1
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Villagra UMM, da Cunha BR, Polachini GM, Henrique T, Stefanini ACB, de Castro TB, da Silva CHTP, Feitosa OA, Fukuyama EE, López RVM, Dias-Neto E, Nunes FD, Severino P, Tajara EH. Expression of Truncated Products at the 5'-Terminal Region of RIPK2 and Evolutive Aspects that Support Their Biological Importance. Genome Biol Evol 2024; 16:evae106. [PMID: 38752399 PMCID: PMC11221433 DOI: 10.1093/gbe/evae106] [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] [Accepted: 05/10/2024] [Indexed: 07/04/2024] Open
Abstract
Alternative splicing is the process of generating different mRNAs from the same primary transcript, which contributes to increase the transcriptome and proteome diversity. Abnormal splicing has been associated with the development of several diseases including cancer. Given that mutations and abnormal levels of the RIPK2 transcript and RIP-2 protein are frequent in tumors, and that RIP-2 modulates immune and inflammatory responses, we investigated alternative splicing events that result in partial deletions of the kinase domain at the N-terminus of RIP-2. We also investigated the structure and expression of the RIPK2 truncated variants and isoforms in different environments. In addition, we searched data throughout Supraprimates evolution that could support the biological importance of RIPK2 alternatively spliced products. We observed that human variants and isoforms were differentially regulated following temperature stress, and that the truncated transcript was more expressed than the long transcript in tumor samples. The inverse was found for the longer protein isoform. The truncated variant was also detected in chimpanzee, gorilla, hare, pika, mouse, rat, and tree shrew. The fact that the same variant has been preserved in mammals with divergence times up to 70 million years raises the hypothesis that it may have a functional significance.
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Affiliation(s)
- Ulises M M Villagra
- Faculty of Exact Sciences, Biotechnology and Molecular Biology Institute (IBBM), National University of La Plata-CCT, CONICET, La Plata, Argentina
| | - Bianca R da Cunha
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Giovana M Polachini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Ana Carolina Buzzo Stefanini
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Tialfi Bergamin de Castro
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Microbial Pathogenesis Department, University of Maryland Baltimore, School of Dentistry, Baltimore, MD, USA
| | - Carlos H T P da Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Olavo A Feitosa
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Erica E Fukuyama
- Head and Neck Surgery Department, Arnaldo Vieira de Carvalho Cancer Institute, São Paulo, SP, Brazil
| | - Rossana V M López
- Comprehensive Center for Precision Oncology, Center for Translational Research in Oncology, State of São Paulo Cancer Institute—ICESP, Clinics Hospital, Sao Paulo University Medical School, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Fabio D Nunes
- Department of Stomatology, School of Dentistry, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Patricia Severino
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
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2
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Riccardi F, Romano G, Licastro D, Pagani F. Age-dependent regulation of ELP1 exon 20 splicing in Familial Dysautonomia by RNA Polymerase II kinetics and chromatin structure. PLoS One 2024; 19:e0298965. [PMID: 38829854 PMCID: PMC11146744 DOI: 10.1371/journal.pone.0298965] [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: 10/14/2023] [Accepted: 02/01/2024] [Indexed: 06/05/2024] Open
Abstract
Familial Dysautonomia (FD) is a rare disease caused by ELP1 exon 20 skipping. Here we clarify the role of RNA Polymerase II (RNAPII) and chromatin on this splicing event. A slow RNAPII mutant and chromatin-modifying chemicals that reduce the rate of RNAPII elongation induce exon skipping whereas chemicals that create a more relaxed chromatin exon inclusion. In the brain of a mouse transgenic for the human FD-ELP1 we observed on this gene an age-dependent decrease in the RNAPII density profile that was most pronounced on the alternative exon, a robust increase in the repressive marks H3K27me3 and H3K9me3 and a decrease of H3K27Ac, together with a progressive reduction in ELP1 exon 20 inclusion level. In HEK 293T cells, selective drug-induced demethylation of H3K27 increased RNAPII elongation on ELP1 and SMN2, promoted the inclusion of the corresponding alternative exons, and, by RNA-sequencing analysis, induced changes in several alternative splicing events. These data suggest a co-transcriptional model of splicing regulation in which age-dependent changes in H3K27me3/Ac modify the rate of RNAPII elongation and affect processing of ELP1 alternative exon 20.
