat. Cell Biol. VL - 23 PB - Nature Portfolio PY - 2021 SN - 1465-7392 ER - TY - JOUR AB - It is generally accepted that epiblast cells ingress into the primitive streak by epithelial-to-mesenchymal transition (EMT) to give rise to the mesoderm; however, it is less clear how the endoderm acquires an epithelial fate. Here, we used embryonic stem cell and mouse embryo knock‐in reporter systems to combine time-resolved lineage labelling with high-resolution single-cell transcriptomics. This allowed us to resolve the morphogenetic programs that segregate the mesoderm from the endoderm germ layer. Strikingly, while the mesoderm is formed by classical EMT, the endoderm is formed independent of the key EMT transcription factor Snail1 by mechanisms of epithelial cell plasticity. Importantly, forkhead box transcription factor A2 (Foxa2) acts as an epithelial gatekeeper and EMT suppressor to shield the endoderm from undergoing a mesenchymal transition. Altogether, these results not only establish the morphogenetic details of germ layer formation, but also have broader implications for stem cell differentiation and cancer metastasis. AU - Scheibner, K. AU - Schirge, S. AU - Burtscher, I. AU - Büttner, M. AU - Sterr, M. AU - Yang, D.* AU - Böttcher, A. AU - Ansarullah AU - Irmler, M. AU - Beckers, J. AU - Cernilogar, F.M.* AU - Schotta, G.* AU - Theis, F.J. AU - Lickert, H. C1 - 62373 C2 - 50697 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 692-703 TI - Epithelial cell plasticity drives endoderm formation during gastrulation. JO - Nat. Cell Biol. VL - 23 IS - 7 PB - Nature Research PY - 2021 SN - 1465-7392 ER - TY - JOUR AB - In the version of this Article originally published, text referencing ATAC-seq data was incorrectly retained. References to ATAC-seq data, which are not included in this study, should be removed from the text in the Results sections ‘In vitro-generated definitive endoderm forms by partial EMT’ and ‘Foxa2 suppresses a complete EMT during endoderm formation’, as well as from the author contributions section. The Methods subsection ‘ChIP-seq and ATAC-seq data visualization’ should also be completely removed. The errors have been corrected. AU - Scheibner, K. AU - Schirge, S. AU - Burtscher, I. AU - Büttner, M. AU - Sterr, M. AU - Yang, D.* AU - Böttcher, A. AU - Ansarullah AU - Irmler, M. AU - Beckers, J. AU - Cernilogar, F.M.* AU - Schotta, G.* AU - Theis, F.J. AU - Lickert, H. C1 - 62627 C2 - 50928 TI - Publisher Correction: Epithelial cell plasticity drives endoderm formation during gastrulation. JO - Nat. Cell Biol. PY - 2021 SN - 1465-7392 ER - TY - JOUR AB - Expression of exon-specific isoforms from alternatively spliced mRNA is a fundamental mechanism that substantially expands the proteome of a cell. However, conventional methods to assess alternative splicing are either consumptive and work-intensive or do not quantify isoform expression longitudinally at the protein level. Here, we therefore developed an exon-specific isoform expression reporter system (EXSISERS), which non-invasively reports the translation of exon-containing isoforms of endogenous genes by scarlessly excising reporter proteins from the nascent polypeptide chain through highly efficient, intein-mediated protein splicing. We applied EXSISERS to quantify the inclusion of the disease-associated exon 10 in microtubule-associated protein tau (MAPT) in patient-derived induced pluripotent stem cells and screened Cas13-based RNA-targeting effectors for isoform specificity. We also coupled cell survival to the inclusion of exon 18b of FOXP1, which is involved in maintaining pluripotency of embryonic stem cells, and confirmed that MBNL1 is a dominant factor for exon 18b exclusion. EXSISERS enables non-disruptive and multimodal monitoring of exon-specific isoform expression with high sensitivity and cellular resolution, and empowers high-throughput screening of exon-specific therapeutic interventions. AU - Truong, D.J.J. AU - Phlairaharn, T. AU - Eßwein, B. AU - Gruber, C. AU - Tümen, D. AU - Baligács, E. AU - Armbrust, N. AU - Vaccaro, F.L. AU - Lederer, E.-M. AU - Beck, E.M. AU - Geilenkeuser, J. AU - Göppert, S. AU - Krumwiede, L. AU - Grätz, C. AU - Raffl, G. AU - Schwarz, D. AU - Zirngibl, M. AU - Živanić, M. AU - Beyer, M. AU - Körner, J.D. AU - Santl, T. AU - Evsyukov, V.* AU - Strauß, T.* AU - Schwarz, S.C.* AU - Höglinger, G.U.* AU - Heutink, P.