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Pradhan UK, Naha S, Das R, Gupta A, Parsad R, Meher PK. RBProkCNN: Deep learning on appropriate contextual evolutionary information for RNA binding protein discovery in prokaryotes. Comput Struct Biotechnol J 2024; 23:1631-1640. [PMID: 38660008 PMCID: PMC11039349 DOI: 10.1016/j.csbj.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
RNA-binding proteins (RBPs) are central to key functions such as post-transcriptional regulation, mRNA stability, and adaptation to varied environmental conditions in prokaryotes. While the majority of research has concentrated on eukaryotic RBPs, recent developments underscore the crucial involvement of prokaryotic RBPs. Although computational methods have emerged in recent years to identify RBPs, they have fallen short in accurately identifying prokaryotic RBPs due to their generic nature. To bridge this gap, we introduce RBProkCNN, a novel machine learning-driven computational model meticulously designed for the accurate prediction of prokaryotic RBPs. The prediction process involves the utilization of eight shallow learning algorithms and four deep learning models, incorporating PSSM-based evolutionary features. By leveraging a convolutional neural network (CNN) and evolutionarily significant features selected through extreme gradient boosting variable importance measure, RBProkCNN achieved the highest accuracy in five-fold cross-validation, yielding 98.04% auROC and 98.19% auPRC. Furthermore, RBProkCNN demonstrated robust performance with an independent dataset, showcasing a commendable 95.77% auROC and 95.78% auPRC. Noteworthy is its superior predictive accuracy when compared to several state-of-the-art existing models. RBProkCNN is available as an online prediction tool (https://iasri-sg.icar.gov.in/rbprokcnn/), offering free access to interested users. This tool represents a substantial contribution, enriching the array of resources available for the accurate and efficient prediction of prokaryotic RBPs.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Ritwika Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Rajender Parsad
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
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2
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Liu Y, Shi Q, Liu Y, Li X, Wang Z, Huang S, Chen Z, He X. Fibrillarin reprograms glucose metabolism by driving the enhancer-mediated transcription of PFKFB4 in liver cancer. Cancer Lett 2024; 602:217190. [PMID: 39182558 DOI: 10.1016/j.canlet.2024.217190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/28/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
DNA- and RNA-binding proteins (DRBPs) are versatile proteins capable of binding to both DNA and RNA molecules. In this study, we identified fibrillarin (FBL) as a key DRBP that is upregulated in liver cancer tissues vs. normal tissues and is correlated with patient prognosis. FBL promotes the proliferation of liver cancer cells both in vitro and in vivo. Mechanistically, FBL interacts with the transcription factor KHSRP, thereby regulating the expression of genes involved in glucose metabolism and leading to the reprogramming of glucose metabolism. Specifically, FBL and KHSRP work together to transcriptionally activate the glycolytic enzyme PFKFB4 by co-occupying enhancer and promoter elements, thereby further promoting liver cancer growth. Collectively, these findings provide compelling evidence highlighting the role of FBL as a transcriptional regulator in liver cancer cells, working in conjunction with KHSRP. The FBL/KHSRP-PFKFB4 regulatory axis holds potential as both a prognostic indicator and a therapeutic target for liver cancer. SIGNIFICANCE: A novel role of FBL in the transcriptional activation of PFKFB4, leading to glucose metabolism reprogramming in liver cancer.
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Affiliation(s)
- Yizhe Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qili Shi
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yanfang Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xinrong Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhen Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
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3
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Cho N, Kim SY, Lee SG, Park C, Choi S, Kim EM, Kim KK. Alternative splicing of PBRM1 mediates resistance to PD-1 blockade therapy in renal cancer. EMBO J 2024:10.1038/s44318-024-00262-7. [PMID: 39375538 DOI: 10.1038/s44318-024-00262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 09/04/2024] [Accepted: 09/20/2024] [Indexed: 10/09/2024] Open
Abstract
Alternative pre-mRNA splicing (AS) is a biological process that results in proteomic diversity. However, implications of AS alterations in cancer remain poorly understood. Herein, we performed a comprehensive AS analysis in cancer driver gene transcripts across fifteen cancer types and found global alterations in inclusion rates of the PBAF SWI/SNF chromatin remodeling complex subunit Polybromo 1 (PBRM1) exon 27 (E27) in most types of cancer tissues compared with those in normal tissues. Further analysis confirmed that PBRM1 E27 is excluded by the direct binding of RBFOX2 to intronic UGCAUG elements. In addition, the E27-included PBRM1 isoform upregulated PD-L1 expression via enhanced PBAF complex recruitment to the PD-L1 promoter. PBRM1 wild-type patients with clear cell renal cell carcinoma were resistant to PD-1 blockade therapy when they expressed low RBFOX2 mRNA levels. Overall, our study suggests targeting of RBFOX2-mediated AS of PBRM1 as a potential therapeutic strategy for immune checkpoint blockade.
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Affiliation(s)
- Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seung-Yeon Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sung-Gwon Lee
- School of Biological Science and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chungoo Park
- School of Biological Science and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Sunkyung Choi
- Department of Biological Sciences, College of Natural Sciences, Keimyung University, Daegu, 42601, Republic of Korea.
| | - Eun-Mi Kim
- Department of Bio & Environmental Technology, College of Science and Convergence Technology, Seoul Women's University, Seoul, 01797, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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4
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Street LA, Rothamel KL, Brannan KW, Jin W, Bokor BJ, Dong K, Rhine K, Madrigal A, Al-Azzam N, Kim JK, Ma Y, Gorhe D, Abdou A, Wolin E, Mizrahi O, Ahdout J, Mujumdar M, Doron-Mandel E, Jovanovic M, Yeo GW. Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. Mol Cell 2024; 84:3790-3809.e8. [PMID: 39303721 DOI: 10.1016/j.molcel.2024.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 04/18/2024] [Accepted: 08/26/2024] [Indexed: 09/22/2024]
Abstract
mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map across the mRNA life cycle in human cells by immunopurification-mass spectrometry (IP-MS) of ∼100 endogenous RBPs with and without RNase, augmented by size exclusion chromatography-mass spectrometry (SEC-MS). We identify 8,742 known and 20,802 unreported interactions between 1,125 proteins and determine that 73% of the IP-MS-identified interactions are RNA regulated. Our interactome links many proteins, some with unknown functions, to specific mRNA life-cycle stages, with nearly half associated with multiple stages. We demonstrate the value of this resource by characterizing the splicing and export functions of enhancer of rudimentary homolog (ERH), and by showing that small nuclear ribonucleoprotein U5 subunit 200 (SNRNP200) interacts with stress granule proteins and binds cytoplasmic RNA differently during stress.
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Affiliation(s)
- Lena A Street
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Katherine L Rothamel
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA
| | - Kristopher W Brannan
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA; Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin J Bokor
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kevin Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kevin Rhine
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Assael Madrigal
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Norah Al-Azzam
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jenny Kim Kim
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Yanzhe Ma
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Darvesh Gorhe
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ahmed Abdou
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Erica Wolin
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Orel Mizrahi
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Ahdout
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mayuresh Mujumdar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ella Doron-Mandel
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Laboratories for Innovative Medicines, San Diego, CA, USA; Sanford Stem Cell Institute, Innovation Center, San Diego, CA, USA.
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5
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Gosztyla ML, Zhan L, Olson S, Wei X, Naritomi J, Nguyen G, Street L, Goda GA, Cavazos FF, Schmok JC, Jain M, Uddin Syed E, Kwon E, Jin W, Kofman E, Tankka AT, Li A, Gonzalez V, Lécuyer E, Dominguez D, Jovanovic M, Graveley BR, Yeo GW. Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. Mol Cell 2024; 84:3826-3842.e8. [PMID: 39303722 DOI: 10.1016/j.molcel.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/19/2024] [Accepted: 08/06/2024] [Indexed: 09/22/2024]
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.
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Affiliation(s)
- Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Jack Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Grady Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lena Street
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Grant A Goda
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Francisco F Cavazos
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Easin Uddin Syed
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; School of Pharmacy, Brac University, Dhaka 1212, Bangladesh
| | - Eunjeong Kwon
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Wenhao Jin
- Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexandra T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Allison Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Valerie Gonzalez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA.
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6
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Nabeel-Shah S, Pu S, Burns JD, Braunschweig U, Ahmed N, Burke GL, Lee H, Radovani E, Zhong G, Tang H, Marcon E, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF. C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes. Mol Cell 2024; 84:3810-3825.e10. [PMID: 39303720 DOI: 10.1016/j.molcel.2024.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
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.
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Affiliation(s)
- Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - James D Burns
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Nujhat Ahmed
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Giovanni L Burke
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Guoqing Zhong
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hua Tang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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7
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Siachisumo C, Luzzi S, Aldalaqan S, Hysenaj G, Dalgliesh C, Cheung K, Gazzara MR, Yonchev ID, James K, Kheirollahi Chadegani M, Ehrmann IE, Smith GR, Cockell SJ, Munkley J, Wilson SA, Barash Y, Elliott DJ. An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression. eLife 2024; 12:RP89705. [PMID: 39356106 PMCID: PMC11446547 DOI: 10.7554/elife.89705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024] Open
Abstract
Previously, we showed that the germ cell-specific nuclear protein RBMXL2 represses cryptic splicing patterns during meiosis and is required for male fertility (Ehrmann et al., 2019). Here, we show that in somatic cells the similar yet ubiquitously expressed RBMX protein has similar functions. RBMX regulates a distinct class of exons that exceed the median human exon size. RBMX protein-RNA interactions are enriched within ultra-long exons, particularly within genes involved in genome stability, and repress the selection of cryptic splice sites that would compromise gene function. The RBMX gene is silenced during male meiosis due to sex chromosome inactivation. To test whether RBMXL2 might replace the function of RBMX during meiosis we induced expression of RBMXL2 and the more distantly related RBMY protein in somatic cells, finding each could rescue aberrant patterns of RNA processing caused by RBMX depletion. The C-terminal disordered domain of RBMXL2 is sufficient to rescue proper splicing control after RBMX depletion. Our data indicate that RBMX and RBMXL2 have parallel roles in somatic tissues and the germline that must have been conserved for at least 200 million years of mammalian evolution. We propose RBMX family proteins are particularly important for the splicing inclusion of some ultra-long exons with increased intrinsic susceptibility to cryptic splice site selection.