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Affiliation(s)
- Federico Riccardi
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Giulia Romano
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Danilo Licastro
- Laboratorio di Genomica ed Epigenomica, AREA Science Park, Padriciano, Trieste, Italy
| | - Franco Pagani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
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3
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Zhang R, Wang D, Ruan GX, Wang R, Li Y, Chen W, Huang H, Wang J, Meng L, Zhu Z, Lei D, Xu S, Ou X. Spliceosome component PHD finger 5A is essential for early B lymphopoiesis. Development 2024; 151:dev202247. [PMID: 38095286 DOI: 10.1242/dev.202247] [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: 08/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The spliceosome, a multi-megadalton ribonucleoprotein complex, is essential for pre-mRNA splicing in the nucleus and ensuring genomic stability. Its precise and dynamic assembly is pivotal for its function. Spliceosome malfunctions can lead to developmental abnormalities and potentially contribute to tumorigenesis. The specific role of the spliceosome in B cell development is poorly understood. Here, we reveal that the spliceosomal U2 snRNP component PHD finger protein 5A (Phf5a) is vital for early B cell development. Loss of Phf5a results in pronounced defects in B cell development, causing an arrest at the transition from pre-pro-B to early pro-B cell stage in the bone marrow of mutant mice. Phf5a-deficient B cells exhibit impaired immunoglobulin heavy (IgH) chain expression due to defective V-to-DJ gene rearrangement. Mechanistically, our findings suggest that Phf5a facilitates IgH gene rearrangement by regulating the activity of recombination-activating gene endonuclease and influencing chromatin interactions at the Igh locus.
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Affiliation(s)
- Rui Zhang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Daoqin Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Gui-Xin Ruan
- Medical School, Taizhou University, Taizhou 318000, China
| | - Ruisi Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxing Li
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenjing Chen
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hengjun Huang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jing Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Limin Meng
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhijian Zhu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dengfeng Lei
- Department of Ophthalmology, Southern University of Science and Technology Hospital, Shenzhen 518055, China
| | - Shengli Xu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Republic of Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive MD9, Singapore 117593, Republic of Singapore
| | - Xijun Ou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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4
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Shenasa H, Bentley DL. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet 2023; 39:672-685. [PMID: 37236814 PMCID: PMC10524715 DOI: 10.1016/j.tig.2023.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Transcription of eukaryotic genes by RNA polymerase II (Pol II) yields RNA precursors containing introns that must be spliced out and the flanking exons ligated together. Splicing is catalyzed by a dynamic ribonucleoprotein complex called the spliceosome. Recent evidence has shown that a large fraction of splicing occurs cotranscriptionally as the RNA chain is extruded from Pol II at speeds of up to 5 kb/minute. Splicing is more efficient when it is tethered to the transcription elongation complex, and this linkage permits functional coupling of splicing with transcription. We discuss recent progress that has uncovered a network of connections that link splicing to transcript elongation and other cotranscriptional RNA processing events.
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Affiliation(s)
- Hossein Shenasa
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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5
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Lim WF, Rinaldi C. RNA Transcript Diversity in Neuromuscular Research. J Neuromuscul Dis 2023:JND221601. [PMID: 37182892 DOI: 10.3233/jnd-221601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Three decades since the Human Genome Project began, scientists have now identified more then 25,000 protein coding genes in the human genome. The vast majority of the protein coding genes (> 90%) are multi-exonic, with the coding DNA being interrupted by intronic sequences, which are removed from the pre-mRNA transcripts before being translated into proteins, a process called splicing maturation. Variations in this process, i.e. by exon skipping, intron retention, alternative 5' splice site (5'ss), 3' splice site (3'ss), or polyadenylation usage, lead to remarkable transcriptome and proteome diversity in human tissues. Given its critical biological importance, alternative splicing is tightly regulated in a tissue- and developmental stage-specific manner. The central nervous system and skeletal muscle are amongst the tissues with the highest number of differentially expressed alternative exons, revealing a remarkable degree of transcriptome complexity. It is therefore not surprising that splicing mis-regulation is causally associated with a myriad of neuromuscular diseases, including but not limited to amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Duchenne muscular dystrophy (DMD), and myotonic dystrophy type 1 and 2 (DM1, DM2). A gene's transcript diversity has since become an integral and an important consideration for drug design, development and therapy. In this review, we will discuss transcript diversity in the context of neuromuscular diseases and current approaches to address splicing mis-regulation.
