Genes & development最新文献

{"title":"The USP11/TCEAL1 complex promotes transcription elongation to sustain oncogenic gene expression in neuroblastoma","authors":"Markus Dehmer, Katrin Trunk, Peter Gallant, Daniel Fleischhauer, Mareike Müller, Steffi Herold, Giacomo Cossa, Francesca Conte, Jan Koster, Florian Sauer, Christina Schülein-Völk, Carsten P. Ade, Raphael Vidal, Caroline Kisker, Rogier Versteeg, Petra Beli, Seychelle M. Vos, Martin Eilers, Gabriele Büchel","doi":"10.1101/gad.352166.124","DOIUrl":"https://doi.org/10.1101/gad.352166.124","url":null,"abstract":"During early transcription, RNA polymerase II (RNAPII) undergoes a series of structural transitions controlled by cyclin-dependent kinases. How protein ubiquitylation and proteasomal degradation control the function of RNAPII is less well understood. Here we show that the deubiquitinating enzyme USP11 forms a complex with TCEAL1, a member of the TFIIS (TCEA)-like protein family. TCEAL1 shares sequence homology with the RNAPII interaction domain of the elongation factor TFIIS (which controls the fate of backtracked RNAPII) and competes with TFIIS for binding to core promoters. USP11 protects TCEAL1 from proteasomal degradation, and TCEAL1 recruits USP11 to RNAPII. Both USP11 and TCEAL1 promote transcription elongation and maintain expression of RPB8, an essential subunit of all three nuclear RNA polymerases. In neuroblastoma, USP11- and TCEAL1-dependent genes define a gene expression program that is characteristic for mesenchymal tumors, which are described as able to escape from many treatments, suggesting that the USP11/TCEAL1 complex promotes transcription elongation to support a critical oncogenic gene expression program.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"31 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A boundary-defining protein facilitates megabase-scale regulatory chromosomal loop formation in Drosophila neurons","authors":"Marion Mouginot, Sahar Hani, Pascal Cousin, Julien Dorier, Arianna Ravera, Maria Cristina Gambetta","doi":"10.1101/gad.352646.125","DOIUrl":"https://doi.org/10.1101/gad.352646.125","url":null,"abstract":"Regulatory elements, such as enhancers and silencers, control transcription by establishing physical proximity to target gene promoters. Neurons in flies and mammals exhibit long-range three-dimensional genome contacts, proposed to connect genes with distal regulatory elements. However, the relevance of these contacts for neuronal gene transcription and the mechanisms underlying their specificity necessitate further investigation. Here, we precisely disrupt several long-range contacts in fly neurons, demonstrating their importance for megabase-range gene regulation and uncovering a hierarchical process in their formation. We further reveal an essential role for the chromosomal boundary-forming protein Cp190 in anchoring many long-range contacts, highlighting a mechanistic interplay between boundary and loop formation. Finally, we develop an unbiased proteomics-based method to systematically identify factors required for specific long-range contacts. Our findings underscore the essential role of architectural proteins such as Cp190 in cell type-specific genome organization in enabling specialized neuronal transcriptional programs.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"24 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Histone chaperones coupled to DNA replication and transcription control divergent chromatin elements to maintain cell fate","authors":"Reuben Franklin, Brian Zhang, Jonah Frazier, Meijuan Chen, Brian T. Do, Sally Padayao, Kun Wu, Matthew G. Vander Heiden, Christopher R. Vakoc, Jae-Seok Roe, Maria Ninova, Jernej Murn, David B. Sykes, Sihem Cheloufi","doi":"10.1101/gad.352316.124","DOIUrl":"https://doi.org/10.1101/gad.352316.124","url":null,"abstract":"The manipulation of DNA replication and transcription can be harnessed to control cell fate. Central to the regulation of these DNA-templated processes are histone chaperones, which in turn are emerging as cell fate regulators. Histone chaperones are a group of proteins with diverse functions that are primarily involved in escorting histones to assemble nucleosomes and maintain the chromatin landscape. Whether distinct histone chaperone pathways control cell fate and whether they function