* AU - Doll, S. AU - Conrad, M. AU - Giesert, F. AU - Wurst, W. AU - Westmeyer, G.G. C1 - 62194 C2 - 51010 CY - Heidelberger Platz 3, Berlin, 14197, Germany SP - 652-663 TI - Non-invasive and high-throughput interrogation of exon-specific isoform expression. JO - Nat. Cell Biol. VL - 23 IS - 6 PB - Nature Research PY - 2021 SN - 1465-7392 ER - TY - JOUR AB - Following fertilization in mammals, the gametes are reprogrammed to create a totipotent zygote, a process that involves de novo establishment of chromatin domains. A major feature occurring during preimplantation development is the dramatic remodelling of constitutive heterochromatin, although the functional relevance of this is unknown. Here, we show that heterochromatin establishment relies on the stepwise expression and regulated activity of SUV39H enzymes. Enforcing precocious acquisition of constitutive heterochromatin results in compromised development and epigenetic reprogramming, which demonstrates that heterochromatin remodelling is essential for natural reprogramming at fertilization. We find that de novo H3K9 trimethylation (H3K9me3) in the paternal pronucleus after fertilization is catalysed by SUV39H2 and that pericentromeric RNAs inhibit SUV39H2 activity and reduce H3K9me3. De novo H3K9me3 is initially non-repressive for gene expression, but instead bookmarks promoters for compaction. Overall, we uncover the functional importance for the restricted transmission of constitutive heterochromatin during reprogramming and a non-repressive role for H3K9me3.Burton et al. show that H3K9me3 deposition catalysed by SUV39H2 and regulated by pericentromeric RNAs in the mouse paternal pronucleus does not suppress gene expression, but bookmarks promoters for compaction. AU - Burton, A. AU - Brochard, V.* AU - Galan, C.* AU - Ruiz-Morales, E.R.* AU - Rovira, Q.* AU - Rodriguez-Terrones, D.* AU - Kruse, K.* AU - Le Gras, S.* AU - Udayakumar, V.S.* AU - Chin, H.G.* AU - Eid, A. AU - Liu, X.* AU - Wang, C.* AU - Gao, S.* AU - Pradhan, S.* AU - Vaquerizas, J.M.* AU - Beaujean, N.* AU - Jenuwein, T.* AU - Torres-Padilla, M.E. C1 - 59539 C2 - 48899 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England SP - 767-778 TI - Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive H3K9me3. JO - Nat. Cell Biol. VL - 22 IS - 7 PB - Nature Publishing Group PY - 2020 SN - 1465-7392 ER - TY - JOUR AB - Following implantation, the naive pluripotent epiblast of the mouse blastocyst generates a rosette, undergoes lumenogenesis and forms the primed pluripotent egg cylinder, which is able to generate the embryonic tissues. How pluripotency progression and morphogenesis are linked and whether intermediate pluripotent states exist remain controversial. We identify here a rosette pluripotent state defined by the co-expression of naive factors with the transcription factor OTX2. Downregulation of blastocyst WNT signals drives the transition into rosette pluripotency by inducing OTX2. The rosette then activates MEK signals that induce lumenogenesis and drive progression to primed pluripotency. Consequently, combined WNT and MEK inhibition supports rosette-like stem cells, a self-renewing naive-primed intermediate. Rosette-like stem cells erase constitutive heterochromatin marks and display a primed chromatin landscape, with bivalently marked primed pluripotency genes. Nonetheless, WNT induces reversion to naive pluripotency. The rosette is therefore a reversible pluripotent intermediate whereby control over both pluripotency progression and morphogenesis pivots from WNT to MEK signals. AU - Neagu, A.* AU - van Genderen, E.* AU - Escudero, I.* AU - Verwegen, L.* AU - Kurek, D.* AU - Lehmann, J.* AU - Stel, J.* AU - Dirks, R.A.M.* AU - van Mierlo, G.* AU - Maas, A.* AU - Eleveld, C.* AU - Ge, Y.* AU - den Dekker, A.T.* AU - Brouwer, R.W.W.* AU - van IJcken, W.F.J.* AU - Modic, M.* AU - Drukker, M. AU - Jansen, J.H.* AU - Rivron, N.C.* AU - Baart, E.B.* AU - Marks, H.* AU - ten Berge, D.