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Affiliation(s)
- Wooi Fang Lim
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Carlo Rinaldi
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
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6
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Liu Q, Zhang H, Yang X, Liu X, Yin F, Guo P, Yin Y, Zheng K, Yang Z, Han Y. Systemic characterization of alternative splicing related to prognosis, immune infiltration, and drug sensitivity analysis in ovarian cancer. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:126. [PMID: 35282039 PMCID: PMC8848412 DOI: 10.21037/atm-21-6422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
Background Alternative splicing (AS) plays an essential role in tumorigenesis and progression. This study intended to construct an innovative prognostic model based on AS events to gain more precise survival prediction and search for potential therapeutic targets in ovarian cancer. Methods Seven types of AS events in ovarian serous cystadenocarcinoma (OV) patients with RNA-seq were obtained using The Cancer Genome Atlas (TCGA) SpliceSeq tool and database. Cox and Kaplan-Meier curve analyses were employed to establish the prognostic models. Relying on drug sensitivity data from the CellMiner database, Genomics of Drug Sensitivity (GDS) was adopted to estimate the platinum-sensitive analysis. Furthermore, a prognostic splicing factor (SF)-AS network was constructed using Cytoscape. Finally, in order to explore the influence of the tumor microenvironment on the prognosis of OV patients, we first combined a similar network fusion and consensus clustering (SNF-CC) algorithm to identify three OV subtypes based on survival-related AS events and then utilized single-sample Gene Set Enrichment Analysis (ssGSEA) method to perform immune cell infiltration analysis. Results A total of 48,049 AS events and 21,841 related genes were selected from 318 OV samples, and 2,206 AS events associated with disease-free survival (DFS) were identified. Multivariate Cox and Kaplan-Meier curve analyses were then employed to establish the prognostic models. Receiver operating characteristic (ROC) analysis from 0.59 to 0.75 showed that these models were highly efficient in distinguishing patient survival. GDS was adopted with the CellMiner database to provide some insights for platinum-sensitive analysis of OV. Furthermore, a prognostic SF-AS network, which discovered a significant connection between SFs and prognostic AS genes, was constructed using Cytoscape. The combined SNF-CC algorithm revealed three distinct OV subtypes based on the prognostic AS events, and the associations between this novel molecular classification and immune cell infiltration were further explored. Conclusions We developed a powerful prognostic AS signature for OV and provided a deeper understanding of SF-AS network regulatory mechanisms, as well as platinum-sensitive and cancer immune microenvironments. These results revealed various candidate biomarkers and potential targets for OV treatment strategies.
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Affiliation(s)
- Qingyang Liu
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Hao Zhang
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Xiaocheng Yang
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Xuesong Liu
- School of Health Professions, Yingkou Vocational and Technical College, Yingkou, China
| | - Fanxing Yin
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Panpan Guo
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Yuhan Yin
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Kaijiang Zheng
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Zhuo Yang
- Department of Gynecology, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, China
| | - Yanshuo Han
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
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7
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Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
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8
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Wang CC, Hsieh HY, Hsieh HL, Tu SL. The Physcomitrella patens chromatin adaptor PpMRG1 interacts with H3K36me3 and regulates light-responsive alternative splicing. PLANT PHYSIOLOGY 2021; 185:1229-1241. [PMID: 33793927 PMCID: PMC8133547 DOI: 10.1093/plphys/kiaa103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Plants perceive dynamic light conditions and optimize their growth and development accordingly by regulating gene expression at multiple levels. Alternative splicing (AS), a widespread mechanism in eukaryotes that post-transcriptionally generates two or more messenger RNAs (mRNAs) from the same pre-mRNA, is rapidly controlled by light. However, a detailed mechanism of light-regulated AS is still not clear. In this study, we demonstrate that histone 3 lysine 36 trimethylation (H3K36me3) rapidly and differentially responds to light at specific gene loci with light-regulated intron retention (IR) of their transcripts in the moss Physcomitrella patens. However, the level of H3K36me3 following exposure to light is inversely related to that of IR events. Physcomitrella patens MORF-related gene 1 (PpMRG1), a chromatin adaptor, bound with higher affinity to H3K36me3 in light conditions than in darkness and was differentially targeted to gene loci showing light-responsive IR. Transcriptome analysis indicated that PpMRG1 functions in the regulation of light-mediated AS. Furthermore, PpMRG1 was also involved in red light-mediated phototropic responses. Our results suggest that light regulates histone methylation, which leads to alterations of AS patterns. The chromatin adaptor PpMRG1 potentially participates in light-mediated AS, revealing that chromatin-coupled regulation of pre-mRNA splicing is an important aspect of the plant's response to environmental changes.
