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Boulanger C, Haidara N, Yague-Sanz C, Larochelle M, Jacques PÉ, Hermand D, Bachand F. Repression of pervasive antisense transcription is the primary role of fission yeast RNA polymerase II CTD serine 2 phosphorylation. Nucleic Acids Res 2024:gkae436. [PMID: 38801067 DOI: 10.1093/nar/gkae436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The RNA polymerase II carboxy-terminal domain (CTD) consists of conserved heptapeptide repeats that can be phosphorylated to influence distinct stages of the transcription cycle, including RNA processing. Although CTD-associated proteins have been identified, phospho-dependent CTD interactions have remained elusive. Proximity-dependent biotinylation (PDB) has recently emerged as an alternative approach to identify protein-protein associations in the native cellular environment. In this study, we present a PDB-based map of the fission yeast RNAPII CTD interactome in living cells and identify phospho-dependent CTD interactions by using a mutant in which Ser2 was replaced by alanine in every repeat of the fission yeast CTD. This approach revealed that CTD Ser2 phosphorylation is critical for the association between RNAPII and the histone methyltransferase Set2 during transcription elongation, but is not required for 3' end processing and transcription termination. Accordingly, loss of CTD Ser2 phosphorylation causes a global increase in antisense transcription, correlating with elevated histone acetylation in gene bodies. Our findings reveal that the fundamental role of CTD Ser2 phosphorylation is to establish a chromatin-based repressive state that prevents cryptic intragenic transcription initiation.
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Affiliation(s)
- Cédric Boulanger
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Nouhou Haidara
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Carlo Yague-Sanz
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Marc Larochelle
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | | | - Damien Hermand
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Francois Bachand
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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2
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Henfrey C, Murphy S, Tellier M. Regulation of mature mRNA levels by RNA processing efficiency. NAR Genom Bioinform 2023; 5:lqad059. [PMID: 37305169 PMCID: PMC10251645 DOI: 10.1093/nargab/lqad059] [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: 10/25/2022] [Revised: 05/13/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
Transcription and co-transcriptional processes, including pre-mRNA splicing and mRNA cleavage and polyadenylation, regulate the production of mature mRNAs. The carboxyl terminal domain (CTD) of RNA polymerase (pol) II, which comprises 52 repeats of the Tyr1Ser2Pro3Thr4Ser5Pro6Ser7 peptide, is involved in the coordination of transcription with co-transcriptional processes. The pol II CTD is dynamically modified by protein phosphorylation, which regulates recruitment of transcription and co-transcriptional factors. We have investigated whether mature mRNA levels from intron-containing protein-coding genes are related to pol II CTD phosphorylation, RNA stability, and pre-mRNA splicing and mRNA cleavage and polyadenylation efficiency. We find that genes that produce a low level of mature mRNAs are associated with relatively high phosphorylation of the pol II CTD Thr4 residue, poor RNA processing, increased chromatin association of transcripts, and shorter RNA half-life. While these poorly-processed transcripts are degraded by the nuclear RNA exosome, our results indicate that in addition to RNA half-life, chromatin association due to a low RNA processing efficiency also plays an important role in the regulation of mature mRNA levels.
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Affiliation(s)
- Callum Henfrey
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael Tellier
- To whom correspondence should be addressed. Tel: +44 1162297011;
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3
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LeBlanc BM, Moreno RY, Escobar EE, Venkat Ramani MK, Brodbelt JS, Zhang Y. What's all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry. RSC Chem Biol 2021; 2:1084-1095. [PMID: 34458825 PMCID: PMC8341212 DOI: 10.1039/d1cb00083g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and its phosphorylation state are critically important in regulating transcription in vivo. Early methods of identifying phosphorylation on the CTD heptad were plagued by issues of low specificity and ambiguous signals. However, advancements in the field of mass spectrometry (MS) have presented the opportunity to gain new insights into well-studied processes as well as explore new frontiers in transcription. By using MS, residues which are modified within the CTD heptad and across repeats are now able to be pinpointed. Likewise, identification of kinase and phosphatase specificity towards residues of the CTD has reached a new level of accuracy. Now, MS is being used to investigate the crosstalk between modified residues of the CTD and may be a critical technique for understanding how phosphorylation plays a role in the new LLPS model of transcription. Herein, we discuss the development of various MS techniques and evaluate their capabilities. By highlighting the pros and cons of each technique, we aim to provide future investigators with a comprehensive overview of how MS can be used to investigate the complexities of RNAP-II mediated transcription.