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Affiliation(s)
- Chileleko Siachisumo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Sara Luzzi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Saad Aldalaqan
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Gerald Hysenaj
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Caroline Dalgliesh
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Kathleen Cheung
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhildelphiaUnited States
| | - Ivaylo D Yonchev
- School of Biosciences, University of SheffieldSheffieldUnited Kingdom
| | - Katherine James
- School of Computing, Newcastle UniversityNewcastleUnited Kingdom
| | | | - Ingrid E Ehrmann
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Graham R Smith
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Simon J Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Jennifer Munkley
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Stuart A Wilson
- School of Biosciences, University of SheffieldSheffieldUnited Kingdom
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhildelphiaUnited States
| | - David J Elliott
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
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8
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Capitanchik C, Wilkins OG, Wagner N, Gagneur J, Ule J. From computational models of the splicing code to regulatory mechanisms and therapeutic implications. Nat Rev Genet 2024:10.1038/s41576-024-00774-2. [PMID: 39358547 DOI: 10.1038/s41576-024-00774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/04/2024]
Abstract
Since the discovery of RNA splicing and its role in gene expression, researchers have sought a set of rules, an algorithm or a computational model that could predict the splice isoforms, and their frequencies, produced from any transcribed gene in a specific cellular context. Over the past 30 years, these models have evolved from simple position weight matrices to deep-learning models capable of integrating sequence data across vast genomic distances. Most recently, new model architectures are moving the field closer to context-specific alternative splicing predictions, and advances in sequencing technologies are expanding the type of data that can be used to inform and interpret such models. Together, these developments are driving improved understanding of splicing regulatory mechanisms and emerging applications of the splicing code to the rational design of RNA- and splicing-based therapeutics.
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Affiliation(s)
- Charlotte Capitanchik
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London, UK
| | - Oscar G Wilkins
- The Francis Crick Institute, London, UK
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nils Wagner
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
| | - Jernej Ule
- The Francis Crick Institute, London, UK.
- UK Dementia Research Institute at King's College London, London, UK.
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London, UK.
- National Institute of Chemistry, Ljubljana, Slovenia.
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9
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Eroglu M, Zocher T, McAuley J, Webster R, Xiao MZX, Yu B, Mok C, Derry WB. Noncanonical inheritance of phenotypic information by protein amyloids. Nat Cell Biol 2024; 26:1712-1724. [PMID: 39223373 DOI: 10.1038/s41556-024-01494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
All known heritable phenotypic information in animals is transmitted by direct inheritance of nucleic acids, their covalent modifications or histone modifications that modulate expression of associated genomic regions. Nonetheless, numerous familial traits and disorders cannot be attributed to known heritable molecular factors. Here we identify amyloid-like protein structures that are stably inherited in wild-type animals and influence traits. Their perturbation by genetic, environmental or pharmacological treatments leads to developmental phenotypes that can be epigenetically passed onto progeny. Injection of amyloids isolated from different phenotypic backgrounds into naive animals recapitulates the associated phenotype in offspring. Genetic and proteomic analyses reveal that the 26S proteasome and its conserved regulators maintain heritable amyloids across generations, which enables proper germ cell sex differentiation. We propose that inheritance of a proteinaceous epigenetic memory coordinates developmental timing and patterning with the environment to confer adaptive fitness.
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Affiliation(s)
- Matthew Eroglu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Tanner Zocher
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacob McAuley
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rachel Webster
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maggie Z X Xiao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bin Yu
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Calvin Mok
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - W Brent Derry
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.
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10
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Grelloni C, Garraffo R, Setti A, Rossi F, Peruzzi G, Cinquanta M, Di Rosa MC, Pierotti MA, Beltran M, Bozzoni I. BRCA1 levels and DNA-damage response are controlled by the competitive binding of circHIPK3 or FMRP to the BRCA1 mRNA. Mol Cell 2024:S1097-2765(24)00773-1. [PMID: 39389065 DOI: 10.1016/j.molcel.2024.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 08/22/2024] [Accepted: 09/13/2024] [Indexed: 10/12/2024]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules widely expressed in eukaryotes and deregulated in several pathologies, including cancer. Many studies point to their activity as microRNAs (miRNAs) and protein sponges; however, we propose a function based on circRNA-mRNA interaction to regulate mRNA fate. We show that the widely tumor-associated circHIPK3 directly interacts in vivo with the BRCA1 mRNA through the back-splicing region in human cancer cells. This interaction increases BRCA1 translation by competing for the binding of the fragile-X mental retardation 1 protein (FMRP) protein, which we identified as a BRCA1 translational repressor. CircHIPK3 depletion or disruption of the circRNA-mRNA interaction decreases BRCA1 protein levels and increases DNA damage, sensitizing several cancer cells to DNA-damage-inducing agents and rendering them susceptible to synthetic lethality. Additionally, blocking FMRP interaction with BRCA1 mRNA with locked nucleic acid (LNA) restores physiological protein levels in BRCA1 hemizygous breast cancer cells, underscoring the importance of this circRNA-mRNA interaction in regulating DNA-damage response.
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Affiliation(s)
- Chiara Grelloni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Raffaele Garraffo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Mario Cinquanta
- Cogentech ltd Benefit C. Registered Office, 20133 Milan, Italy
| | | | | | - Manuel Beltran
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy.
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy.
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11
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Harris SE, Alexis MS, Giri G, Cavazos FF, Hu Y, Murn J, Aleman MM, Burge CB, Dominguez D. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. Nat Commun 2024; 15:8400. [PMID: 39333159 PMCID: PMC11436793 DOI: 10.1038/s41467-024-52231-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/28/2024] [Indexed: 09/29/2024] Open
Abstract
While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examine interspecies differences in RNA-protein interactions using the conserved neuronal RNA-binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstitute the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.
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Affiliation(s)
- Sarah E Harris
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Maria S Alexis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Remix Therapeutics, Cambridge, MA, USA
| | - Gilbert Giri
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Francisco F Cavazos
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Yue Hu
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Maria M Aleman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Dominguez
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA.
- RNA Discovery Center, University of North Carolina, Chapel Hill, NC, USA.
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12
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Karam JAQ, Fréreux C, Mohanty BK, Dalton AC, Dincman TA, Palanisamy V, Howley BV, Howe PH. The RNA binding protein PCBP1 modulates transcription by recruiting the G-quadruplex-specific helicase DHX9. J Biol Chem 2024:107830. [PMID: 39342995 DOI: 10.1016/j.jbc.2024.107830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/12/2024] [Accepted: 09/15/2024] [Indexed: 10/01/2024] Open
Abstract
PCBP1, polycytosine (poly(C)) binding protein 1, an RNA and single-stranded DNA (ssDNA) binding protein, binds poly(C) DNA tracts but it remains unclear whether its ability to bind ssDNA contributes to transcriptional regulation. Here, we report that PCBP1's DNA binding sites are enriched at transcription start sites and that by binding to promoter regions, PCBP1 regulates transcription in addition to splicing and translation. At PCBP1 target genes, we show that PCBP1 interacts with several RNA/DNA hybrid (R-loop) associated G-quadruplex resolving helicases. Furthermore, we find that PCBP1 interacts with RNA Helicase A (DHX9) to modulate transcription by regulating DHX9 accumulation and activity. PCBP1 depletion leads to defects in R-loop processing and dysregulation of transcription of PCBP1 target genes. PCBP1's high sequence specificity and interaction with helicases suggest that its mechanism in transcription involves guiding helicases to specific loci during transcription, thereby modulating their activity.
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Affiliation(s)
- Joseph A Q Karam
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Cécile Fréreux
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Bidyut K Mohanty
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine, Spartanburg, SC, United States
| | - Annamarie C Dalton
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Toros A Dincman
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Department of Medicine, Division of Hematology and Oncology Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Division of Molecular Medicine, Department of Internal Medicine, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Breege V Howley
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, United States.
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13
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Gallardo-Dodd CJ, Kutter C. The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer. Hum Genomics 2024; 18:109. [PMID: 39334294 PMCID: PMC11437681 DOI: 10.1186/s40246-024-00678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024] Open
Abstract
Biological systems encompass intricate networks governed by RNA-protein interactions that play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the mammalian cell weight, respectively, orchestrate vital processes from genome organization to translation. To date, disentangling the functional fraction of the human genome has presented a major challenge, particularly for noncoding regions, yet recent discoveries have started to unveil a host of regulatory functions for noncoding RNAs (ncRNAs). While ncRNAs exist at different sizes, structures, degrees of evolutionary conservation and abundances within the cell, they partake in diverse roles either alone or in combination. However, certain ncRNA subtypes, including those that have been described or remain to be discovered, are poorly characterized given their heterogeneous nature. RNA activity is in most cases coordinated through interactions with RNA-binding proteins (RBPs). Extensive efforts are being made to accurately reconstruct RNA-RBP regulatory networks, which have provided unprecedented insight into cellular physiology and human disease. In this review, we provide a comprehensive view of RNAs and RBPs, focusing on how their interactions generate functional signals in living cells, particularly in the context of post-transcriptional regulatory processes and cancer.
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Affiliation(s)
- Carlos J Gallardo-Dodd
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden.