using related mechanisms remain unclear. To address this, we performed a screen to assess the requirement of diverse histone chaperones in the self-renewal of hematopoietic stem and progenitor cells. Remarkably, all candidates were required to maintain cell fate to differing extents, with no clear correlation with their specific histone partners or DNA-templated process. Among all the histone chaperones, the loss of the transcription-coupled histone chaperone SPT6 most strongly promoted differentiation, even more than the major replication-coupled chromatin assembly factor complex CAF-1. To directly compare how DNA replication- and transcription-coupled histone chaperones maintain stem cell self-renewal, we generated an isogenic dual-inducible system to perturb each pathway individually. We found that SPT6 and CAF-1 perturbations required cell division to induce differentiation but had distinct effects on cell cycle progression, chromatin accessibility, and lineage choice. CAF-1 depletion led to S-phase accumulation, increased heterochromatic accessibility (particularly at H3K27me3 sites), and aberrant multilineage gene expression. In contrast, SPT6 loss triggered cell cycle arrest, altered accessibility at promoter elements, and drove lineage-specific differentiation, which is in part influenced by AP-1 transcription factors. Thus, CAF-1 and SPT6 histone chaperones maintain cell fate through distinct mechanisms, highlighting how different chromatin assembly pathways can be leveraged to alter cell fate.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"38 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An imbalance between proliferation and differentiation underlies the development of microRNA-defective pineoblastoma","authors":"Claudette R. Fraire, Kavita Desai, Indumathy Jagadeeswaran, Uma A. Obalapuram, Lindsay K. Mendyka, Veena Rajaram, Teja Sebastian, Yemin Wang, Kenan Onel, Jeon Lee, Stephen X. Skapek, Kenneth S. Chen","doi":"10.1101/gad.352485.124","DOIUrl":"https://doi.org/10.1101/gad.352485.124","url":null,"abstract":"Mutations in the microRNA processing genes <em>DROSHA</em> and <em>DICER1</em> drive several cancers that resemble embryonic progenitors. To understand how microRNAs regulate tumorigenesis, we ablated <em>Drosha</em> or <em>Dicer1</em> in the developing pineal gland to emulate the pathogenesis of pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. Accordingly, these mice develop pineal tumors marked by loss of microRNAs, particularly the let-7/miR-98-5p family, and derepression of microRNA target genes. Pineal tumors driven by loss of <em>Drosha</em> or <em>Dicer1</em> mimic tumors driven by <em>Rb1</em> loss, as they exhibit upregulation of S-phase genes and homeobox transcription factors that regulate pineal development. Blocking proliferation of these tumors facilitates expression of pinealocyte maturation markers, with a concomitant reduction in embryonic markers. Select embryonic markers remain elevated, however, as the microRNAs that normally repress these target genes remain absent. One such microRNA target gene is the oncofetal transcription factor <em>Plagl2</em>, which regulates expression of progrowth genes, and inhibiting their signaling impairs tumor growth. Thus, we demonstrate that tumors driven by loss of microRNA processing may be therapeutically targeted by inhibiting downstream drivers of proliferation.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"5 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IRX2 and NPTX1 differential regulation of β-catenin underlies MEK-mediated proliferation in human neuroglial cells","authors":"Alexander Chen, Hannah Wang, Xuanwei Li, Corina Anastasaki, David H. Gutmann","doi":"10.1101/gad.352508.124","DOIUrl":"https://doi.org/10.1101/gad.352508.124","url":null,"abstract":"The two major genomic alterations in pediatric pilocytic astrocytoma (PA) are <em>NF1</em> loss and <em>KIAA1549:BRAF</em> rearrangement. Although these molecular changes result in increased MEK activity and tumor growth, it is not clear exactly how MEK controls human neuroglial cell proliferation. Leveraging human-induced pluripotent stem cells harboring these PA-associated alterations, we used a combination of genetic and pharmacological approaches to demonstrate that MEK-regulated cell growth is mediated by β-catenin through independent mechanisms involving IRX2 control of <em>CTNNB1</em> transcription and NPTX1 stabilization of β-catenin protein levels. These results provide new mechanistic insights into MEK regulation of human brain cell function.