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Affiliation(s)
- Blase M LeBlanc
- Department of Molecular Biosciences, University of Texas Austin USA
| | - R Yvette Moreno
- Department of Molecular Biosciences, University of Texas Austin USA
| | | | | | | | - Yan Zhang
- Department of Molecular Biosciences, University of Texas Austin USA
- Institute of Cellular and Molecular Biology, University of Texas Austin USA
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4
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Yang G, Wang Y, Xiao J, Zhao F, Qiu J, Liu Y, Chen G, Cao Z, You L, Zheng L, Zhang T, Zhao Y. CREPT serves as a biomarker of poor survival in pancreatic ductal adenocarcinoma. Cell Oncol (Dordr) 2021; 44:345-355. [PMID: 33125631 DOI: 10.1007/s13402-020-00569-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive human malignancies. Cell-cycle-related and expression-elevated protein in tumor (CREPT) plays an important role in the phosphorylation of RNA Pol II, and has been implicated in the development of several types of cancer. As yet, however, there have been no reports on its role in PDAC. Here, we aimed to explore the value of CREPT as a prognostic biomarker in PDAC. METHODS CREPT expression was assessed by immunohistochemistry (IHC) on a tissue microarray containing samples from 375 PDAC patients. Kaplan-Meier and Cox regression analyses were performed to explore the independent prognostic value of CREPT expression for the disease-free survival (DFS) and overall survival (OS) of PDAC patients. A Cell Counting Kit-8 (CCK8) assay was used to determine the growth rates and gemcitabine sensitivities of PDAC cells, while a Transwell assay was used to determine the migration and invasion abilities of PDAC cells. Subcutaneous xenografts were used to explore the effect of CREPT expression on tumor growth in vivo. RESULTS We found that CREPT is highly expressed in tumor tissues and may serve as an independent prognostic biomarker for DFS and OS of PDAC patients. In vitro assays revealed that CREPT expression promotes the proliferation, migration, invasion and gemcitabine resistance of PDAC cells, and in vivo assays showed that CREPT expression knockdown led to inhibition of PDAC tumor growth. CONCLUSIONS We conclude that high CREPT expression enhances the proliferation, migration, invasion and gemcitabine resistance of PDAC cells. In addition, we conclude that CREPT may serve as an independent prognostic biomarker and therapeutic target for PDAC patients.
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Affiliation(s)
- Gang Yang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Yicheng Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Jianchun Xiao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Fangyu Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Jiangdong Qiu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Yueze Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Guangyu Chen
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Zhe Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China
| | - Lianfang Zheng
- Department of Nuclear Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Taiping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing Street, Beijing, 100730, China.
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5
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Wenquan L, Hongqing X, Yuhua L, Lili W, Wang Z, Ziwei Z, Chuang W, Aizhen C, Xiaosong W, Bo W, Lin C. MiR-139-5p inhibits the proliferation of gastric cancer cells by targeting Regulation of Nuclear Pre-mRNA Domain Containing 1B. Biochem Biophys Res Commun 2020; 527:393-400. [PMID: 32327260 DOI: 10.1016/j.bbrc.2020.04.067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 12/13/2022]
Abstract
Regulation of Nuclear Pre-mRNA Domain Containing 1B (RPRD1B) has been of great interest in the field of oncology in recent years. The relationship between miRNAs and RPRD1B in gastric cancer (GC) has not been adequately reported. This study was designed to screen RPRD1B-targeted miRNAs and investigate its regulatory mechanism in GC cells. Quantitative RT-PCR and in situ hybridization were used to detect miRNA expression in GC tissues. Colony formation, EdU cell proliferation assay, and flow cytometry were used to analyze the cell cycle. Database-assisted gene expression analysis revealed that RPRD1B was targeted and regulated by miRNA-139-5p in GC. miRNA-139-5p expression was higher in GC tissue than in normal tissues and significantly correlated with tumor size, pathological stage, and disease-free survival of GC (p < 0.05). MiRNA-139-5p regulates GC cell proliferation and affects the transition from G1 to S phase. It binds explicitly to the 2013-2019 sites of the 3'UTR of RPRD1B and negatively regulates RPRD1B expression. We demonstrated that the ability of miR-139-5p to regulate GC cell proliferation depends on RPRD1B. This process is accompanied by changes in Cyclin D1 protein expression. We established a miR-139-5p/RPRD1B/tumor proliferation axis in GC, which may serve as novel biomarkers and drug targets for GC.