* C1 - 59176 C2 - 48619 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England SP - 534-545 TI - In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states. JO - Nat. Cell Biol. VL - 22 IS - 5 PB - Nature Publishing Group PY - 2020 SN - 1465-7392 ER - TY - JOUR AB - Genotoxic DNA double-strand breaks (DSBs) can be repaired by error-free homologous recombination (HR) or mutagenic non-homologous end-joining(1). HR supresses tumorigenesis(1), but is restricted to the S and G2 phases of the cell cycle when a sister chromatid is present(2). Breast cancer type 1 susceptibility protein (BRCA1) promotes HR by antagonizing the anti-resection factor TP53-binding protein 1(53BP1) (refs. (2-5)), but it remains unknown how BRCA1 function is limited to the S and G2 phases. We show that BRCA1 recruitment requires recognition of histone H4 unmethylated at lysine 20 (H4K2OmeO), linking DSB repair pathway choice directly to sister chromatid availability. We identify the ankyrin repeat domain of BRCA1-associated RING domain protein 1 (BARD1)-the obligate BRCA1 binding partner(3)-as a reader of H4K2OmeO present on new histones in post-replicative chromatin(6). BARD1 ankyrin repeat domain mutations disabling H4K2OmeO recognition abrogate accumulation of BRCA1 at DSBs, causing aberrant build-up of 53BP1, and allowing anti-resection activity to prevail in S and G2. Consequently, BARD1 recognition of H4K2OmeO is required for HR and resistance to poly (ADP-ribose) polymerase inhibitors. Collectively, this reveals that BRCA1-BARD1 monitors the replicative state of the genome to oppose 53BP1 function, routing only DSBs within sister chromatids to HR. AU - Nakamura, K.* AU - Saredi, G.* AU - Becker, J.R.* AU - Foster, B. AU - Nguyen, N.V.* AU - Beyer, T.E.* AU - Cesa, L.C.* AU - Faull, P.A.* AU - Lukauskas, S. AU - Frimurer, T.* AU - Chapman, J.R.* AU - Bartke, T. AU - Groth, A.* C1 - 55668 C2 - 46390 CY - Macmillan Building, 4 Crinan St, London N1 9xw, England SP - 311-318 TI - H4K20meO recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. JO - Nat. Cell Biol. VL - 21 IS - 3 PB - Nature Publishing Group PY - 2019 SN - 1465-7392 ER - TY - JOUR AB - During fetal development, mammalian back-skin undergoes a natural transition in response to injury, from scarless regeneration to skin scarring. Here, we characterize dermal morphogenesis and follow two distinct embryonic fibroblast lineages, based on their history of expression of the engrailed 1 gene. We use single-cell fate-mapping, live three dimensional confocal imaging and in silico analysis coupled with immunolabelling to reveal unanticipated structural and regional complexity and dynamics within the dermis. We show that dermal development and regeneration are driven by engrailed 1-history-naive fibroblasts, whose numbers subsequently decline. Conversely, engrailed 1-history-positive fibroblasts possess scarring abilities at this early stage and their expansion later on drives scar emergence. The transition can be reversed, locally, by transplanting engrailed 1-naive cells. Thus, fibroblastic lineage replacement couples the decline of regeneration with the emergence of scarring and creates potential clinical avenues to reduce scarring. AU - Jiang, D. AU - Correa-Gallegos, D. AU - Christ, S. AU - Stefanska, A. AU - Liu, J. AU - Ramesh, P. AU - Rajendran, V. AU - De Santis, M. AU - Wagner, D.E. AU - Rinkevich, Y. C1 - 53338 C2 - 44576 CY - London SP - 422-431 TI - Two succeeding fibroblastic lineages drive dermal development and the transition from regeneration to scarring. JO - Nat. Cell Biol. VL - 20 IS - 4 PB - Nature Publishing Group PY - 2018 SN - 1465-7392 ER - TY - JOUR AB - End-binding proteins (EBs) are adaptors that recruit functionally diverse microtubule plus-end-tracking proteins (+TIPs) to growing microtubule plus ends. To test with high spatial and temporal accuracy how, when and where + TIP complexes contribute to dynamic cell biology, we developed a photo-inactivated EB1 variant (pi-EB1) by inserting a blue-light-sensitive protein-protein interaction module between the microtubule-binding and + TIP-binding domains of EB1 pi-EB1 replaces endogenous EB1 function in the absence of blue light. By contrast, blue-light-mediated pi-EB1 photodissociation results in rapid + TIP complex disassembly, and acutely and reversibly attenuates microtubule growth independent of microtubule end association of the microtubule polymerase CKAP5 (also known as ch-TOG and XMAP215). Local pi-EB1 photodissociation allows subcellular control of microtubule dynamics at the second and micrometre scale, and elicits aversive turning of migrating cancer cells. Importantly, light-mediated domain splitting can serve as a template to optically control other intracellular protein activities. AU - van Haren, J.* AU - Charafeddine, R.A.* AU - Ettinger, A. AU - Wang, H.* AU - Hahn, K.M.* AU - Wittmann, T.