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"20 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gap resection matters in BRCA mutant cancer","authors":"Lee Zou","doi":"10.1101/gad.352827.125","DOIUrl":"https://doi.org/10.1101/gad.352827.125","url":null,"abstract":"Cancer cells deficient in BRCA1/2 have impaired DNA repair, making them sensitive to PARP inhibitors (PARPis). In this issue of <em>Genes &amp; Development</em>, Seppa and colleagues (doi:10.1101/gad.352421.124) investigated how BRCA1 protects single-stranded DNA gaps from nucleolytic processing. They showed that PARPi-induced gaps are rapidly resected by several exonucleases bidirectionally and filled by translesion synthesis. In BRCA1-deficient cells, gaps become larger and persistent due to excessive resection. These gaps do not convert to DNA double-stranded breaks (DSBs) via endonuclease activity but cause DSBs through replication fork collisions in a cell cycle-dependent manner. This research clarifies how BRCA1 loss contributes to PARPi sensitivity in BRCA mutant tumors.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"59 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CDK4 loss-of-function mutations cause microcephaly and short stature","authors":"Aitana Verdu Schlie, Andrea Leitch, Maria Izabel Arismendi, Colin Stok, Andrea Castro Leal, David A. Parry, Antonio Marcondes Lerario, Margaret E. Harley, Bruna Lucheze, Paula L. Carroll, Kamila I. Musialik, Julia M.T. Auer, Carol-Anne Martin, Lukas Gerasimavicius, Alan J. Quigley, Joya Emilie de Menezes Correia-Deur, Joseph A. Marsh, Martin A.M. Reijns, Anne K. Lampe, Andrew P. Jackson, Alexander A.L. Jorge, Lukas Tamayo-Orrego","doi":"10.1101/gad.352311.124","DOIUrl":"https://doi.org/10.1101/gad.352311.124","url":null,"abstract":"Cell number is a major determinant of organism size in mammals. In humans, gene mutations in cell cycle components result in restricted growth through reduced cell numbers. Here we identified biallelic mutations in <em>CDK4</em> as a cause of microcephaly and short stature. <em>CDK4</em> encodes a key cell cycle kinase that associates with D-type cyclins during G1 of the cell cycle to promote S-phase entry and cell proliferation through retinoblastoma (RB) phosphorylation. CDK4 and CDK6 are believed to be functionally redundant and are targeted jointly by chemotherapeutic CDK4/6 inhibitors. Using molecular and cell biology approaches, we show that functional CDK4 protein is not detectable in cells with <em>CDK4</em> mutations. Cells display impaired RB phosphorylation in G1, leading to G1/S-phase transition defects and reduced cell proliferation, consistent with complete loss of cellular CDK4 enzymatic activity. Together, these findings demonstrate that CDK4 is itself required for cell proliferation, human growth, and brain size determination during development.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"183 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ribosome-associated quality control factor TCF25 imposes K48 specificity on Listerin-mediated ubiquitination of nascent chains by binding and specifically orienting the acceptor ubiquitin","authors":"Irina S. Abaeva, Alexander G. Bulakhov, Christopher U.T. Hellen, Tatyana V. Pestova","doi":"10.1101/gad.352389.124","DOIUrl":"https://doi.org/10.1101/gad.352389.124","url":null,"abstract":"Polypeptides arising from interrupted translation undergo proteasomal degradation by the ribosome-associated quality control (RQC) pathway. The ASC-1 complex splits stalled ribosomes into 40S subunits and nascent chain–tRNA-associated 60S subunits (60S RNCs). 