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Affiliation(s)
- Liang Wenquan
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Xi Hongqing
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China
| | - Liu Yuhua
- Institute of Army Hospital Management, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Wang Lili
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China
| | - Zhang Wang
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Zhuang Ziwei
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Wang Chuang
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Cai Aizhen
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China
| | - Wu Xiaosong
- Medical Management Office, Chinese PLA General Hospital, Beijing, China.
| | - Wei Bo
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China.
| | - Chen Lin
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital, Beijing, China.
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6
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Mora Gallardo C, Sánchez de Diego A, Gutiérrez Hernández J, Talavera-Gutiérrez A, Fischer T, Martínez-A C, van Wely KHM. Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing. Nucleic Acids Res 2019; 47:5381-5394. [PMID: 30931476 PMCID: PMC6547428 DOI: 10.1093/nar/gkz235] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing is facilitated by accessory proteins that guide spliceosome subunits to the primary transcript. Many of these splicing factors recognize the RNA polymerase II tail, but SFPQ is a notable exception even though essential for mammalian RNA processing. This study reveals a novel role for Dido3, one of three Dido gene products, in alternative splicing. Binding of the Dido3 amino terminus to histones and to the polymerase jaw domain was previously reported, and here we show interaction between its carboxy terminus and SFPQ. We generated a mutant that eliminates Dido3 but preserves other Dido gene products, mimicking reduced Dido3 levels in myeloid neoplasms. Dido mutation suppressed SFPQ binding to RNA and increased skipping for a large group of exons. Exons bearing recognition sequences for alternative splicing factors were nonetheless included more efficiently. Reduced SFPQ recruitment may thus account for increased skipping of SFPQ-dependent exons, but could also generate a splicing factor surplus that becomes available to competing splice sites. Taken together, our data indicate that Dido3 is an adaptor that controls SFPQ utilization in RNA splicing. Distributing splicing factor recruitment over parallel pathways provides mammals with a simple mechanism to regulate exon usage while maintaining RNA splicing efficiency.
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Affiliation(s)
- Carmen Mora Gallardo
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Ainhoa Sánchez de Diego
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Julio Gutiérrez Hernández
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Amaia Talavera-Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Thierry Fischer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Carlos Martínez-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Karel H M van Wely
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)/CSIC, Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
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7
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Crump NT, Milne TA. Why are so many MLL lysine methyltransferases required for normal mammalian development? Cell Mol Life Sci 2019; 76:2885-2898. [PMID: 31098676 PMCID: PMC6647185 DOI: 10.1007/s00018-019-03143-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022]
Abstract
The mixed lineage leukemia (MLL) family of proteins became known initially for the leukemia link of its founding member. Over the decades, the MLL family has been recognized as an important class of histone H3 lysine 4 (H3K4) methyltransferases that control key aspects of normal cell physiology and development. Here, we provide a brief history of the discovery and study of this family of proteins. We address two main questions: why are there so many H3K4 methyltransferases in mammals; and is H3K4 methylation their key function?
