Molecular Cell最新文献_第9页

C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes C2H2-锌指转录因子与 RNA 结合并在多种转录后调控过程中发挥作用

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-19 DOI: 10.1016/j.molcel.2024.08.037

Syed Nabeel-Shah, Shuye Pu, James D. Burns, Ulrich Braunschweig, Nujhat Ahmed, Giovanni L. Burke, Hyunmin Lee, Ernest Radovani, Guoqing Zhong, Hua Tang, Edyta Marcon, Zhaolei Zhang, Timothy R. Hughes, Benjamin J. Blencowe, Jack F. Greenblatt

{"title":"C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes","authors":"Syed Nabeel-Shah, Shuye Pu, James D. Burns, Ulrich Braunschweig, Nujhat Ahmed, Giovanni L. Burke, Hyunmin Lee, Ernest Radovani, Guoqing Zhong, Hua Tang, Edyta Marcon, Zhaolei Zhang, Timothy R. Hughes, Benjamin J. Blencowe, Jack F. Greenblatt","doi":"10.1016/j.molcel.2024.08.037","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.08.037","url":null,"abstract":"Cys2-His2 zinc-finger proteins (C2H2-ZNFs) constitute the largest class of DNA-binding transcription factors (TFs) yet remain largely uncharacterized. Although certain family members, e.g., GTF3A, have been shown to bind both DNA and RNA, the extent to which C2H2-ZNFs interact with—and regulate—RNA-associated processes is not known. Using UV crosslinking and immunoprecipitation (CLIP), we observe that 148 of 150 analyzed C2H2-ZNFs bind directly to RNA in human cells. By integrating CLIP sequencing (CLIP-seq) RNA-binding maps for 50 of these C2H2-ZNFs with data from chromatin immunoprecipitation sequencing (ChIP-seq), protein-protein interaction assays, and transcriptome profiling experiments, we observe that the RNA-binding profiles of C2H2-ZNFs are generally distinct from their DNA-binding preferences and that they regulate a variety of post-transcriptional processes, including pre-mRNA splicing, cleavage and polyadenylation, and m6A modification of mRNA. Our results thus define a substantially expanded repertoire of C2H2-ZNFs that bind RNA and provide an important resource for elucidating post-transcriptional regulatory programs.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"5 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246010","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}

引用次数: 0

Transcription regulation through selective partitioning: Weak interactions with a strong foundation 通过选择性分区进行转录调控：基础牢固的弱相互作用

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-19 DOI: 10.1016/j.molcel.2024.08.029

Megan Palacio, Dylan J. Taatjes

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Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation 锌指蛋白的多组学综合分析揭示其在 RNA 调控中的作用

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-19 DOI: 10.1016/j.molcel.2024.08.010

Maya L. Gosztyla, Lijun Zhan, Sara Olson, Xintao Wei, Jack Naritomi, Grady Nguyen, Lena Street, Grant A. Goda, Francisco F. Cavazos, Jonathan C. Schmok, Manya Jain, Easin Uddin Syed, Eunjeong Kwon, Wenhao Jin, Eric Kofman, Alexandra T. Tankka, Allison Li, Valerie Gonzalez, Eric Lécuyer, Daniel Dominguez, Gene W. Yeo

{"title":"Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation","authors":"Maya L. Gosztyla, Lijun Zhan, Sara Olson, Xintao Wei, Jack Naritomi, Grady Nguyen, Lena Street, Grant A. Goda, Francisco F. Cavazos, Jonathan C. Schmok, Manya Jain, Easin Uddin Syed, Eunjeong Kwon, Wenhao Jin, Eric Kofman, Alexandra T. Tankka, Allison Li, Valerie Gonzalez, Eric Lécuyer, Daniel Dominguez, Gene W. Yeo","doi":"10.1016/j.molcel.2024.08.010","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.08.010","url":null,"abstract":"RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc-finger families. We show that multiple ZFPs are previously unknown regulators of RNA splicing, alternative polyadenylation, stability, or translation. The examined ZFPs show widespread sequence-specific RNA binding and preferentially bind proximal to transcription start sites. Additionally, several ZFPs associate with their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DNA/RNA-associated protein that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"13 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246241","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}

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Ubiquitylation: Sword and shield in the bacterial arsenal 泛素化：细菌武库中的剑与盾