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14
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Liu Z, Deng K, Su Y, Zhang Z, Shi C, Wang J, Fan Y, Zhang G, Wang F. IGF2BP1-mediated the stability and protein translation of FGFR1 mRNA regulates myogenesis through the ERK signaling pathway. Int J Biol Macromol 2024; 280:135989. [PMID: 39326619 DOI: 10.1016/j.ijbiomac.2024.135989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 08/21/2024] [Accepted: 09/22/2024] [Indexed: 09/28/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent post-transcriptional modification of RNAs and plays a key regulatory role in various biological processes. As a member of the insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) family, IGF2BP1 has recently demonstrated its ability to specifically bind m6A-modified sites within mRNAs and effectively regulate their mRNA stability. However, the precise roles of IGF2BP1 in mammalian skeletal muscle development, along with its downstream mRNA targets during myogenesis, have yet to be fully elucidated. Here, we observed that IGF2BP1 expression significantly decreased during myogenic differentiation. Knockdown of IGF2BP1 significantly inhibited myoblast proliferation while promoted myogenic differentiation. In contrast, IGF2BP1 overexpression robustly stimulated myoblast proliferation but suppressed their differentiation. Combined analysis of high-throughput sequencing and RNA stability assays revealed that IGF2BP1 can enhance fibroblast growth factor receptor 1 (FGFR1) mRNA stability and promote its translation in an m6A-dependent manner, thereby regulating its expression level and the Extracellular Signal-Regulated Kinase (ERK) pathway. Additionally, knockdown of FGFR1 rescued the phenotypic changes (namely increased cell proliferation and suppressed differentiation) induced by IGF2BP1 overexpression via attenuating ERK signaling. Taken together, our findings suggest that IGF2BP1 maintains the stability and translation of FGFR1 mRNA in an m6A-dependent manner, thereby inhibiting skeletal myogenesis through activation of the ERK signaling pathway. This study further enriches the understanding of the molecular mechanisms by which RNA methylation regulates myogenesis, providing valuable insights into the role of IGF2BP1-mediated post-transcriptional regulation in muscle development.
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Affiliation(s)
- Zhipeng Liu
- Sanya Research Institute of Nanjing Agricultural University & Hainan Seed Industry laborator, Nanjing Agricultural University, Sanya 572025, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaiping Deng
- Sanya Research Institute of Nanjing Agricultural University & Hainan Seed Industry laborator, Nanjing Agricultural University, Sanya 572025, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Yalong Su
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Congyu Shi
- Sanya Research Institute of Nanjing Agricultural University & Hainan Seed Industry laborator, Nanjing Agricultural University, Sanya 572025, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingang Wang
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Yixuan Fan
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China
| | - Guoming Zhang
- Sanya Research Institute of Nanjing Agricultural University & Hainan Seed Industry laborator, Nanjing Agricultural University, Sanya 572025, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China; College of veterinary medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Wang
- Sanya Research Institute of Nanjing Agricultural University & Hainan Seed Industry laborator, Nanjing Agricultural University, Sanya 572025, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
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15
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Alsina FC, Lupan BM, Lin LJ, Musso CM, Mosti F, Newman CR, Wood LM, Suzuki A, Agostino M, Moore JK, Silver DL. The RNA-binding protein EIF4A3 promotes axon development by direct control of the cytoskeleton. Cell Rep 2024; 43:114666. [PMID: 39182224 DOI: 10.1016/j.celrep.2024.114666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 02/28/2024] [Accepted: 08/06/2024] [Indexed: 08/27/2024] Open
Abstract
The exon junction complex (EJC), nucleated by EIF4A3, is indispensable for mRNA fate and function throughout eukaryotes. We discover that EIF4A3 directly controls microtubules, independent of RNA, which is critical for neural wiring. While neuronal survival in the developing mouse cerebral cortex depends upon an intact EJC, axonal tract development requires only Eif4a3. Using human cortical organoids, we show that EIF4A3 disease mutations also impair neuronal growth, highlighting conserved functions relevant for neurodevelopmental pathology. Live imaging of growing neurons shows that EIF4A3 is essential for microtubule dynamics. Employing biochemistry and competition experiments, we demonstrate that EIF4A3 directly binds to microtubules, mutually exclusive of the EJC. Finally, in vitro reconstitution assays and rescue experiments demonstrate that EIF4A3 is sufficient to promote microtubule polymerization and that EIF4A3-microtubule association is a major contributor to axon growth. This reveals a fundamental mechanism by which neurons re-utilize core gene expression machinery to directly control the cytoskeleton.
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Affiliation(s)
- Fernando C Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Bianca M Lupan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lydia J Lin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Camila M Musso
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Federica Mosti
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Carly R Newman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lisa M Wood
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Curtin Medical School, and Curtin Institute for Computation, Curtin University, Bentley, WA 6102, Australia
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences and Duke Regeneration Center, Duke University Medical Center, Durham, NC 27710, USA.
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16
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Noguchi K, Suzuki H, Abe R, Horiuchi K, Onoguchi-Mizutani R, Akimitsu N, Ogawa S, Akiyama T, Ike Y, Ino Y, Kimura Y, Ryo A, Doi H, Tanaka F, Suzuki Y, Toyoda A, Yamaguchi Y, Takahashi H. Multi-omics analysis using antibody-based in situ biotinylation technique suggests the mechanism of Cajal body formation. Cell Rep 2024; 43:114734. [PMID: 39283744 DOI: 10.1016/j.celrep.2024.114734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 04/30/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024] Open
Abstract
Membrane-less subcellular compartments play important roles in various cellular functions. Although techniques exist to identify components of cellular bodies, a comprehensive method for analyzing both static and dynamic states has not been established. Here, we apply an antibody-based in situ biotinylation proximity-labeling technique to identify components of static and dynamic nuclear bodies. Using this approach, we comprehensively identify DNA, RNA, and protein components of Cajal bodies (CBs) and then clarify their interactome. By inhibiting transcription, we capture dynamic changes in CBs. Our analysis reveals that nascent small nuclear RNAs (snRNAs) transcribed in CBs contribute to CB formation by assembling RNA-binding proteins, including frontotemporal dementia-related proteins, RNA-binding motif proteins, and heterogeneous nuclear ribonucleoproteins.
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Affiliation(s)
- Keisuke Noguchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Rena Onoguchi-Mizutani
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Nobuyoshi Akimitsu
- R&D Department, Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ike
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yoko Ino
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Yayoi Kimura
- Advance Medical Research Center, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 216-0004, Japan; Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa 226-8501, Japan.
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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17
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Song Z, Bae B, Schnabl S, Yuan F, De Zoysa T, Akinyi M, Le Roux C, Choquet K, Whipple A, Van Nostrand E. Mapping snoRNA-target RNA interactions in an RNA binding protein-dependent manner with chimeric eCLIP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613955. [PMID: 39345503 PMCID: PMC11429978 DOI: 10.1101/2024.09.19.613955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs that function in ribosome and spliceosome biogenesis, primarily by guiding modifying enzymes to specific sites on ribosomal RNA (rRNA) and spliceosomal RNA (snRNA). However, many orphan snoRNAs remain uncharacterized, with unidentified or unvalidated targets, and studies on additional snoRNA-associated proteins are limited. We adapted an enhanced chimeric eCLIP approach to comprehensively profile snoRNA-target RNA interactions using both core and accessory snoRNA binding proteins as baits. Using core snoRNA binding proteins, we confirmed most annotated snoRNA-rRNA and snoRNA-snRNA interactions in mouse and human cell lines and called novel, high-confidence interactions for orphan snoRNAs. While some of these interactions result in chemical modification, others may have modification-independent functions. We then showed that snoRNA ribonucleoprotein complexes containing certain accessory proteins, like WDR43 and NOLC1, enriched for specific subsets of snoRNA-target RNA interactions with distinct roles in ribosome and spliceosome biogenesis. Notably, we discovered that SNORD89 guides 2'-O-methylation at two neighboring sites in U2 snRNA that are important for activating splicing, but also appear to ensure imperfect splicing for a subset of near-constitutive exons. Thus, chimeric eCLIP of snoRNA-associating proteins enables a comprehensive framework for studying snoRNA-target interactions in an RNA binding protein-dependent manner, revealing novel interactions and regulatory roles in RNA biogenesis.
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Affiliation(s)
- Zhuoyi Song
- Therapeutic Innovation Center & the Verna Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, TX USA
| | - Bongmin Bae
- Department of Molecular & Cellular Biology, Harvard University, Cambridge MA USA
| | - Simon Schnabl
- Department of Molecular & Cellular Biology, Harvard University, Cambridge MA USA
| | - Fei Yuan
- Therapeutic Innovation Center & the Verna Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, TX USA
| | - Thareendra De Zoysa
- Department of Molecular & Cellular Biology, Harvard University, Cambridge MA USA
| | - Maureen Akinyi
- Therapeutic Innovation Center & the Verna Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, TX USA
| | - Charlotte Le Roux
- Therapeutic Innovation Center & the Verna Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, TX USA
| | - Karine Choquet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Québec CA
| | - Amanda Whipple
- Department of Molecular & Cellular Biology, Harvard University, Cambridge MA USA
| | - Eric Van Nostrand
- Therapeutic Innovation Center & the Verna Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, TX USA
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18
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Corso-Díaz X, Liang X, Preston K, Tegshee B, English MA, Nellissery J, Yadav SP, Marchal C, Swaroop A. Maf-family bZIP transcription factor NRL interacts with RNA-binding proteins and R-loops in retinal photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613899. [PMID: 39345562 PMCID: PMC11430021 DOI: 10.1101/2024.09.19.613899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
RNA-binding proteins (RBPs) perform diverse functions including the regulation of chromatin dynamics and the coupling of transcription with RNA processing. However, our understanding of their actions in mammalian neurons remains limited. Using affinity purification, yeast-two-hybrid and proximity ligation assays, we identified interactions of multiple RBPs with NRL, a Maf-family bZIP transcription factor critical for retinal rod photoreceptor development and function. In addition to splicing, many NRL-interacting RBPs are associated with R-loops, which form during transcription and increase during photoreceptor maturation. Focusing on DHX9 RNA helicase, we demonstrate that its expression is modulated by NRL and that the NRL-DHX9 interaction is positively influenced by R-loops. ssDRIP-Seq analysis reveals both stranded and unstranded R-loops at distinct genomic elements, characterized by active and inactive epigenetic signatures and enriched at neuronal genes. NRL binds to both types of R-loops, suggesting an epigenetically independent function. Our findings suggest additional functions of NRL during transcription and highlight complex interactions among transcription factors, RBPs, and R-loops in regulating photoreceptor gene expression in the mammalian retina.