* C1 - 52872 C2 - 44466 CY - London SP - 252–261 TI - Local control of intracellular microtubule dynamics by EB1 photodissociation. JO - Nat. Cell Biol. VL - 20 IS - 3 PB - Nature Publishing Group PY - 2018 SN - 1465-7392 ER - TY - JOUR AB - Transcription factor (TF) networks are thought to regulate embryonic stem cell (ESC) pluripotency. However, TF expression dynamics and regulatory mechanisms are poorly understood. We use reporter mouse ESC lines allowing non-invasive quantification of Nanog or Oct4 protein levels and continuous long-term single-cell tracking and quantification over many generations to reveal diverse TF protein expression dynamics. For cells with low Nanog expression, we identified two distinct colony types: one re-expressed Nanog in a mosaic pattern, and the other did not re-express Nanog over many generations. Although both expressed pluripotency markers, they exhibited differences in their TF protein correlation networks and differentiation propensities. Sister cell analysis revealed that differences in Nanog levels are not necessarily accompanied by differences in the expression of other pluripotency factors. Thus, regulatory interactions of pluripotency TFs are less stringently implemented in individual self-renewing ESCs than assumed at present. AU - Filipczyk, A. AU - Marr, C. AU - Hastreiter, S. AU - Feigelman, J. AU - Schwarzfischer, M. AU - Hoppe, P.S. AU - Loeffler, D. AU - Kokkaliaris, K.D. AU - Endele, M. AU - Schauberger, B. AU - Hilsenbeck, O. AU - Skylaki, S. AU - Hasenauer, J. AU - Anastassiadis, K.* AU - Theis, F.J. AU - Schroeder, T. C1 - 46889 C2 - 39012 SP - 1235-1246 TI - Network plasticity of pluripotency transcription factors in embryonic stem cells. JO - Nat. Cell Biol. VL - 17 IS - 10 PY - 2015 SN - 1465-7392 ER - TY - JOUR AB - Senescent cells secrete a combination of factors collectively known as the senescence-associated secretory phenotype (SASP). The SASP reinforces senescence and activates an immune surveillance response, but it can also show pro-tumorigenic properties and contribute to age-related pathologies. In a drug screen to find new SASP regulators, we uncovered the mTOR inhibitor rapamycin as a potent SASP suppressor. Here we report a mechanism by which mTOR controls the SASP by differentially regulating the translation of the MK2 (also known as MAPKAPK2) kinase through 4EBP1. In turn, MAPKAPK2 phosphorylates the RNA-binding protein ZFP36L1 during senescence, inhibiting its ability to degrade the transcripts of numerous SASP components. Consequently, mTOR inhibition or constitutive activation of ZFP36L1 impairs the non-cell-autonomous effects of senescent cells in both tumour-suppressive and tumour-promoting contexts. Altogether, our results place regulation of the SASP as a key mechanism by which mTOR could influence cancer, age-related diseases and immune responses. AU - Herranz, N.* AU - Gallage, S.* AU - Mellone, M.* AU - Wuestefeld, T.* AU - Klotz, S.* AU - Hanley, C.J.* AU - Raguz, S.* AU - Acosta, J.C.* AU - Innes, A.J.* AU - Banito, A.* AU - Georgilis, A.* AU - Montoya, A.* AU - Wolter, K.* AU - Dharmalingam, G.* AU - Faull, P.* AU - Carroll, T.* AU - Martínez-Barbera, J.P.* AU - Cutillas, P.* AU - Reisinger, F. AU - Heikenwälder, M. AU - Miller, R.A.* AU - Withers, D.* AU - Zender, L.* AU - Thomas, G.J.* AU - Gil, J.* C1 - 46585 C2 - 37698 SP - 1205-1217 TI - mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype. JO - Nat. Cell Biol. VL - 17 IS - 9 PY - 2015 SN - 1465-7392 ER - TY - JOUR AB - Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease. AU - Wheway, G.* AU - Schmidts, M.* AU - Mans, D.A.* AU - Szymanska, K.* AU - Nguyen, T.T.* AU - Racher, H.* AU - Phelps, I.G.* AU - Toedt, G.* AU - Kennedy, J.* AU - Wunderlich, K.A.* AU - Sorusch, N.* AU - Abdelhamed, Z.A.* AU - Natarajan, S.* AU - Herridge, W.* AU - van Reeuwijk, J.* AU - Horn, N.* AU - Boldt, K.* AU - Parry, D.A.* AU - Letteboer, S.J.* AU - Roosing, S.* AU - Adams, M.* AU - Bell, S.M.* AU - Bond, J.* AU - Higgins, J.* AU - Morrison, E.E.* AU - Tomlinson, D.C.* AU - Slaats, G.G.* AU - van Dam, T.J.* AU - Huang, L.* AU - Kessler, K.* AU - Giessl, A.* AU - Logan, C.V.* AU - Boyle, E.A.* AU - Shendure, J.* AU - Anazi, S.* AU - Aldahmesh, M.* AU - Al Hazzaa, S.* AU - Hegele, R.A.* AU - Ober, C.* AU - Frosk, P.* AU - Mhanni, A.A.* AU - Chodirker, B.N.* AU - Chudley, A.E.* AU - Lamont, R.* AU - Bernier, F.P.* AU - Beaulieu, C.L.* AU - Gordon, P.M.* AU - Pon, R.T.* AU - Donahue, C.* AU - Barkovich, A.J.* AU - Wolf, L.* AU - Toomes, C.* AU - Thiel, C.T.* AU - Boycott, K.M.* AU - McKibbin, M.* AU - Inglehearn, C.F.* AU - Stewart, F.* AU - Omran, H.* AU - Huynen, M.A.* AU - Sergouniotis, P.I.* AU - Alkuraya, F.S.