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Affiliation(s)
- Chien-Chang Wang
- Institute of Plant and Microbial biology, Academia Sinica, Taipei, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yu Hsieh
- Institute of Plant and Microbial biology, Academia Sinica, Taipei, Taiwan
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial biology, Academia Sinica, Taipei, Taiwan
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9
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Zhou Y, Zheng X, Xu B, Deng H, Chen L, Jiang J. Histone methyltransferase SETD2 inhibits tumor growth via suppressing CXCL1-mediated activation of cell cycle in lung adenocarcinoma. Aging (Albany NY) 2020; 12:25189-25206. [PMID: 33223508 PMCID: PMC7803529 DOI: 10.18632/aging.104120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022]
Abstract
The histone H3 lysine 36 methyltransferase SET-domain-containing 2 (SETD2) has been reported to be frequently mutated or deleted in many types of human cancer. However, the role of SETD2 in lung adenocarcinoma (LUAD) has not been well documented. In the present study, we found that SETD2 was significantly down-regulated both in LUAD tissues and cell lines. Functionally, the increased expression of SETD2 significantly attenuated the proliferation of cancer cells by affecting the cell cycle, whereas SETD2 deficiency dramatically improved these proliferative abilities of cancer cells. Through conjoint analysis of RNA-seq and ChIP data, we identified a functional target gene of SETD2, CXCL1, and its expression was negatively correlated with that of SETD2. Moreover, SETD2 deletion stimulated cell cycle-related proteins to promote LUAD. Further mechanistic studies demonstrated that histone H3 lysine 36 trimethylation (H3K36me3) catalyzed by SETD2 interacted with the promoter of CXCL1 to regulate its transcription and downstream signaling pathways, contributing to tumorigenesis in vitro and in vivo. Our findings suggested that SETD2 inhibited tumor growth via suppressing CXCL1-mediated activation of cell cycle, indicating that the regulation of H3K36me3 level by targeting SETD2 and/or the administration of downstream CXCL1 might represent a potential therapeutic way for new treatment in LUAD.
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Affiliation(s)
- You Zhou
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Xiao Zheng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Bin Xu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Haifeng Deng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Lujun Chen
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Jiangsu Engineering Research Center for Tumor Immunotherapy, Changzhou 213003, China.,Institute of Cell Therapy, Soochow University, Changzhou 213003, China
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10
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Tang SJ, Shen H, An O, Hong H, Li J, Song Y, Han J, Tay DJT, Ng VHE, Bellido Molias F, Leong KW, Pitcheshwar P, Yang H, Chen L. Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development. Nat Commun 2020; 11:799. [PMID: 32034135 PMCID: PMC7005744 DOI: 10.1038/s41467-020-14621-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/16/2020] [Indexed: 12/18/2022] Open
Abstract
RNA editing and splicing are the two major processes that dynamically regulate human transcriptome diversity. Despite growing evidence of crosstalk between RNA editing enzymes (mainly ADAR1) and splicing machineries, detailed mechanistic explanations and their biological importance in diseases, such as cancer are still lacking. Herein, we identify approximately a hundred high-confidence splicing events altered by ADAR1 and/or ADAR2, and ADAR1 or ADAR2 protein can regulate cassette exons in both directions. We unravel a binding tendency of ADARs to dsRNAs that involves GA-rich sequences for editing and splicing regulation. ADAR1 edits an intronic splicing silencer, leading to recruitment of SRSF7 and repression of exon inclusion. We also present a mechanism through which ADAR2 binds to dsRNA formed between GA-rich sequences and polypyrimidine (Py)-tract and precludes access of U2AF65 to 3' splice site. Furthermore, we find these ADARs-regulated splicing changes per se influence tumorigenesis, not merely byproducts of ADARs editing and binding.
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Affiliation(s)
- Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Fernando Bellido Molias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Ka Wai Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Priyankaa Pitcheshwar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore.