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Affiliation(s)
- Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Stanford, California, USA
| | - Xulong Liang
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
| | - Kiam Preston
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
| | - Bilguun Tegshee
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
| | - Milton A. English
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
| | - Jacob Nellissery
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
| | - Sharda Prasad Yadav
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
| | - Claire Marchal
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
- In silichrom Ltd, 15 Digby road, RG14 1TS Newbury, United Kingdom
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, Maryland, 20892 USA
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19
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Bolikhova AK, Buyan AI, Mariasina SS, Rudenko AY, Chekh DS, Mazur AM, Prokhortchouk EB, Dontsova OA, Sergiev PV. Study of the RNA splicing kinetics via in vivo 5-EU labeling. RNA (NEW YORK, N.Y.) 2024; 30:1356-1373. [PMID: 39048310 PMCID: PMC11404452 DOI: 10.1261/rna.079937.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
Splicing is an important step of gene expression in all eukaryotes. Splice sites might be used with different efficiency, giving rise to alternative splicing products. At the same time, splice sites might be used at a variable rate. We used 5-ethynyl uridine labeling to sequence a nascent transcriptome of HeLa cells and deduced the rate of splicing for each donor and acceptor splice site. The following correlation analysis showed a correspondence of primary transcript features with the rate of splicing. Some dependencies we revealed were anticipated, such as a splicing rate decrease with a decreased complementarity of the donor splice site to U1 and acceptor sites to U2 snRNAs. Other dependencies were more surprising, like a negative influence of a distance to the 5' end on the rate of the acceptor splicing site utilization, or the differences in splicing rate between long, short, and RBM17-dependent introns. We also observed a deceleration of last intron splicing with an increase of the distance to the poly(A) site, which might be explained by the cooperativity of the splicing and polyadenylation. Additional analysis of splicing kinetics of SF3B4 knockdown cells suggested the impairment of a U2 snRNA recognition step. As a result, we deconvoluted the effects of several examined features on the splicing rate into a single regression model. The data obtained here are useful for further studies in the field, as they provide general splicing rate dependencies as well as help to justify the existence of slowly removed splice sites.
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Affiliation(s)
- Anastasiia K Bolikhova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Andrey I Buyan
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sofia S Mariasina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Y Rudenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Daria S Chekh
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander M Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Egor B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Petr V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119991, Russia
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20
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Ruan X, Hu K, Yang Y, Yang R, Tseng E, Kang B, Kauffman A, Zhong R, Zhang X. Cell-type-specific splicing of transcription regulators and Ptbp1 by Rbfox1/2/3 in the developing neocortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612108. [PMID: 39314274 PMCID: PMC11419088 DOI: 10.1101/2024.09.09.612108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
How master splicing regulators crosstalk with each other and to what extent transcription regulators are differentially spliced remain unclear in the developing brain. Here, cell-type-specific RNA-Seq of the developing neocortex uncover that transcription regulators are enriched for differential splicing, altering protein isoforms or inducing nonsense-mediated mRNA decay. Transient expression of Rbfox proteins in radial glia progenitors induces neuronal splicing events preferentially in transcription regulators such as Meis2 and Tead1. Surprisingly, Rbfox proteins promote the inclusion of a mammal-specific alternative exon and a previously undescribed poison exon in Ptbp1. Simultaneous ablation of Rbfox1/2/3 in the neocortex downregulates neuronal isoforms and disrupts radial neuronal migration. Furthermore, the progenitor isoform of Meis2 promotes Tgfb3 transcription, while the Meis2 neuron isoform promotes neuronal differentiation. These observations indicate that transcription regulators are differentially spliced between cell types in the developing neocortex.
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Affiliation(s)
- Xiangbin Ruan
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Equal contributions
| | - Kaining Hu
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Equal contributions
| | - Yalan Yang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Equal contributions
| | - Runwei Yang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | | | - Bowei Kang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Aileen Kauffman
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Rong Zhong
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaochang Zhang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- The Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
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21
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Khoroshkin M, Buyan A, Dodel M, Navickas A, Yu J, Trejo F, Doty A, Baratam R, Zhou S, Lee SB, Joshi T, Garcia K, Choi B, Miglani S, Subramanyam V, Modi H, Carpenter C, Markett D, Corces MR, Mardakheh FK, Kulakovskiy IV, Goodarzi H. Systematic identification of post-transcriptional regulatory modules. Nat Commun 2024; 15:7872. [PMID: 39251607 PMCID: PMC11385195 DOI: 10.1038/s41467-024-52215-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we perform a systematic annotation of RBP combinatorial interactions via multimodal data integration. We build a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we use CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generate an integrated map of functional RBP interactions. We then use this map to match RBPs to their context-specific functions and validate the predicted functions biochemically for four RBPs. This study provides a detailed map of RBP interactions and deconvolves them into distinct regulatory modules with annotated functions and target regulons. This multimodal and integrative framework provides a principled approach for studying post-transcriptional regulatory processes and enriches our understanding of their underlying mechanisms.
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Affiliation(s)
- Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Andrey Buyan
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Institut Curie, UMR3348 CNRS, Inserm, Orsay, France
| | - Johnny Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Fathima Trejo
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Anthony Doty
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Rithvik Baratam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Shaopu Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sean B Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tanvi Joshi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sohit Miglani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Vishvak Subramanyam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Carpenter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Markett
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
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22
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Seitz H. A new perspective on microRNA-guided gene regulation specificity, and its potential generalization to transcription factors and RNA-binding proteins. Nucleic Acids Res 2024; 52:9360-9368. [PMID: 39149906 PMCID: PMC11381331 DOI: 10.1093/nar/gkae694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
Our conception of gene regulation specificity has undergone profound changes over the last 20 years. Previously, regulators were considered to control few genes, recognized with exquisite specificity by a 'lock and key' mechanism. However, recently genome-wide exploration of regulator binding site occupancy (whether on DNA or RNA targets) revealed extensive lists of molecular targets for every studied regulator. Such poor biochemical specificity suggested that each regulator controls many genes, collectively contributing to biological phenotypes. Here, I propose a third model, whereby regulators' biological specificity is only partially due to 'lock and key' biochemistry. Rather, regulators affect many genes at the microscopic scale, but biological consequences for most interactions are attenuated at the mesoscopic scale: only a few regulatory events propagate from microscopic to macroscopic scale; others are made inconsequential by homeostatic mechanisms. This model is well supported by the microRNA literature, and data suggest that it extends to other regulators. It reconciles contradicting observations from biochemistry and comparative genomics on one hand and in vivo genetics on the other hand, but this conceptual unification is obscured by common misconceptions and counter-intuitive modes of graphical display. Profound understanding of gene regulation requires conceptual clarification, and better suited statistical analyses and graphical representation.
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Affiliation(s)
- Hervé Seitz
- Institut de Génétique Humaine (UMR 9002), CNRS, 141, rue de la Cardonille, 34396 Montpellier, France
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23
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Abood A, Mesner LD, Jeffery ED, Murali M, Lehe MD, Saquing J, Farber CR, Sheynkman GM. Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease. Am J Hum Genet 2024; 111:1914-1931. [PMID: 39079539 PMCID: PMC11393689 DOI: 10.1016/j.ajhg.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 08/07/2024] Open
Abstract
A major fraction of loci identified by genome-wide association studies (GWASs) mediate alternative splicing, but mechanistic interpretation is hindered by the technical limitations of short-read RNA sequencing (RNA-seq), which cannot directly link splicing events to full-length protein isoforms. Long-read RNA-seq represents a powerful tool to characterize transcript isoforms, and recently, infer protein isoform existence. Here, we present an approach that integrates information from GWASs, splicing quantitative trait loci (sQTLs), and PacBio long-read RNA-seq in a disease-relevant model to infer the effects of sQTLs on the ultimate protein isoform products they encode. We demonstrate the utility of our approach using bone mineral density (BMD) GWAS data. We identified 1,863 sQTLs from the Genotype-Tissue Expression (GTEx) project in 732 protein-coding genes that colocalized with BMD associations (H4PP ≥ 0.75). We generated PacBio Iso-Seq data (N = ∼22 million full-length reads) on human osteoblasts, identifying 68,326 protein-coding isoforms, of which 17,375 (25%) were unannotated. By casting the sQTLs onto protein isoforms, we connected 809 sQTLs to 2,029 protein isoforms from 441 genes expressed in osteoblasts. Overall, we found that 74 sQTLs influenced isoforms likely impacted by nonsense-mediated decay and 190 that potentially resulted in the expression of unannotated protein isoforms. Finally, we functionally validated colocalizing sQTLs in TPM2, in which siRNA-mediated knockdown in osteoblasts showed two TPM2 isoforms with opposing effects on mineralization but exhibited no effect upon knockdown of the entire gene. Our approach should be to generalize across diverse clinical traits and to provide insights into protein isoform activities modulated by GWAS loci.
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Affiliation(s)
- Abdullah Abood
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Larry D Mesner
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Mayank Murali
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Micah D Lehe
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Jamie Saquing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Charles R Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
| | - Gloria M Sheynkman
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA; UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA.