* AU - Parboosingh, J.S.* AU - Innes, A.M.* AU - Willoughby, C.E.* AU - Giles, R.H.* AU - Webster, A.R.* AU - Ueffing, M. AU - Blacque, O.E.* AU - Gleeson, J.G.* AU - Wolfrum, U.* AU - Beales, P.L.* AU - Gibson, T.J.* AU - Doherty, D.* AU - Mitchison, H.M.* AU - Roepman, R.* AU - Johnson, C.A.* C1 - 46327 C2 - 37591 CY - London SP - 1074-1087 TI - An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. JO - Nat. Cell Biol. VL - 17 IS - 8 PB - Nature Publishing Group PY - 2015 SN - 1465-7392 ER - TY - JOUR AB - Ferroptosis is a non-apoptotic form of cell death induced by small molecules in specific tumour types, and in engineered cells overexpressing oncogenic RAS. Yet, its relevance in non-transformed cells and tissues is unexplored and remains enigmatic. Here, we provide direct genetic evidence that the knockout of glutathione peroxidase 4 (Gpx4) causes cell death in a pathologically relevant form of ferroptosis. Using inducible Gpx4(-/-) mice, we elucidate an essential role for the glutathione/Gpx4 axis in preventing lipid-oxidation-induced acute renal failure and associated death. We furthermore systematically evaluated a library of small molecules for possible ferroptosis inhibitors, leading to the discovery of a potent spiroquinoxalinamine derivative called Liproxstatin-1, which is able to suppress ferroptosis in cells, in Gpx4(-/-) mice, and in a pre-clinical model of ischaemia/reperfusion-induced hepatic damage. In sum, we demonstrate that ferroptosis is a pervasive and dynamic form of cell death, which, when impeded, promises substantial cytoprotection. AU - Friedmann Angeli, J.P.F.* AU - Schneider, M.* AU - Proneth, B. AU - Tyurina, Y.Y.* AU - Tyurin, V.A.* AU - Hammond, V.J.* AU - Herbach, N.* AU - Aichler, M. AU - Walch, A.K. AU - Eggenhofer, E.* AU - Basavarajappa, D.* AU - Rådmark, O.* AU - Kobayashi, S. AU - Seibt, T. AU - Beck, H.* AU - Neff, F. AU - Esposito, I.* AU - Wanke, R.* AU - Förster, H. AU - Yefremova, O. AU - Heinrichmeyer, M. AU - Bornkamm, G.W. AU - Geissler, E.K.* AU - Thomas, S.B.* AU - Stockwell, B.R.* AU - O'Donnell, V.B.* AU - Kagan, V.E.* AU - Schick, J. AU - Conrad, M. C1 - 42780 C2 - 35335 SP - 1180-1191 TI - Inactivation of the ferroptosis regulator Gpx4 triggers acute renal failure in mice. JO - Nat. Cell Biol. VL - 16 IS - 12 PY - 2014 SN - 1465-7392 ER - TY - JOUR AB - The spindle assembly checkpoint is a conserved signalling pathway that protects genome integrity. Given its central importance, this checkpoint should withstand stochastic fluctuations and environmental perturbations, but the extent of and mechanisms underlying its robustness remain unknown. We probed spindle assembly checkpoint signalling by modulating checkpoint protein abundance and nutrient conditions in fission yeast. For core checkpoint proteins, a mere 20% reduction can suffice to impair signalling, revealing a surprising fragility. Quantification of protein abundance in single cells showed little variability (noise) of critical proteins, explaining why the checkpoint normally functions reliably. Checkpoint-mediated stoichiometric inhibition of the anaphase activator Cdc20 (Slp1 in Schizosaccharomyces pombe) can account for the tolerance towards small fluctuations in protein abundance and explains our observation that some perturbations lead to non-genetic variation in the checkpoint response. Our work highlights low gene expression noise as an important determinant of reliable checkpoint signalling. AU - Heinrich, S.* AU - Geissen, E.M.* AU - Kamenz, J.* AU - Trautmann, S.* AU - Widmer, C.* AU - Drewe, P.* AU - Knop, M.* AU - Radde, N.* AU - Hasenauer, J. AU - Hauf, S.* C1 - 28102 C2 - 32936 SP - 1328-1239 TI - Determinants of robustness in spindle assembly checkpoint signalling. JO - Nat. Cell Biol. VL - 15 IS - 11 PB - Nature Publishing PY - 2013 SN - 1465-7392 ER - TY - JOUR AB - Cellular decision-making is mediated by a complex interplay of external stimuli with the intracellular environment, in particular transcription factor regulatory networks. Here we have determined the expression of a network of 18 key haematopoietic transcription factors in 597 single primary blood stem and progenitor cells isolated from mouse bone marrow. We demonstrate that different stem/progenitor populations are characterized by distinctive transcription factor expression states, and through comprehensive bioinformatic analysis reveal positively and negatively correlated transcription factor pairings, including previously unrecognized relationships between Gata2, Gfi1 and Gfi1b. Validation using transcriptional and transgenic assays confirmed direct regulatory interactions consistent with a regulatory triad in immature blood stem cells, where Gata2 may function to modulate cross-inhibition between Gfi1 and Gfi1b. Single-cell expression profiling therefore identifies network states and allows reconstruction of network hierarchies involved in controlling stem cell fate choices, and provides a blueprint for studying both normal development and human disease. AU - Moignard, V.