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-19 DOI: 10.1016/j.molcel.2024.08.034

Jonathan N. Pruneda, Felix Randow

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Finish the unfinished: Chd1 resolving hexasome-nucleosome complex with FACT 完成未完成的工作Chd1 与 FACT 一起解析六聚体-核小体复合物

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-19 DOI: 10.1016/j.molcel.2024.08.031

Hongxin Yin, Yang Liu

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Coming in out of the cold: Rho-dependent termination contributes to adaptation to cold shock 从寒冷中走来依赖 Rho 的终止有助于适应冷休克

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-19 DOI: 10.1016/j.molcel.2024.08.033

Teppei Morita, Susan Gottesman

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A TBK1-independent primordial function of STING in lysosomal biogenesis STING 在溶酶体生物发生过程中的原始功能与 TBK1 无关

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-19 DOI: 10.1016/j.molcel.2024.08.026

Bo Lv, William A. Dion, Haoxiang Yang, Jinrui Xun, Do-Hyung Kim, Bokai Zhu, Jay Xiaojun Tan

{"title":"A TBK1-independent primordial function of STING in lysosomal biogenesis","authors":"Bo Lv, William A. Dion, Haoxiang Yang, Jinrui Xun, Do-Hyung Kim, Bokai Zhu, Jay Xiaojun Tan","doi":"10.1016/j.molcel.2024.08.026","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.08.026","url":null,"abstract":"Stimulator of interferon genes (STING) is activated in many pathophysiological conditions, leading to TBK1-dependent interferon production in higher organisms. However, primordial functions of STING independent of TBK1 are poorly understood. Here, through proteomics and bioinformatics approaches, we identify lysosomal biogenesis as an unexpected function of STING. Transcription factor EB (TFEB), an evolutionarily conserved regulator of lysosomal biogenesis and host defense, is activated by STING from multiple species, including humans, mice, and frogs. STING-mediated TFEB activation is independent of TBK1, but it requires STING trafficking and its conserved proton channel. GABARAP lipidation, stimulated by the channel of STING, is key for STING-dependent TFEB activation. STING stimulates global upregulation of TFEB-target genes, mediating lysosomal biogenesis and autophagy. TFEB supports cell survival during chronic sterile STING activation, a common condition in aging and age-related diseases. These results reveal a primordial function of STING in the biogenesis of lysosomes, essential organelles in immunity and cellular stress resistance.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"195 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246009","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}

引用次数: 0

Spatial omics advances for in situ RNA biology 空间全息技术在原位 RNA 生物学方面的进展

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-12 DOI: 10.1016/j.molcel.2024.08.002

Jingyi Ren, Shuchen Luo, Hailing Shi, Xiao Wang

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Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT 通过 Chd1 和 FACT 分解转录诱导的六聚体-核小体复合物

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-12 DOI: 10.1016/j.molcel.2024.08.022

Maik Engeholm, Johann J. Roske, Elisa Oberbeckmann, Christian Dienemann, Michael Lidschreiber, Patrick Cramer, Lucas Farnung

引用次数: 0

RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages RAPIDASH：无标记核糖体相关蛋白富集揭示胚胎组织、癌细胞和巨噬细胞中的组成动态

IF 16 1区生物学

Molecular Cell Pub Date : 2024-09-10 DOI: 10.1016/j.molcel.2024.08.023

Teodorus Theo Susanto, Victoria Hung, Andrew G. Levine, Yuxiang Chen, Craig H. Kerr, Yongjin Yoo, Juan A. Oses-Prieto, Lisa Fromm, Zijian Zhang, Travis C. Lantz, Kotaro Fujii, Marius Wernig, Alma L. Burlingame, Davide Ruggero, Maria Barna

{"title":"RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages","authors":"Teodorus Theo Susanto, Victoria Hung, Andrew G. Levine, Yuxiang Chen, Craig H. Kerr, Yongjin Yoo, Juan A. Oses-Prieto, Lisa Fromm, Zijian Zhang, Travis C. Lantz, Kotaro Fujii, Marius Wernig, Alma L. Burlingame, Davide Ruggero, Maria Barna","doi":"10.1016/j.molcel.2024.08.023","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.08.023","url":null,"abstract":"Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including Dhx30 and Llph, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed that RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"103 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160994","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}

引用次数: 0