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11
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Luo J, Ye H, Hao L, Sun Y, Li R, Li Y, Yang Z. SRSFs mediate the function of AR in the ovarian granulosa cells of patients with PCOS. Genes Dis 2019; 8:94-109. [PMID: 33569518 PMCID: PMC7859457 DOI: 10.1016/j.gendis.2019.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/26/2019] [Accepted: 09/04/2019] [Indexed: 12/04/2022] Open
Abstract
Ovarian hyperandrogenism is one of the characteristics of polycystic ovary syndrome (PCOS) and androgen receptor (AR) in ovarian granulosa cells (GCs) functions as an important element to the accumulation of androgens. This study verified the existence of alternative splicing variant of AR (AR-SVs) in the GCs of PCOS patients and found that the function of AR decreased significantly in the presence of AR-SVs. And compared to the normal individuals, the expression of Serine/arginine-rich splicing factor 2(SRSF2) was higher and the expression of SRSF3 was lower in the GCs of patients with AR-SVs. More importantly, we found that the expression of SRSF2 was inhibited and that the expression of AR was decreased after the successful upregulation of miRNA-183, and testostrone (T) concentrations in the culture medium were increased. The results also showed that the expression of SRSF3 decreased when miRNA-124 was successfully upregulated, while the expression of AR significantly increased; however, the function of AR was also inhibited when T concentration in the culture medium was increased. This study has proved that SRSFs are regulated by corresponding miRNAs, and the altered expression of SRSFs interferenced the alternative splicing process of AR and ultimately decreased the function of AR, leading to the accumulation of androgens in the ovary.
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Affiliation(s)
- Jing Luo
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Hong Ye
- Gynecologic Endocrinology of Chongqing Health Center for Women and Children, Chongqing, PR China
| | - Lijuan Hao
- Gynecologic Endocrinology of Chongqing Health Center for Women and Children, Chongqing, PR China
| | - Yixuan Sun
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Ruohan Li
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Yanxi Li
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Zhu Yang
- Gynecology and Obstetrics of the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
- Corresponding author.
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12
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Balestra D, Branchini A. Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. Int J Mol Sci 2019; 20:ijms20123036. [PMID: 31234407 PMCID: PMC6627357 DOI: 10.3390/ijms20123036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular strategies tailored to promote/correct the expression and/or processing of defective coagulation factors would represent innovative therapeutic approaches beyond standard substitutive therapy. Here, we focus on the molecular mechanisms and determinants underlying innovative approaches acting at DNA, mRNA and protein levels in inherited coagulation factor deficiencies, and in particular on: (i) gene editing approaches, which have permitted intervention at the DNA level through the specific recognition, cleavage, repair/correction or activation of target sequences, even in mutated gene contexts; (ii) the rescue of altered pre-mRNA processing through the engineering of key spliceosome components able to promote correct exon recognition and, in turn, the synthesis and secretion of functional factors, as well as the effects on the splicing of missense changes affecting exonic splicing elements; this section includes antisense oligonucleotide- or siRNA-mediated approaches to down-regulate target genes; (iii) the rescue of protein synthesis/function through the induction of ribosome readthrough targeting nonsense variants or the correction of folding defects caused by amino acid substitutions. Overall, these approaches have shown the ability to rescue the expression and/or function of potentially therapeutic levels of coagulation factors in different disease models, thus supporting further studies in the future aimed at evaluating the clinical translatability of these new strategies.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
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13
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In Vitro System for Coupling RNAP II Transcription to Primary microRNA Processing and a Three-Way System for RNAP II Transcription/Splicing/microRNA Processing. Methods Mol Biol 2019; 1823:43-50. [PMID: 29959672 DOI: 10.1007/978-1-4939-8624-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
In the genome, primary microRNAs (pri-miRNAs) are encoded either as independent transcriptional units with their own promoters (intergenic miRNAs) or within the introns of other genes (intronic miRNAs). Here, we report two methods, one that we established for coupled RNAP II transcription and pri-miRNA processing and the other that is a three-way system for RNAP II transcription, pri-miRNA processing, and pre-mRNA splicing. In these systems, CMV-DNA constructs encoding the processing substrates are incubated in HeLa cell nuclear extracts in the presence of 32P-UTP to generate the nascent RNAP II transcripts, which are processed efficiently by the endogenous RNA processing machineries in nuclear extracts.