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24
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Quintas A, Harvey RF, Horvilleur E, Garland GD, Schmidt T, Kalmar L, Dezi V, Marini A, Fulton AM, Pöyry TAA, Cole CH, Turner M, Sawarkar R, Chapman MA, Bushell M, Willis AE. Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs. Nucleic Acids Res 2024:gkae767. [PMID: 39225047 DOI: 10.1093/nar/gkae767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/13/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
RNA binding proteins drive proliferation and tumorigenesis by regulating the translation and stability of specific subsets of messenger RNAs (mRNAs). We have investigated the role of eukaryotic initiation factor 4B (eIF4B) in this process and identify 10-fold more RNA binding sites for eIF4B in tumour cells from patients with diffuse large B-cell lymphoma compared to control B cells and, using individual-nucleotide resolution UV cross-linking and immunoprecipitation, find that eIF4B binds the entire length of mRNA transcripts. eIF4B stimulates the helicase activity of eIF4A, thereby promoting the unwinding of RNA structure within the 5' untranslated regions of mRNAs. We have found that, in addition to its well-documented role in mRNA translation, eIF4B additionally interacts with proteins associated with RNA turnover, including UPF1 (up-frameshift protein 1), which plays a key role in histone mRNA degradation at the end of S phase. Consistent with these data, we locate an eIF4B binding site upstream of the stem-loop structure in histone mRNAs and show that decreased eIF4B expression alters histone mRNA turnover and delays cell cycle progression through S phase. Collectively, these data provide insight into how eIF4B promotes tumorigenesis.
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Affiliation(s)
- Ana Quintas
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Robert F Harvey
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Emilie Horvilleur
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Gavin D Garland
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lajos Kalmar
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Veronica Dezi
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alberto Marini
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alexander M Fulton
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Tuija A A Pöyry
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Cameron H Cole
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Martin Turner
- Immunology Programme, Babraham Institute, Babraham Science Campus, Cambridgeshire CB22 3AT, UK
| | - Ritwick Sawarkar
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Michael A Chapman
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
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25
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Xu H, Ye J, Zhang KX, Hu Q, Cui T, Tong C, Wang M, Geng H, Shui KM, Sun Y, Wang J, Hou X, Zhang K, Xie R, Yin Y, Chen N, Chen JY. Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA. Nat Chem 2024:10.1038/s41557-024-01609-7. [PMID: 39223307 DOI: 10.1038/s41557-024-01609-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/17/2024] [Indexed: 09/04/2024]
Abstract
Triplex DNA structures, formed when a third DNA strand wraps around the major groove of DNA, are key molecular regulators and genomic threats. However, the regulatory network governing triplex DNA dynamics remains poorly understood. Here we reveal the binding and functional repertoire of proteins that interact with triplex DNA through chemoproteomic profiling in living cells. We develop a chemical probe that exhibits exceptional specificity towards triplex DNA. By employing a co-binding-mediated proximity capture strategy, we enrich triplex DNA interactome for quantitative proteomics analysis. This enables the identification of a comprehensive list of proteins that interact with triplex DNA, characterized by diverse binding properties and regulatory mechanisms in their native chromatin context. As a demonstration, we validate DDX3X as an ATP-independent triplex DNA helicase to unwind substrates with a 5' overhang to prevent DNA damage. Overall, our study provides a valuable resource for exploring the biology and translational potential of triplex DNA.
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Affiliation(s)
- Hongzhan Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Jing Ye
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Kui-Xing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Qingxi Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Chong Tong
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengqi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Huichao Geng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Kun-Ming Shui
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Yan Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Jian Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Xiaomeng Hou
- ChomiX Biotech (Nanjing) Co. Ltd., Nanjing, China
| | - Kai Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nan Chen
- ChomiX Biotech (Nanjing) Co. Ltd., Nanjing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China.
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, China.
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26
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Guarnacci M, Zhang PH, Kanchi M, Hung YT, Lin H, Shirokikh NE, Yang L, Preiss T. Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover. Life Sci Alliance 2024; 7:e202402613. [PMID: 38986569 PMCID: PMC11235314 DOI: 10.26508/lsa.202402613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Maps of the RNA modification 5-methylcytosine (m5C) often diverge markedly not only because of differences in detection methods, data depand analysis pipelines but also biological factors. We re-analysed bisulfite RNA sequencing datasets from five human cell lines and seven tissues using a coherent m5C site calling pipeline. With the resulting union list of 6,393 m5C sites, we studied site distribution, enzymology, interaction with RNA-binding proteins and molecular function. We confirmed tRNA:m5C methyltransferases NSUN2 and NSUN6 as the main mRNA m5C "writers," but further showed that the rRNA:m5C methyltransferase NSUN5 can also modify mRNA. Each enzyme recognises mRNA features that strongly resemble their canonical substrates. By analysing proximity between mRNA m5C sites and footprints of RNA-binding proteins, we identified new candidates for functional interactions, including the RNA helicases DDX3X, involved in mRNA translation, and UPF1, an mRNA decay factor. We found that lack of NSUN2 in HeLa cells affected both steady-state levels of, and UPF1-binding to, target mRNAs. Our studies emphasise the emerging diversity of m5C writers and readers and their effect on mRNA function.
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Affiliation(s)
- Marco Guarnacci
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Pei-Hong Zhang
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Molecular Medicine, Children's Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Madhu Kanchi
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Yu-Ting Hung
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Hanrong Lin
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Nikolay E Shirokikh
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Thomas Preiss
- https://ror.org/019wvm592 Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Sydney, Australia
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27
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Wang B, Mount S. Latent Dirichlet allocation mixture models for nucleotide sequence analysis. NAR Genom Bioinform 2024; 6:lqae099. [PMID: 39131816 PMCID: PMC11310860 DOI: 10.1093/nargab/lqae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/13/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
Strings of nucleotides carrying biological information are typically described as sequence motifs represented by weight matrices or consensus sequences. However, many signals in DNA or RNA are recognized by multiple factors in temporal sequence, consist of distinct alternative motifs, or are best described by base composition. Here we apply the latent Dirichlet allocation (LDA) mixture model to nucleotide sequences. Using positions in an alignment of human or Drosophila splice sites as samples, we show that LDA readily identifies motifs, including such elusive cases as the intron branch site. Using whole sequences with positional k-mers as features, LDA can identify sequence subtypes enriched in long vs. short introns. LDA with bulk k-mers can reliably distinguish reading frame and species of origin in coding sequences from humans and Drosophila. We find that LDA is a useful model for describing heterogeneous signals, for assigning individual sequences to subtypes, and for identifying and characterizing sequences that do not fit recognized subtypes. Because LDA topic models are interpretable, they also aid the discovery of new motifs, even those present in a small fraction of samples. In summary, LDA can identify and characterize signals in nucleotide sequences, including candidate regulatory factors involved in biological processes.
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Affiliation(s)
- Bixuan Wang
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen M Mount
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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28
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Yao J, Xu H, Ferrick-Kiddie EA, Nottingham RM, Wu DC, Ares M, Lambowitz AM. Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers. PLoS Genet 2024; 20:e1011416. [PMID: 39325823 PMCID: PMC11460701 DOI: 10.1371/journal.pgen.1011416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 10/08/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024] Open
Abstract
A previous study using Thermostable Group II Intron Reverse Transcriptase sequencing (TGIRT-seq) found human plasma contains short (≤300 nt) structured full-length excised linear intron (FLEXI) RNAs with potential to serve as blood-based biomarkers. Here, TGIRT-seq identified >9,000 different FLEXI RNAs in human cell lines, including relatively abundant FLEXIs with cell-type-specific expression patterns. Analysis of public CLIP-seq datasets identified 126 RNA-binding proteins (RBPs) that have binding sites within the region corresponding to the FLEXI or overlapping FLEXI splice sites in pre-mRNAs, including 53 RBPs with binding sites for ≥30 different FLEXIs. These included splicing factors, transcription factors, a chromatin remodeling protein, cellular growth regulators, and proteins with cytoplasmic functions. Analysis of ENCODE datasets identified subsets of these RBPs whose knockdown impacted FLEXI host gene mRNA levels or proximate alternative splicing, indicating functional interactions. Hierarchical clustering identified six subsets of RBPs whose FLEXI binding sites were co-enriched in six subsets of functionally related host genes: AGO1-4 and DICER, including but not limited to agotrons or mirtron pre-miRNAs; DKC1, NOLC1, SMNDC1, and AATF (Apoptosis Antagonizing Transcription Factor), including but not limited to snoRNA-encoding FLEXIs; two subsets of alternative splicing factors; and two subsets that included RBPs with cytoplasmic functions (e.g., LARP4, PABPC4, METAP2, and ZNF622) together with regulatory proteins. Cell fractionation experiments showed cytoplasmic enrichment of FLEXI RNAs with binding sites for RBPs with cytoplasmic functions. The subsets of host genes encoding FLEXIs with binding sites for different subsets of RBPs were co-enriched with non-FLEXI other short and long introns with binding sites for the same RBPs, suggesting overarching mechanisms for coordinately regulating expression of functionally related genes. Our findings identify FLEXIs as a previously unrecognized large class of cellular RNAs and provide a comprehensive roadmap for further analyzing their biological functions and the relationship of their RBPs to cellular regulatory mechanisms.
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Affiliation(s)
- Jun Yao
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Elizabeth A. Ferrick-Kiddie
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Ryan M. Nottingham
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Douglas C. Wu
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Manuel Ares
- Department of Molecular, Cell, and Developmental Biology University of California, Santa Cruz, California, United States of America
| | - Alan M. Lambowitz
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
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29
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Gadekar V, Munk AW, Miladi M, Junge A, Backofen R, Seemann S, Gorodkin J. Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. NAR Genom Bioinform 2024; 6:lqae089. [PMID: 39131818 PMCID: PMC11310781 DOI: 10.1093/nargab/lqae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/26/2024] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
RNA secondary structures play essential roles in the formation of the tertiary structure and function of a transcript. Recent genome-wide studies highlight significant potential for RNA structures in the mammalian genome. However, a major challenge is assigning functional roles to these structured RNAs. In this study, we conduct a guilt-by-association analysis of clusters of computationally predicted conserved RNA structure (CRSs) in human untranslated regions (UTRs) to associate them with gene functions. We filtered a broad pool of ∼500 000 human CRSs for UTR overlap, resulting in 4734 and 24 754 CRSs from the 5' and 3' UTR of protein-coding genes, respectively. We separately clustered these CRSs for both sets using RNAscClust, obtaining 793 and 2403 clusters, each containing an average of five CRSs per cluster. We identified overrepresented binding sites for 60 and 43 RNA-binding proteins co-localizing with the clustered CRSs. Furthermore, 104 and 441 clusters from the 5' and 3' UTRs, respectively, showed enrichment for various Gene Ontologies, including biological processes such as 'signal transduction', 'nervous system development', molecular functions like 'transferase activity' and the cellular components such as 'synapse' among others. Our study shows that significant functional insights can be gained by clustering RNA structures based on their structural characteristics.