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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8
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Gregersen LH, Mitter R, Ugalde AP, Nojima T, Proudfoot NJ, Agami R, Stewart A, Svejstrup JQ. SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. Cell 2019; 177:1797-1813.e18. [PMID: 31104839 PMCID: PMC6579486 DOI: 10.1016/j.cell.2019.04.038] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/30/2022]
Abstract
Accurate regulation of mRNA termination is required for correct gene expression. Here, we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation (polyA) sites. The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) phosphorylated on both Ser2 and Ser5 and are detected at early, alternative polyA sites. Concomitant knockout of human SCAF4 and SCAF8 results in altered polyA selection and subsequent early termination, leading to expression of truncated mRNAs and proteins lacking functional domains and is cell lethal. While SCAF4 and SCAF8 work redundantly to suppress early mRNA termination, they also have independent, non-essential functions. SCAF8 is an RNAPII elongation factor, whereas SCAF4 is required for correct termination at canonical, distal transcription termination sites in the presence of SCAF8. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, ensuring correct polyA site selection and RNAPII transcriptional termination in human cells.
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Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alejandro P Ugalde
- The Netherlands Cancer Institute (NKI-AVL), Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Reuven Agami
- The Netherlands Cancer Institute (NKI-AVL), Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Aengus Stewart
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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9
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Ali I, Ruiz DG, Ni Z, Johnson JR, Zhang H, Li PC, Khalid MM, Conrad RJ, Guo X, Min J, Greenblatt J, Jacobson M, Krogan NJ, Ott M. Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Mol Cell 2019; 74:1164-1174.e4. [PMID: 31054975 DOI: 10.1016/j.molcel.2019.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/26/2019] [Accepted: 03/30/2019] [Indexed: 01/01/2023]
Abstract
Post-translational modifications of the RNA polymerase II C-terminal domain (CTD) coordinate the transcription cycle. Crosstalk between different modifications is poorly understood. Here, we show how acetylation of lysine residues at position 7 of characteristic heptad repeats (K7ac)-only found in higher eukaryotes-regulates phosphorylation of serines at position 5 (S5p), a conserved mark of polymerases initiating transcription. We identified the regulator of pre-mRNA-domain-containing (RPRD) proteins as reader proteins of K7ac. K7ac enhanced CTD peptide binding to the CTD-interacting domain (CID) of RPRD1A and RPRD1B proteins in isothermal calorimetry and molecular modeling experiments. Deacetylase inhibitors increased K7ac- and decreased S5-phosphorylated polymerases, consistent with acetylation-dependent S5 dephosphorylation by an RPRD-associated S5 phosphatase. Consistent with this model, RPRD1B knockdown increased S5p but enhanced K7ac, indicating that RPRD proteins recruit K7 deacetylases, including HDAC1. We also report autoregulatory crosstalk between K7ac and S5p via RPRD proteins and their interactions with acetyl- and phospho-eraser proteins.
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Affiliation(s)
- Ibraheem Ali
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zuyao Ni
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Heng Zhang
- Structural Genomics Consortium, University of Toronto, ON, Canada
| | - Pao-Chen Li
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Mir M Khalid
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ryan J Conrad
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Xinghua Guo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, ON, Canada
| | | | - Matthew Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences (QBC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences (QBC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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10
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Cornella N, Tebaldi T, Gasperini L, Singh J, Padgett RA, Rossi A, Macchi P. The hnRNP RALY regulates transcription and cell proliferation by modulating the expression of specific factors including the proliferation marker E2F1. J Biol Chem 2017; 292:19674-19692. [PMID: 28972179 DOI: 10.1074/jbc.m117.795591] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/18/2017] [Indexed: 12/31/2022] Open
Abstract
The heterogeneous nuclear ribonucleoproteins (hnRNP) form a large family of RNA-binding proteins that exert numerous functions in RNA metabolism. RALY is a member of the hnRNP family that binds poly-U-rich elements within several RNAs and regulates the expression of specific transcripts. RALY is up-regulated in different types of cancer, and its down-regulation impairs cell cycle progression. However, the RALY's role in regulating RNA levels remains elusive. Here, we show that numerous genes coding for factors involved in transcription and cell cycle regulation exhibit an altered expression in RALY-down-regulated HeLa cells, consequently causing impairments in transcription, cell proliferation, and cell cycle progression. Interestingly, by comparing the list of RALY targets with the list of genes affected by RALY down-regulation, we found an enrichment of RALY mRNA targets in the down-regulated genes upon RALY silencing. The affected genes include the E2F transcription factor family. Given its role as proliferation-promoting transcription factor, we focused on E2F1. We demonstrate that E2F1 mRNA stability and E2F1 protein levels are reduced in cells lacking RALY expression. Finally, we also show that RALY interacts with transcriptionally active chromatin in both an RNA-dependent and -independent manner and that this association is abolished in the absence of active transcription. Taken together, our results highlight the importance of RALY as an indirect regulator of transcription and cell cycle progression through the regulation of specific mRNA targets, thus strengthening the possibility of a direct gene expression regulation exerted by RALY.