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14
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Chen W, Song X, Lin H. Combinatorial Pattern of Histone Modifications in Exon Skipping Event. Front Genet 2019; 10:122. [PMID: 30833963 PMCID: PMC6387913 DOI: 10.3389/fgene.2019.00122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/04/2019] [Indexed: 11/18/2022] Open
Abstract
Histone modifications are associated with alternative splicing. It has been suggested that histone modifications act in combinational patterns in gene expression regulation. However, how they interact with each other and what is their casual relationships in the process of RNA splicing remain unclear. In this study, the combinatorial patterns of 38 kinds of histone modifications in the exon skipping event of the CD4+ T cell were analyzed by constructing Bayesian networks. Distinct combinatorial patterns of histone modifications that illustrating their casual relationships were observed in excluded/included exons and the surrounding intronic regions. The Bayesian networks also indicate that some histone modifications directly correlate with RNA splicing. We anticipate that this work could provide novel insights into the effects of histone modifications on RNA splicing regulation.
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Affiliation(s)
- Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Key Laboratory for Neuro-Information of Ministry of Education, Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoming Song
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
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15
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Savisaar R, Hurst LD. Exonic splice regulation imposes strong selection at synonymous sites. Genome Res 2018; 28:1442-1454. [PMID: 30143596 PMCID: PMC6169883 DOI: 10.1101/gr.233999.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/31/2018] [Indexed: 01/17/2023]
Abstract
What proportion of coding sequence nucleotides have roles in splicing, and how strong is the selection that maintains them? Despite a large body of research into exonic splice regulatory signals, these questions have not been answered. This is because, to our knowledge, previous investigations have not explicitly disentangled the frequency of splice regulatory elements from the strength of the evolutionary constraint under which they evolve. Current data are consistent both with a scenario of weak and diffuse constraint, enveloping large swaths of sequence, as well as with well-defined pockets of strong purifying selection. In the former case, natural selection on exonic splice enhancers (ESEs) might primarily act as a slight modifier of codon usage bias. In the latter, mutations that disrupt ESEs are likely to have large fitness and, potentially, clinical effects. To distinguish between these scenarios, we used several different methods to determine the distribution of selection coefficients for new mutations within ESEs. The analyses converged to suggest that ∼15%-20% of fourfold degenerate sites are part of functional ESEs. Most of these sites are under strong evolutionary constraint. Therefore, exonic splice regulation does not simply impose a weak bias that gently nudges coding sequence evolution in a particular direction. Rather, the selection to preserve these motifs is a strong force that severely constrains the evolution of a substantial proportion of coding nucleotides. Thus synonymous mutations that disrupt ESEs should be considered as a potentially common cause of single-locus genetic disorders.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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16
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Filippenkov IB, Sudarkina OY, Limborska SA, Dergunova LV. Multi-step splicing of sphingomyelin synthase linear and circular RNAs. Gene 2018; 654:14-22. [DOI: 10.1016/j.gene.2018.02.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/01/2018] [Accepted: 02/12/2018] [Indexed: 12/13/2022]
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17
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Nissen KE, Homer CM, Ryan CJ, Shales M, Krogan NJ, Patrick KL, Guthrie C. The histone variant H2A.Z promotes splicing of weak introns. Genes Dev 2017; 31:688-701. [PMID: 28446597 PMCID: PMC5411709 DOI: 10.1101/gad.295287.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/22/2017] [Indexed: 12/12/2022]
Abstract
In this study, Nissen et al. investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast S. pombe. The findings suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading ATPases. Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe. Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A.Z, we uncovered evidence for functional interactions with components of the spliceosome. In support of these genetic connections, splicing-specific microarrays show that H2A.Z and the Swr1 ATPase are required during temperature stress for the efficient splicing of a subset of introns. Notably, affected introns are enriched for H2A.Z occupancy and more likely to contain nonconsensus splice sites. To test the significance of the latter correlation, we mutated the splice sites in an affected intron to consensus and found that this suppressed the requirement for H2A.Z in splicing of that intron. These data suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading ATPases. Consistent with this model, we show that overexpression of splicing ATPase Prp16 suppresses both the growth and splicing defects seen in the absence of H2A.Z.