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Affiliation(s)
- Veerendra P Gadekar
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Ridebanevej 9, 1870 Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, 1870 Frederiksberg, Denmark
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India
| | - Alexander Welford Munk
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Ridebanevej 9, 1870 Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, 1870 Frederiksberg, Denmark
| | - Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
| | - Alexander Junge
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Ridebanevej 9, 1870 Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, 1870 Frederiksberg, Denmark
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stefan E Seemann
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Ridebanevej 9, 1870 Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, 1870 Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Ridebanevej 9, 1870 Frederiksberg, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, 1870 Frederiksberg, Denmark
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30
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Schmok JC, Jain M, Street LA, Tankka AT, Schafer D, Her HL, Elmsaouri S, Gosztyla ML, Boyle EA, Jagannatha P, Luo EC, Kwon EJ, Jovanovic M, Yeo GW. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nat Biotechnol 2024; 42:1429-1441. [PMID: 38168984 PMCID: PMC11389820 DOI: 10.1038/s41587-023-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification-mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.
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Affiliation(s)
- Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lena A Street
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alex T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sara Elmsaouri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ester J Kwon
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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31
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Bakulin A, Teyssier NB, Kampmann M, Khoroshkin M, Goodarzi H. pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease. PLoS Comput Biol 2024; 20:e1012346. [PMID: 39236079 PMCID: PMC11421795 DOI: 10.1371/journal.pcbi.1012346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/24/2024] [Accepted: 07/22/2024] [Indexed: 09/07/2024] Open
Abstract
Inferring the driving regulatory programs from comparative analysis of gene expression data is a cornerstone of systems biology. Many computational frameworks were developed to address this problem, including our iPAGE (information-theoretic Pathway Analysis of Gene Expression) toolset that uses information theory to detect non-random patterns of expression associated with given pathways or regulons. Our recent observations, however, indicate that existing approaches are susceptible to the technical biases that are inherent to most real world annotations. To address this, we have extended our information-theoretic framework to account for specific biases and artifacts in biological networks using the concept of conditional information. To showcase pyPAGE, we performed a comprehensive analysis of regulatory perturbations that underlie the molecular etiology of Alzheimer's disease (AD). pyPAGE successfully recapitulated several known AD-associated gene expression programs. We also discovered several additional regulons whose differential activity is significantly associated with AD. We further explored how these regulators relate to pathological processes in AD through cell-type specific analysis of single cell and spatial gene expression datasets. Our findings showcase the utility of pyPAGE as a precise and reliable biomarker discovery in complex diseases such as Alzheimer's disease.
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Affiliation(s)
- Artemy Bakulin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Noam B. Teyssier
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Arc Institute, Palo Alto, California, United States of America
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32
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Shen J, Shentu J, Zhong C, Huang Q, Duan S. RNA splicing factor RBFOX2 is a key factor in the progression of cancer and cardiomyopathy. Clin Transl Med 2024; 14:e1788. [PMID: 39243148 PMCID: PMC11380049 DOI: 10.1002/ctm2.1788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Alternative splicing of pre-mRNA is a fundamental regulatory process in multicellular eukaryotes, significantly contributing to the diversification of the human proteome. RNA-binding fox-1 homologue 2 (RBFOX2), a member of the evolutionarily conserved RBFOX family, has emerged as a critical splicing regulator, playing a pivotal role in the alternative splicing of pre-mRNA. This review provides a comprehensive analysis of RBFOX2, elucidating its splicing activity through direct and indirect binding mechanisms. RBFOX2 exerts substantial influence over the alternative splicing of numerous transcripts, thereby shaping essential cellular processes such as differentiation and development. MAIN BODY OF THE ABSTRACT Dysregulation of RBFOX2-mediated alternative splicing has been closely linked to a spectrum of cardiovascular diseases and malignant tumours, underscoring its potential as a therapeutic target. Despite significant progress, current research faces notable challenges. The complete structural characterisation of RBFOX2 remains elusive, limiting in-depth exploration beyond its RNA-recognition motif. Furthermore, the scarcity of studies focusing on RBFOX2-targeting drugs poses a hindrance to translating research findings into clinical applications. CONCLUSION This review critically assesses the existing body of knowledge on RBFOX2, highlighting research gaps and limitations. By delineating these areas, this analysis not only serves as a foundational reference for future studies but also provides strategic insights for bridging these gaps. Addressing these challenges will be instrumental in unlocking the full therapeutic potential of RBFOX2, paving the way for innovative and effective treatments in various diseases.
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Affiliation(s)
- Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Jianqiao Shentu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Chenming Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, China
| | - Qiankai Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
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Besouro-Duarte A, Carrasqueiro B, Sousa S, Xavier JM, Maia AT. Colocalised Genetic Associations Reveal Alternative Splicing Variants as Candidate Causal Links for Breast Cancer Risk in 10 Loci. Cancers (Basel) 2024; 16:3020. [PMID: 39272878 PMCID: PMC11394352 DOI: 10.3390/cancers16173020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/23/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Genome-wide association studies (GWASs) have revealed numerous loci associated with breast cancer risk, yet the precise causal variants, their impact on molecular mechanisms, and the affected genes often remain elusive. We hypothesised that specific variants exert their influence by affecting cis-regulatory alternative splice elements. An analysis of splicing quantitative trait loci (sQTL) in healthy breast tissue from female individuals identified multiple variants linked to alterations in splicing ratios. Through colocalisation analysis, we pinpointed 43 variants within twelve genes that serve as candidate causal links between sQTL and GWAS findings. In silico splice analysis highlighted a potential mechanism for three genes-FDPS, SGCE, and MRPL11-where variants in proximity to or on the splice site modulate usage, resulting in alternative splice transcripts. Further in vitro/vivo studies are imperative to fully understand how these identified changes contribute to breast oncogenesis. Moreover, investigating their potential as biomarkers for breast cancer risk could enhance screening strategies and early detection methods for breast cancer.
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Affiliation(s)
- André Besouro-Duarte
- CINTESIS@RISE, Universidade do Algarve, 8005-139 Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, Gambelas Campus, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Beatriz Carrasqueiro
- Faculty of Medicine and Biomedical Sciences, Gambelas Campus, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Sofia Sousa
- Faculty of Medicine and Biomedical Sciences, Gambelas Campus, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Joana M Xavier
- CINTESIS@RISE, Universidade do Algarve, 8005-139 Faro, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Ana-Teresa Maia
- CINTESIS@RISE, Universidade do Algarve, 8005-139 Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, Gambelas Campus, Universidade do Algarve, 8005-139 Faro, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
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Stocks J, Gilbert N. Nuclear RNA: a transcription-dependent regulator of chromatin structure. Biochem Soc Trans 2024; 52:1605-1615. [PMID: 39082979 DOI: 10.1042/bst20230787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/29/2024]
Abstract
Although the majority of RNAs are retained in the nucleus, their significance is often overlooked. However, it is now becoming clear that nuclear RNA forms a dynamic structure through interacting with various proteins that can influence the three-dimensional structure of chromatin. We review the emerging evidence for a nuclear RNA mesh or gel, highlighting the interplay between DNA, RNA and RNA-binding proteins (RBPs), and assessing the critical role of protein and RNA in governing chromatin architecture. We also discuss a proposed role for the formation and regulation of the nuclear gel in transcriptional control. We suggest that it may concentrate the transcriptional machinery either by direct binding or inducing RBPs to form microphase condensates, nanometre sized membraneless structures with distinct properties to the surrounding medium and an enrichment of particular macromolecules.
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Affiliation(s)
- Jon Stocks
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, U.K
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, U.K
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Nguyen E, Sosa JA, Cassidy KC, Berman AJ. Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution. PLoS One 2024; 19:e0308574. [PMID: 39190712 DOI: 10.1371/journal.pone.0308574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
TOR (target of rapamycin), a ubiquitous protein kinase central to cellular homeostasis maintenance, fundamentally regulates ribosome biogenesis in part by its target La-related protein 1 (LARP1). Among other target transcripts, LARP1 specifically binds TOP (terminal oligopyrimidine) mRNAs encoding all 80 ribosomal proteins in a TOR-dependent manner through its C-terminal region containing the DM15 module. Though the functional implications of the LARP1 interaction with target mRNAs is controversial, it is clear that the TOP-LARP1-TOR axis is critical to cellular health in humans. Its existence and role in evolutionarily divergent animals remain less understood. We focused our work on expanding our knowledge of the first arm of the axis: the connection between LARP1-DM15 and the 5' TOP motif. We show that the overall DM15 architecture observed in humans is conserved in fruit fly and zebrafish. Both adopt familiar curved arrangements of HEAT-like repeats that bind 5' TOP mRNAs on the same conserved surface, although molecular dynamics simulations suggest that the N-terminal fold of the fruit fly DM15 is predicted to be unstable and unfold. We demonstrate that each ortholog interacts with TOP sequences with varying affinities. Importantly, we determine that the ability of the DM15 region to bind some TOP sequences but not others might amount to the context of the RNA structure, rather than the ability of the module to recognize some sequences but not others. We propose that TOP mRNAs may retain similar secondary structures to regulate LARP1 DM15 recognition.