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Affiliation(s)
- Nicola Cornella
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Toma Tebaldi
- the Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Lisa Gasperini
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | | | | | - Annalisa Rossi
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy,
| | - Paolo Macchi
- From the Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento, Italy,
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11
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Chen X, Li B, Luo R, Cai S, Zhang C, Cao X. Analysis of the function of microRNA-375 in humans using bioinformatics. Biomed Rep 2017; 6:561-566. [PMID: 28515914 DOI: 10.3892/br.2017.889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/14/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-375 (miR-375) is expressed at low levels in many types of solid tumor, particularly in gastrointestinal tumors. It is considered to be important in the development of cancer and certain diseases. Thus, more detailed knowledge is required on the particular functions of miR-375. miRs function by regulating target genes. Therefore, in the current study, miRWalk (which includes the data from 10 prediction software programs) was used to predict the target genes of miR-375. The genes, which were co-predicted using five different software programs were further analyzed using Database for Annotation, Visualization and Integrated Discovery online software [including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis]. Subsequently, the online tool, Search Tool for the Retrieval of Interacting Genes, was used to analyze the protein-protein interaction and construct modules using Cytoscape. The result demonstrated 6,574 predicted genes, 1,325 of which were co-predicted. The GO analysis result indicated that, in biological processes, the co-predicted genes were significantly enriched in the regulation of nervous system development and cell differentiation, and the highest enrichment of molecular function was ion binding. In KEGG analysis, the genes were enriched in the Hippo signaling pathway, glutamatergic synapse, circadian entrainment and the phosphoinositide 3-kinase (PI3K)-Akt signaling pathway. The top 10 hub proteins were mechanistic target of rapamycin, PH domain and leucine rich repeat protein phosphatase 1, ubiquitously transcribed tetratricopeptide repeat containing, Y-linked, histone deacetylase 2, F-box and leucine rich repeat protein 19, KIT proto-oncogene receptor tyrosine kinase, angiotensinogen, Janus kinase 2, fibroblast growth factor 2 and RNA polymerase II subunit A. These proteins predominantly regulate the development and progression of cancer, hypertension, essential thrombocythemia and inflammation. The genes in the top seven modules selected were identified to be primarily enriched in chemokines, extracellular matrix-receptor interaction, focal adhesion, the PI3K-Akt signaling pathway, amoebiasis and protein processing signaling pathway. Thus, the target genes and hub proteins that were predicted in the current study were identified to be important in regulating the development and progression of cancer and certain diseases. Furthermore, they present potential novel biomarkers for tumor diagnosis and candidate targets for treatment, and indicate that further research is required to establish the functions of miR-375.
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Affiliation(s)
- Xiaohua Chen
- Department of Oncology, Panyu Central Hospital, Cancer Institute of Panyu, Guangzhou, Guangdong 511400, P.R. China
| | - Baoxia Li
- Department of Oncology, South China State Laboratory, Cancer Center of Sun Yat-sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Rongcheng Luo
- Department of Oncology, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Sina Cai
- Department of Oncology, The Hospital of Third Affiliated Southern Medical University, Guangzhou, Guangdong 510630, P.R. China
| | - Cao Zhang
- Department of Oncology, Panyu Central Hospital, Cancer Institute of Panyu, Guangzhou, Guangdong 511400, P.R. China
| | - Xiaolong Cao
- Department of Oncology, Panyu Central Hospital, Cancer Institute of Panyu, Guangzhou, Guangdong 511400, P.R. China
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