60S RNCs associate with NEMF that promotes recruitment of the RING-type E3 ubiquitin (Ub) ligase Listerin (Ltn1 in yeast), which ubiquitinates nascent chains. RING-type E3s mediate the transfer of Ub directly from the E2∼Ub conjugate, implying that the specificity of Ub linkage is determined by the given E2. Listerin is most efficient when it is paired with promiscuous Ube2D E2s. We previously found that TCF25 (Rqc1 in yeast) can impose K48 specificity on Listerin paired with Ube2D E2s. To determine the mechanism of TCF25's action, we combined functional biochemical studies and AlphaFold3 modeling and now report that TCF25 specifically interacts with the RING domain of Listerin and the acceptor ubiquitin (Ub^A) and imposes K48 specificity by orienting Ub^A such that its K48 is directly positioned to attack the thioester bond of the Ube2D1∼Ub conjugate. We also found that TCF25 itself undergoes K48-specific ubiquitination by Listerin, suggesting a mechanism for the reported upregulation of Rqc1 in the absence of Ltn1 and the observed degradation of TCF25 by the proteasome in vivo.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"32 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vivo CRISPR screening reveals epigenetic regulators of hepatobiliary plasticity","authors":"Jonathan H. Sussman, Hector W. Cure, Salina Yuan, Kenji Ito, Irfan A. Asangani, Benjamin A. Garcia, Ben Z. Stanger, Takeshi Katsuda","doi":"10.1101/gad.352420.124","DOIUrl":"https://doi.org/10.1101/gad.352420.124","url":null,"abstract":"Following prolonged liver injury, a small fraction of hepatocytes undergoes reprogramming to become cholangiocytes or biliary epithelial cells (BECs). This physiological process involves chromatin and transcriptional remodeling, but the epigenetic mediators are largely unknown. Here, we exploited a lineage-traced model of liver injury to investigate the role of histone post-translational modification in biliary reprogramming. Using mass spectrometry, we defined the repertoire of histone marks that are globally altered in quantity during reprogramming. Next, applying an in vivo CRISPR screening approach, we identified seven histone-modifying enzymes that alter the efficiency of hepatobiliary reprogramming. Among these, the histone methyltransferase and demethylase <em>Nsd1</em> and <em>Kdm2a</em> were found to have reciprocal effects on H3K36 methylation that regulated the early and late stages of reprogramming, respectively. Although loss of <em>Nsd1</em> and <em>Kdm2a</em> affected reprogramming efficiency, cells ultimately acquired the same transcriptomic states. These findings reveal that multiple chromatin regulators exert dynamic and complementary activities to achieve robust cell fate switching, serving as a model for the cell identity changes that occur in various forms of physiological metaplasia or reprogramming.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"16 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cognition and behavior in neurofibromatosis type 1: report and perspective from the Cognition and Behavior in NF1 (CABIN) Task Force","authors":"David H. Gutmann, Corina Anastasaki, Aditi Gupta, Yang Hou, Stephanie M. Morris, Jonathan M. Payne, Jacob Raber, Seth M. Tomchik, Linda Van Aelst, James A. Walker, Kaleb H. Yohay, on behalf of the CABIN Task Force","doi":"10.1101/gad.352629.125","DOIUrl":"https://doi.org/10.1101/gad.352629.125","url":null,"abstract":"Individuals with neurofibromatosis type 1 (NF1) are prone to the evolution of neurodevelopmental symptomatology including motor delays, learning disabilities, autism, and attention deficits. Caused by heterozygous germline mutations in the <em>NF1</em> gene, this monogenic condition offers unique opportunities to study the genetic etiologies for neurodevelopmental disorders and the mechanisms that underlie their formation. Although numerous small animal models have been generated to elucidate the causes of these alterations, there is little consensus on how to align preclinical observations with clinical outcomes, harmonize findings across species, and consolidate these insights to chart a cohesive path forward. Capitalizing on expertise from clinicians; human, animal, and cellular model research scientists; and bioinformatics researchers, the first Cognition and Behavior in NF1 (CABIN) meeting was convened at the Banbury Center of Cold Spring Harbor Laboratory in October 2024. This Perspective summarizes the state of our understanding and a proposed plan for future investigation and exploration to improve the quality of life of those with NF1.","PeriodicalId":12591,"journal":{"name":"Genes & development","volume":"61 1","pages":""},"PeriodicalIF":10.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143695665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}