* AU - Macaulay, I.C.* AU - Swiers, G.* AU - Buettner, F. AU - Schütte, J.* AU - Calero-Nieto, F.J.* AU - Kinston, S.* AU - Joshi, A.* AU - Hannah, R.* AU - Theis, F.J. AU - Jacobsen, S.E.* AU - de Bruijn, M.F.* AU - Göttgens, B.* C1 - 24243 C2 - 31354 SP - 363-372 TI - Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. JO - Nat. Cell Biol. VL - 15 IS - 4 PB - Nature Publishing Group PY - 2013 SN - 1465-7392 ER - TY - JOUR AB - The adult mouse subependymal zone (SEZ) harbours adult neural stem cells (aNSCs) that give rise to neuronal and oligodendroglial progeny. However it is not known whether the same aNSC can give rise to neuronal and oligodendroglial progeny or whether these distinct progenies constitute entirely separate lineages. Continuous live imaging and single-cell tracking of aNSCs and their progeny isolated from the mouse SEZ revealed that aNSCs exclusively generate oligodendroglia or neurons, but never both within a single lineage. Moreover, activation of canonical Wnt signalling selectively stimulated proliferation within the oligodendrogliogenic lineage, resulting in a massive increase in oligodendrogliogenesis without changing lineage choice or proliferation within neurogenic clones. In vivo activation or inhibition of canonical Wnt signalling respectively increased or decreased the number of Olig2 and PDGFR-alpha positive cells, suggesting that this pathway contributes to the fine tuning of oligodendrogliogenesis in the adult SEZ. AU - Ortega, F.* AU - Gascón, S. AU - Masserdotti, G. AU - Deshpande, A.* AU - Simon, C.* AU - Fischer, J. AU - Dimou, L. AU - Lie, D.C.C.* AU - Schroeder, T. AU - Berninger, B. C1 - 25743 C2 - 31917 SP - 602-613 TI - Oligodendrogliogenic and neurogenic adult subependymal zone neural stem cells constitute distinct lineages and exhibit differential responsiveness to Wnt signalling. JO - Nat. Cell Biol. VL - 15 IS - 6 PB - Nature Publishing PY - 2013 SN - 1465-7392 ER - TY - JOUR AB - Aquaporins are membrane channels that facilitate water movement across cell membranes. In plants, aquaporins contribute to water relations. Here, we establish a new link between aquaporin-dependent tissue hydraulics and auxin-regulated root development in Arabidopsis thaliana. We report that most aquaporin genes are repressed during lateral root formation and by exogenous auxin treatment. Auxin reduces root hydraulic conductivity both at the cell and whole-organ levels. The highly expressed aquaporin PIP2;1 is progressively excluded from the site of the auxin response maximum in lateral root primordia (LRP) whilst being maintained at their base and underlying vascular tissues. Modelling predicts that the positive and negative perturbations of PIP2;1 expression alter water flow into LRP, thereby slowing lateral root emergence (LRE). Consistent with this mechanism, pip2;1 mutants and PIP2;1-overexpressing lines exhibit delayed LRE. We conclude that auxin promotes LRE by regulating the spatial and temporal distribution of aquaporin-dependent root tissue water transport. AU - Péret, B.* AU - Li, G.* AU - Zhao, J.* AU - Band, L.R.* AU - Voß, U.* AU - Postaire, O.* AU - Luu, D.T.* AU - Da Ines, O. AU - Casimiro, I.* AU - Lucas, M.* AU - Wells, D.M.* AU - Lazzerini, L.* AU - Nacry, P.* AU - King, J.R.* AU - Jensen, O.E.* AU - Schäffner, A. AU - Maurel, C.* AU - Bennett, M.J.