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Affiliation(s)
- Elaine Nguyen
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Jahree A Sosa
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Kevin C Cassidy
- BIOVIA, Dassault Systèmes, Waltham, MA, United States of America
| | - Andrea J Berman
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States of America
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36
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Li M, Fang Q, Xiao P, Yin Z, Mei G, Wang C, Xiang Y, Zhao X, Qu L, Xu T, Zhang J, Liu K, Li X, Dong H, Xiao R, Zhou R. KHSRP ameliorates acute liver failure by regulating pre-mRNA splicing through its interaction with SF3B1. Cell Death Dis 2024; 15:618. [PMID: 39187547 PMCID: PMC11347664 DOI: 10.1038/s41419-024-06886-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 08/28/2024]
Abstract
Acute liver failure (ALF) is characterized by the rapidly progressive deterioration of hepatic function, which, without effective medical intervention, results in high mortality and morbidity. Here, using proteomic and transcriptomic analyses in murine ALF models, we found that the expression of multiple splicing factors was downregulated in ALF. Notably, we found that KH-type splicing regulatory protein (KHSRP) has a protective effect in ALF. Knockdown of KHSRP resulted in dramatic splicing defects, such as intron retention, and led to the exacerbation of liver injury in ALF. Moreover, we demonstrated that KHSRP directly interacts with splicing factor 3b subunit 1 (SF3B1) and enhances the binding of SF3B1 to the intronic branch sites, thereby promoting pre-mRNA splicing. Using splicing inhibitors, we found that Khsrp protects against ALF by regulating pre-mRNA splicing in vivo. Overall, our findings demonstrate that KHSRP is an important splicing activator and promotes the expression of genes associated with ALF progression by interacting with SF3B1; thus, KHSRP could be a possible target for therapeutic intervention in ALF.
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Affiliation(s)
- Mingxuan Li
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Qian Fang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Pingping Xiao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Zhinang Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Guangbo Mei
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Cheng Wang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Ying Xiang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Xuejun Zhao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Lihua Qu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Tian Xu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Jiaxi Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Kejun Liu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Xiaoqing Li
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Huifen Dong
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Ruijing Xiao
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
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Leclair NK, Lucas CHG, Mirchia K, McCortney K, Horbinski CM, Raleigh DR, Anczukow O. The RNA-binding protein IGF2BP1 regulates stability of mRNA transcribed from FOXM1 target genes in hypermitotic meningiomas. Acta Neuropathol 2024; 148:28. [PMID: 39179895 PMCID: PMC11343784 DOI: 10.1007/s00401-024-02788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024]
Affiliation(s)
- Nathan K Leclair
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Calixto-Hope G Lucas
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Kanish Mirchia
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen McCortney
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Craig M Horbinski
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
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Holmes ME, Hertel KJ. Interdependent regulation of alternative splicing by SR and hnRNP proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608666. [PMID: 39229091 PMCID: PMC11370404 DOI: 10.1101/2024.08.19.608666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Alternative pre-mRNA splicing is a combinatorial process involving SR and hnRNP splicing factors. These proteins can silence or enhance splicing based on their expression levels and binding positions. To better understand their combinatorial and interdependent regulation, computational analyses were performed using HepG2 and K562 cell knockdown and binding datasets from the ENCODE Project. Analyses of diMerential splicing for 6 SR proteins and 13 hnRNP knockdowns revealed statistically significant exon overlap among most RBP combinations, albeit at diMerent levels. Neither SR proteins nor hnRNPs showed strong preferences for collaborating with specific RBP classes in mediating exon inclusion. While SRSF1, hnRNPK, and hnRNPC stand out as major influencers of alternative splicing, they do so predominantly independent of other RBPs. Meanwhile, minor influencers of alternative splicing such as hnRNPAB and hnRNPA0 predominantly regulate exon inclusion in concert with other RBPs, indicating that inclusion can be mediated by both single and multiple RBPs. Interestingly, the higher the number of RBPs that regulate the inclusion of an exon, the more variable exon inclusion preferences become. Interdependently regulated exons are more modular and have diMerent physical characteristics such as reduced exon length compared to their independent counterparts. A comparison of RBP interdependence between HepG2 and K562 cells provides the framework that explains cell-type-specific alternative splicing. Our study highlights the importance of the interdependent regulation of alternative exons and identifies characteristics of interdependently regulated exons that diMer from independently regulated exons.
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Yang Y, Li G, Pang K, Cao W, Zhang Z, Li X. Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2407013. [PMID: 39159140 DOI: 10.1002/advs.202407013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/23/2024] [Indexed: 08/21/2024]
Abstract
The 3' untranslated regions (3'UTRs) of messenger RNAs contain many important cis-regulatory elements that are under functional and evolutionary constraints. It is hypothesized that these constraints are similar to grammars and syntaxes in human languages and can be modeled by advanced natural language techniques such as Transformers, which has been very effective in modeling complex protein sequence and structures. Here 3UTRBERT is described, which implements an attention-based language model, i.e., Bidirectional Encoder Representations from Transformers (BERT). 3UTRBERT is pre-trained on aggregated 3'UTR sequences of human mRNAs in a task-agnostic manner; the pre-trained model is then fine-tuned for specific downstream tasks such as identifying RBP binding sites, m6A RNA modification sites, and predicting RNA sub-cellular localizations. Benchmark results show that 3UTRBERT generally outperformed other contemporary methods in each of these tasks. More importantly, the self-attention mechanism within 3UTRBERT allows direct visualization of the semantic relationship between sequence elements and effectively identifies regions with important regulatory potential. It is expected that 3UTRBERT model can serve as the foundational tool to analyze various sequence labeling tasks within the 3'UTR fields, thus enhancing the decipherability of post-transcriptional regulatory mechanisms.
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Affiliation(s)
- Yuning Yang
- School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Gen Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Kuan Pang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Wuxinhao Cao
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, 130012, China
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Anglada-Girotto M, Ciampi L, Bonnal S, Head SA, Miravet-Verde S, Serrano L. In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications. Nat Commun 2024; 15:7039. [PMID: 39147755 PMCID: PMC11327330 DOI: 10.1038/s41467-024-51380-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/06/2024] [Indexed: 08/17/2024] Open
Abstract
Alternative splicing is crucial for cancer progression and can be targeted pharmacologically, yet identifying driver exons genome-wide remains challenging. We propose identifying such exons by associating statistically gene-level cancer dependencies from knockdown viability screens with splicing profiles and gene expression. Our models predict the effects of splicing perturbations on cell proliferation from transcriptomic data, enabling in silico RNA screening and prioritizing targets for splicing-based therapies. We identified 1,073 exons impacting cell proliferation, many from genes not previously linked to cancer. Experimental validation confirms their influence on proliferation, especially in highly proliferative cancer cell lines. Integrating pharmacological screens with splicing dependencies highlights the potential driver exons affecting drug sensitivity. Our models also allow predicting treatment outcomes from tumor transcriptomes, suggesting applications in precision oncology. This study presents an approach to identifying cancer driver exon and their therapeutic potential, emphasizing alternative splicing as a cancer target.
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Affiliation(s)
- Miquel Anglada-Girotto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sarah A Head
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain.
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Wang J, Zhang XZ, Sun XY, Tian WJ, Wang XJ. Cellular RNA-binding proteins LARP4 and PABPC1 synergistically facilitate viral translation of coronavirus PEDV. Vet Microbiol 2024; 298:110219. [PMID: 39182469 DOI: 10.1016/j.vetmic.2024.110219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/10/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024]
Abstract
Coronaviruses are causing epizootic diseases and thus are a substantial threat for both domestic and wild animals. These viruses depend on the host translation machinery to complete their life cycle. The current paper identified cellular RNA-binding proteins (RBPs), La-related protein 4 (LARP4) and polyadenylate-binding protein cytoplasmic 1 (PABPC1), as critical regulators of efficient translation of the coronavirus porcine epidemic diarrhea virus (PEDV) mRNA. In Vero cells, PEDV infection caused LARP4 to migrate from the nucleus to the cytoplasm in a chromosome region maintenance1 (CRM1)-independent pathway. In the absence of the nuclear export signal of LARP4, viral translation was not promoted by LARP4. A further study unveiled that the cytoplasmic LARP4 binds to the 3'-terminal untranslated region (3'UTR) of PEDV mRNA with the assistance of PABPC1 to facilitate viral translation. LARP4 knockdown reduced the promotion of the PABPC1-induced 3'UTR translation activity. Moreover, the rabbit reticulocyte lysate (RRL) system revealed that the prokaryotic expressed protein LARP4 and PABPC1 enhance PEDV mRNA translation. To our knowledge, this is the first study demonstrating that PEDV induces nucleo-cytoplasmic shuttling of LARP4 to enhance its own replication, which broadens our insights into how viruses use host's RBPs for the efficient translation of viral mRNA.
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Affiliation(s)
- Jing Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiu-Zhong Zhang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xin-Yue Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wen-Jun Tian
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiao-Jia Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Johnson OD, Paul S, Gutierrez JA, Russell WK, Ward MC. DNA damage-associated protein co-expression network in cardiomyocytes informs on tolerance to genetic variation and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607863. [PMID: 39185220 PMCID: PMC11343126 DOI: 10.1101/2024.08.14.607863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Cardiovascular disease (CVD) is associated with both genetic variants and environmental factors. One unifying consequence of the molecular risk factors in CVD is DNA damage, which must be repaired by DNA damage response proteins. However, the impact of DNA damage on global cardiomyocyte protein abundance, and its relationship to CVD risk remains unclear. We therefore treated induced pluripotent stem cell-derived cardiomyocytes with the DNA-damaging agent Doxorubicin (DOX) and a vehicle control, and identified 4,178 proteins that contribute to a network comprising 12 co-expressed modules and 403 hub proteins with high intramodular connectivity. Five modules correlate with DOX and represent distinct biological processes including RNA processing, chromatin regulation and metabolism. DOX-correlated hub proteins are depleted for proteins that vary in expression across individuals due to genetic variation but are enriched for proteins encoded by loss-of-function intolerant genes. While proteins associated with genetic risk for CVD, such as arrhythmia are enriched in specific DOX-correlated modules, DOX-correlated hub proteins are not enriched for known CVD risk proteins. Instead, they are enriched among proteins that physically interact with CVD risk proteins. Our data demonstrate that DNA damage in cardiomyocytes induces diverse effects on biological processes through protein co-expression modules that are relevant for CVD, and that the level of protein connectivity in DNA damage-associated modules influences the tolerance to genetic variation.