* C1 - 10522 C2 - 30271 SP - 991-998 TI - Auxin regulates aquaporin function to facilitate lateral root emergence. JO - Nat. Cell Biol. VL - 14 IS - 10 PB - Macmillan Publishers Ltd. PY - 2012 SN - 1465-7392 ER - TY - JOUR AB - Kinases and phosphatases regulate messenger RNA synthesis through post-translational modification of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (ref. 1). In yeast, the phosphatase Cdc14 is required for mitotic exit2, 3 and for segregation of repetitive regions4. Cdc14 is also a subunit of the silencing complex RENT (refs 5, 6), but no roles in transcriptional repression have been described. Here we report that inactivation of Cdc14 causes silencing defects at the intergenic spacer sequences of ribosomal genes during interphase and at Y′ repeats in subtelomeric regions during mitosis. We show that the role of Cdc14 in silencing is independent of the RENT deacetylase subunit Sir2. Instead, Cdc14 acts directly on RNA polymerase II by targeting CTD phosphorylation at Ser 2 and Ser 5. We also find that the role of Cdc14 as a CTD phosphatase is conserved in humans. Finally, telomere segregation defects in cdc14 mutants4 correlate with the presence of subtelomeric Y′ elements and can be rescued by transcriptional inhibition of RNA polymerase II. AU - Clemente-Blanco, A.* AU - Sen, N.* AU - Mayan-Santos, M.* AU - Sacristán, M.P.* AU - Graham, B.* AU - Jarmuz, A.* AU - Giess, A.* AU - Webb, E.* AU - Game, L.* AU - Eick, D. AU - Bueno, A.* AU - Merkenschlager, M* AU - Aragón, L.* C1 - 6661 C2 - 29059 SP - 1450-1456 TI - Cdc14 phosphatase promotes segregation of telomeres through repression of RNA polymerase II transcription. JO - Nat. Cell Biol. VL - 13 IS - 12 PB - Nature Publ. Group PY - 2011 SN - 1465-7392 ER - TY - JOUR AB - Gene expression reprogramming governs cellular processes such as proliferation, differentiation and cell migration through the complex and tightly regulated control of transcriptional cofactors that exist in multiprotein complexes. Here we describe SCAI (suppressor of cancer cell invasion), a novel and highly conserved protein that regulates invasive cell migration through three-dimensional matrices. SCAI acts on the RhoA-Dia1 signal transduction pathway and localizes in the nucleus, where it binds and inhibits the myocardin-related transcription factor MAL by forming a ternary complex with serum response factor (SRF). Genomewide expression analysis surprisingly reveals that one of the strongest upregulated genes after suppression of SCAI is beta(1)-integrin. Decreased levels of SCAI are tightly correlated with increased invasive cell migration, and SCAI is downregulated in several human tumours. Functional analysis of the beta(1)-integrin gene strongly argues that SCAI is a novel transcriptional cofactor that controls gene expression downstream of Dia1 to dictate changes in cell invasive behaviour. AU - Brandt, D.T.* AU - Baarlink, C.* AU - Kitzing, T.M.* AU - Kremmer, E. AU - Ivaska, J.* AU - Nollau, P.* AU - Grosse, R.* C1 - 2901 C2 - 26508 SP - 557-568 TI - SCAI acts as a suppressor of cancer cell invasion through the transcriptional control of β₁-integrin. JO - Nat. Cell Biol. VL - 11 IS - 5 PB - Nature Publ. Group PY - 2009 SN - 1465-7392 ER - TY - JOUR AB - EpCAM was found to be overexpressed on epithelial progenitors, carcinomas and cancer-initiating cells. The role of EpCAM in proliferation, and its association with cancer is poorly explained by proposed cell adhesion functions. Here we show that regulated intramembrane proteolysis activates EpCAM as a mitogenic signal transducer in vitro and in vivo. This involves shedding of its ectodomain EpEX and nuclear translocation of its intracellular domain EpICD. Cleavage of EpCAM is sequentially catalysed by TACE and presenilin-2. Pharmacological inhibition or genetic silencing of either protease impairs growth-promoting signalling by EpCAM, which is compensated for by EpICD. Released EpICD associates with FHL2, beta-catenin and Lef-1 to form a nuclear complex that contacts DNA at Lef-1 consensus sites, induces gene transcription and is oncogenic in immunodeficient mice. In patients, EpICD was found in nuclei of colon carcinoma but not of normal tissue. Nuclear signalling of EpCAM explains how EpCAM functions in cell proliferation. AU - Maetzel, D. AU - Denzel, S. AU - Mack, B.* AU - Canis, M.* AU - Went, P.* AU - Benk, M. AU - Kieu, C.* AU - Papior, P. AU - Baeuerle, P.A.* AU - Münz, M. AU - Gires, O. C1 - 230 C2 - 26965 SP - 162-171 TI - Nuclear signalling by tumour-associated antigen EpCAM. JO - Nat. Cell Biol. VL - 11 IS - 2 PB - Nature Publ. Group PY - 2009 SN - 1465-7392 ER - TY - JOUR AB - The let-7 miRNA and its target gene Lin-28 interact in a regulatory circuit controlling pluripotency. We investigated an additional let-7 target, mLin41 (mouse homologue of lin-41), as a potential contributor to this circuit. We demonstrate the presence of mLin41 protein in several stem cell niches, including the embryonic ectoderm, epidermis and male germ line. mLin41 colocalized to cytoplasmic foci with P-body markers and the miRNA pathway proteins Ago2, Mov10 and Tnrc6b. In co-precipitation assays, mLin41 interacted with Dicer and the Argonaute proteins Ago1, Ago2 and Ago4. Moreover, we show that mLin41 acts as an E3 ubiquitin ligase in an auto-ubiquitylation assay and that mLin41 mediates ubiquitylation of Ago2 in vitro and in vivo. Overexpression and depletion of mLin41 led to inverse changes in the level of Ago2 protein, implicating mLin41 in the regulation of Ago2 turnover. mLin41 interfered with silencing of target mRNAs for let-7 and miR-124, at least in part by antagonizing Ago2. Furthermore, mLin41 cooperated with the pluripotency factor Lin-28 in suppressing let-7 activity, revealing a dual control mechanism regulating let-7 in stem cells. AU - Rybak, A.* AU - Fuchs, H.* AU - Hadian, K. AU - Smirnova, L.* AU - Wulczyn, E.A.* AU - Michel, G.* AU - Nitsch, R.* AU - Krappmann, D. AU - Wulczyn, F.G.* C1 - 263 C2 - 26703 CY - London SP - 1411-1420 TI - The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2. JO - Nat. Cell Biol. VL - 11 IS - 12 PB - Nature Publ. Group PY - 2009 SN - 1465-7392 ER - TY - JOUR AB - ES-cell-based cardiovascular repair requires an in-depth understanding of the molecular mechanisms underlying the differentiation of cardiovascular ES cells. A candidate cardiovascular-fate inducer is the bHLH transcription factor MesP1. As one of the earliest markers, it is expressed specifically in almost all cardiovascular precursors and is required for cardiac morphogenesis. Here we show that MesP1 is a key factor sufficient to induce the formation of ectopic heart tissue in vertebrates and increase cardiovasculogenesis by ES cells. Electrophysiological analysis showed all subtypes of cardiac ES-cell differentiation. MesP1 overexpression and knockdown experiments revealed a prominent function of MesP1 in a gene regulatory cascade, causing Dkk-1-mediated blockade of canonical Wnt-signalling. Independent evidence from ChIP and in vitro DNA-binding studies, expression analysis in wild-type and MesP knockout mice, and reporter assays confirm that Dkk-1 is a direct target of MesP1. Further analysis of the regulatory networks involving MesP1 will be required to preprogramme ES cells towards a cardiovascular fate for cell therapy and cardiovascular tissue engineering. This may also provide a tool to elicit cardiac transdifferentiation in native human adult stem cells. AU - David, R.* AU - Brenner, C.* AU - Stieber, J.* AU - Schwarz, F.* AU - Brunner, S.* AU - Vollmer, M. AU - Mentele, E.* AU - Müller-Höcker, J.* AU - Kitajima, S.* AU - Lickert, H. AU - Rupp, R.* AU - Franz, W.M.* C1 - 2706 C2 - 25144 SP - 338-345 TI - MesP1 drives vertebrate cardiovascular differentiation through Dkk-1-mediated blockade of Wnt-signalling. JO - Nat. Cell Biol. VL - 10 IS - 3 PB - Nature Publ. Group PY - 2008 SN - 1465-7392 ER - TY - JOUR AB - Integrin transmembrane receptors mediate cell adhesion through intracellular linker proteins that connect to the cytoskeleton. Of the numerous linker proteins identified, only a few, including Talin and Integrin-linked-kinase (ILK), are essential and evolutionarily conserved. The wech gene encodes a newly discovered and highly conserved regulator of integrin-mediated adhesion in Drosophila melanogaster. Embryos deficient in wech have very similar phenotypes to integrin-null or Talin-null embryos, including muscle detachment from the body wall. The Wech protein contains a B-box zinc-finger and a coiled-coil domain, which is also found in RBCC/TRIM family members, and an NHL domain. In beta-integrin or Talin mutants, Wech is mislocalized, whereas ILK localization depends on Wech. We provide evidence that Wech interacts with the head domain of Talin and the kinase domain of ILK, and propose that Wech is required to connect both core proteins of the linker complex during embryonic muscle attachment. Both the NHL and the B-box/coiled-coil domains of Wech are required for proper interaction with Talin and ILK. The single murine Wech orthologue is also colocalized with Talin and ILK in muscle tissue. We propose that Wech proteins are crucial and evolutionarily conserved regulators of the integrin-cytoskeleton link. AU - Löer, B.* AU - Bauer, R.* AU - Bornheim, R.* AU - Grell, J.* AU - Kremmer, E. AU - Kolanus, W.* AU - Hoch, M.* C1 - 3209 C2 - 25697 SP - 422-428 TI - The NHL-domain protein Wech is crucial for the integrin-cytoskeleton link. JO - Nat. Cell Biol. VL - 10 IS - 4 PB - Nature Publ. Group PY - 2008 SN - 1465-7392 ER -