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Affiliation(s)
- Omar D. Johnson
- Biochemistry, Cellular and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, USA
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Sayan Paul
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jose A. Gutierrez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - William K. Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Michelle C. Ward
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
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Mironov A, Franchitti L, Ghosh S, Ritz MF, Hutter G, De Bortoli M, Zavolan M. Leveraging multi-omics data to infer regulators of mRNA 3' end processing in glioblastoma. Front Mol Biosci 2024; 11:1363933. [PMID: 39188787 PMCID: PMC11345230 DOI: 10.3389/fmolb.2024.1363933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
Alterations in mRNA 3' end processing and polyadenylation are widely implicated in the biology of many cancer types, including glioblastoma (GBM), one the most aggressive tumor types. Although several RNA-binding proteins (RBPs) responsible for alternative polyadenylation (APA) were identified from functional studies in cell lines, their contribution to the APA landscape in tumors in vivo was not thoroughly addressed. In this study we analyzed a large RNA-seq data set of glioblastoma (GBM) samples from The Cancer Genome Atlas (TCGA) to identify APA patterns differentiating the main molecular subtypes of GBM. We superimposed these to RBP footprinting data and to APA events occurring upon depletion of individual RBPs from a large panel tested by the ENCODE Consortium. Our analysis revealed 22 highly concordant and statistically significant RBP-APA associations, whereby changes in RBP expression were accompanied by APA in both TCGA and ENCODE datasets. Among these, we found a previously unknown PTBP1-regulated APA event in the PRRC2B gene and an HNRNPU-regulated event in the SC5D gene. Both of these were further supported by RNA-sequencing data of paired tumor center-periphery GBM samples obtained at the University Hospital of Basel. In addition, we validated the regulation of APA in PRRC2B by PTBP1 in siRNA-knockdown and overexpression experiments followed by RNA-sequencing in two glioblastoma cell lines. The transcriptome analysis workflow that we present here enables the identification of concordant RBP-APA associations in cancers.
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Affiliation(s)
| | - Lorenzo Franchitti
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | | | | | - Gregor Hutter
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
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44
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Liu Y, Hoskins I, Geng M, Zhao Q, Chacko J, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Rao S, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.11.607360. [PMID: 39149359 PMCID: PMC11326257 DOI: 10.1101/2024.08.11.607360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Characterization of shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of Translation Efficiency Covariation (TEC), identifying coordinated translation patterns across cell types. We nominate potential mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and helps uncover gene functions. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish translational covariation as a conserved organizing principle of mammalian transcriptomes.
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Affiliation(s)
- Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Geng
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kangsheng Qi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Yochen Zhong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Present address: Sail Biomedicines, Cambridge, MA, 02141, USA
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45
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Hervoso JL, Amoah K, Dodson J, Choudhury M, Bhattacharya A, Quinones-Valdez G, Pasaniuc B, Xiao X. Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia. Am J Hum Genet 2024; 111:1573-1587. [PMID: 38925119 PMCID: PMC11339621 DOI: 10.1016/j.ajhg.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with genome-wide association studies to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-sequencing datasets, BrainGVEX and CommonMind, revealing 137 and 88 trait-associated exons (in 84 and 67 genes), respectively. Enriched biological functions in the associated gene sets converged on neuronal function and development, immune cell activation, and cellular transport, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein binding sites, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level, identifying 36 genes and 48 exons as putatively causal for SCZ. We highlight VPS45 and APOPT1, where splicing of specific exons was associated with disease risk, eluding detection by conventional gene expression analysis. Collectively, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ, providing a valuable approach for future investigations in this area.
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Affiliation(s)
- Jonatan L Hervoso
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kofi Amoah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jack Dodson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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46
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Masuda A, Okamoto T, Kawachi T, Takeda JI, Hamaguchi T, Ohno K. Blending and separating dynamics of RNA-binding proteins develop architectural splicing networks spreading throughout the nucleus. Mol Cell 2024; 84:2949-2965.e10. [PMID: 39053456 DOI: 10.1016/j.molcel.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/28/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
The eukaryotic nucleus has a highly organized structure. Although the spatiotemporal arrangement of spliceosomes on nascent RNA drives splicing, the nuclear architecture that directly supports this process remains unclear. Here, we show that RNA-binding proteins (RBPs) assembled on RNA form meshworks in human and mouse cells. Core and accessory RBPs in RNA splicing make two distinct meshworks adjacently but distinctly distributed throughout the nucleus. This is achieved by mutual exclusion dynamics between the charged and uncharged intrinsically disordered regions (IDRs) of RBPs. These two types of meshworks compete for spatial occupancy on pre-mRNA to regulate splicing. Furthermore, the optogenetic enhancement of the RBP meshwork causes aberrant splicing, particularly of genes involved in neurodegeneration. Genetic mutations associated with neurodegenerative diseases are often found in the IDRs of RBPs, and cells harboring these mutations exhibit impaired meshwork formation. Our results uncovered the spatial organization of RBP networks to drive RNA splicing.
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Affiliation(s)
- Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Takaaki Okamoto
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshihiko Kawachi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan; Graduate School of Nutritional Sciences, Nagoya University of Arts and Sciences, Nisshin, Japan
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47
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Fierro-Monti I. RBPs: an RNA editor's choice. Front Mol Biosci 2024; 11:1454241. [PMID: 39165644 PMCID: PMC11333368 DOI: 10.3389/fmolb.2024.1454241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/25/2024] [Indexed: 08/22/2024] Open
Abstract
RNA-binding proteins (RBPs) play a key role in gene expression and post-transcriptional RNA regulation. As integral components of ribonucleoprotein complexes, RBPs are susceptible to genomic and RNA Editing derived amino acid substitutions, impacting functional interactions. This article explores the prevalent RNA Editing of RBPs, unravelling the complex interplay between RBPs and RNA Editing events. Emphasis is placed on their influence on single amino acid variants (SAAVs) and implications for disease development. The role of Proteogenomics in identifying SAAVs is briefly discussed, offering insights into the RBP landscape. RNA Editing within RBPs emerges as a promising target for precision medicine, reshaping our understanding of genetic and epigenetic variations in health and disease.
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48
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Dao K, Jungers CF, Djuranovic S, Mustoe AM. U-rich elements drive pervasive cryptic splicing in 3' UTR massively parallel reporter assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606557. [PMID: 39149310 PMCID: PMC11326173 DOI: 10.1101/2024.08.05.606557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Non-coding RNA sequences play essential roles in orchestrating gene expression. However, the sequence codes and mechanisms underpinning post-transcriptional regulation remain incompletely understood. Here, we revisit the finding from a prior massively parallel reporter assay (MPRA) that AU-rich (U-rich) elements in 3' untranslated regions (3' UTRs) can drive upregulation or downregulation of mRNA expression depending on 3' UTR context. We unexpectedly discover that this variable regulation arises from widespread cryptic splicing, predominately from an unannotated splice donor in the coding sequence of GFP to diverse acceptor sites in reporter 3' UTRs. Splicing is activated by U-rich sequences, which function as potent position-dependent regulators of 5' and 3' splice site choice and overall splicing efficiency. Splicing has diverse impacts on reporter expression, causing both increases and decreases in reporter expression via multiple mechanisms. We further provide evidence that cryptic splicing impacts between 10 to 50% of measurements made by other published 3' UTR MPRAs. Overall, our work emphasizes U-rich sequences as principal drivers of splicing and provides strategies to minimize cryptic splicing artifacts in reporter assays.
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Affiliation(s)
- Khoa Dao
- Therapeutic Innovation Center (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston TX
| | - Courtney F. Jungers
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis MO
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis MO
| | - Anthony M. Mustoe
- Therapeutic Innovation Center (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX
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49
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Kerkhofs K, Guydosh NR, Bayfield MA. Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606199. [PMID: 39131278 PMCID: PMC11312563 DOI: 10.1101/2024.08.02.606199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Viral infection often triggers eukaryotic initiator factor 2α (eIF2α) phosphorylation, leading to global 5'-cap-dependent translation inhibition. RSV encodes messenger RNAs (mRNAs) mimicking 5'-cap structures of host mRNAs and thus inhibition of cap-dependent translation initiation would likely also reduce viral translation. We confirmed that RSV limits widespread translation initiation inhibition and unexpectedly found that the fraction of ribosomes within polysomes increases during infection, indicating higher ribosome loading on mRNAs during infection. We found that AU-rich host transcripts that are less efficiently translated under normal conditions become more efficient at recruiting ribosomes, similar to RSV transcripts. Viral transcripts are transcribed in cytoplasmic inclusion bodies, where the viral AU-rich binding protein M2-1 has been shown to bind viral transcripts and shuttle them into the cytoplasm. We further demonstrated that M2-1 is found on polysomes, and that M2-1 might deliver host AU-rich transcripts for translation.
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Affiliation(s)
- Kyra Kerkhofs
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
| | - Nicholas R. Guydosh
- Section on mRNA Regulation and Translation, Laboratory of Biochemistry & Genetics. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark A. Bayfield
- Department of Biology, Faculty of Science, York University, Toronto, Ontario N3J 1P3, Canada
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50
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Xu Z, Sziraki A, Lee J, Zhou W, Cao J. Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. Nat Biotechnol 2024; 42:1218-1223. [PMID: 37749268 PMCID: PMC10961254 DOI: 10.1038/s41587-023-01948-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
We present a combinatorial indexing method, PerturbSci-Kinetics, for capturing whole transcriptomes, nascent transcriptomes and single guide RNA (sgRNA) identities across hundreds of genetic perturbations at the single-cell level. Profiling a pooled CRISPR screen targeting various biological processes, we show the gene expression regulation during RNA synthesis, processing and degradation, miRNA biogenesis and mitochondrial mRNA processing, systematically decoding the genome-wide regulatory network that underlies RNA temporal dynamics at scale.
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Affiliation(s)
- Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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