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Affiliation(s)
- Kelly E Nissen
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
| | - Christina M Homer
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco 94158, California, USA.,California Institute for Quantitative Biosciences (QB3), San Francisco 94158, California, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco 94158, California, USA.,California Institute for Quantitative Biosciences (QB3), San Francisco 94158, California, USA.,J. David Gladstone Institutes, San Francisco 94158, California, USA
| | - Kristin L Patrick
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA.,Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas 77807, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco 94158, California, USA
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18
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Yuan H, Li N, Fu D, Ren J, Hui J, Peng J, Liu Y, Qiu T, Jiang M, Pan Q, Han Y, Wang X, Li Q, Qin J. Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis. J Clin Invest 2017; 127:3375-3391. [PMID: 28825595 DOI: 10.1172/jci94292] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/23/2017] [Indexed: 12/27/2022] Open
Abstract
The histone H3K36 methyltransferase SETD2 is frequently mutated or deleted in a variety of human tumors. Nevertheless, the role of SETD2 loss in oncogenesis remains largely undefined. Here, we found that SETD2 counteracts Wnt signaling and its inactivation promotes intestinal tumorigenesis in mouse models of colorectal cancer (CRC). SETD2 was not required for intestinal homeostasis under steady state; however, upon irradiation, genetic inactivation of Setd2 in mouse intestinal epithelium facilitated the self-renewal of intestinal stem/progenitor cells as well as tissue regeneration. Furthermore, depletion of SETD2 enhanced the susceptibility to tumorigenesis in the context of dysregulated Wnt signaling. Mechanistic characterizations indicated that SETD2 downregulation affects the alternative splicing of a subset of genes implicated in tumorigenesis. Importantly, we uncovered that SETD2 ablation reduces intron retention of dishevelled segment polarity protein 2 (DVL2) pre-mRNA, which would otherwise be degraded by nonsense-mediated decay, thereby augmenting Wnt signaling. The signaling cascades mediated by SETD2 were further substantiated by a CRC patient cohort analysis. Together, our studies highlight SETD2 as an integral regulator of Wnt signaling through epigenetic regulation of RNA processing during tissue regeneration and tumorigenesis.
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Affiliation(s)
- Huairui Yuan
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Ni Li
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiale Ren
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Junjie Peng
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yongfeng Liu
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Tong Qiu
- Department of Obstetrics, Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Min Jiang
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Qiang Pan
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Ying Han
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaoming Wang
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Qintong Li
- Department of Obstetrics, Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jun Qin
- The Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Shanghai, China
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19
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Savisaar R, Hurst LD. Estimating the prevalence of functional exonic splice regulatory information. Hum Genet 2017; 136:1059-1078. [PMID: 28405812 PMCID: PMC5602102 DOI: 10.1007/s00439-017-1798-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/04/2017] [Indexed: 12/14/2022]
Abstract
In addition to coding information, human exons contain sequences necessary for correct splicing. These elements are known to be under purifying selection and their disruption can cause disease. However, the density of functional exonic splicing information remains profoundly uncertain. Several groups have experimentally investigated how mutations at different exonic positions affect splicing. They have found splice information to be distributed widely in exons, with one estimate putting the proportion of splicing-relevant nucleotides at >90%. These results suggest that splicing could place a major pressure on exon evolution. However, analyses of sequence conservation have concluded that the need to preserve splice regulatory signals only slightly constrains exon evolution, with a resulting decrease in the average human rate of synonymous evolution of only 1–4%. Why do these two lines of research come to such different conclusions? Among other reasons, we suggest that the methods are measuring different things: one assays the density of sites that affect splicing, the other the density of sites whose effects on splicing are visible to selection. In addition, the experimental methods typically consider short exons, thereby enriching for nucleotides close to the splice junction, such sites being enriched for splice-control elements. By contrast, in part owing to correction for nucleotide composition biases and to the assumption that constraint only operates on exon ends, the conservation-based methods can be overly conservative.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
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20
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Jubin T, Kadam A, Gani AR, Singh M, Dwivedi M, Begum R. Poly ADP-ribose polymerase-1: Beyond transcription and towards differentiation. Semin Cell Dev Biol 2017; 63:167-179. [PMID: 27476447 DOI: 10.1016/j.semcdb.2016.07.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
Abstract
Gene regulation mediates the processes of cellular development and differentiation leading to the origin of different cell types each having their own signature gene expression profile. However, the compact chromatin structure and the timely recruitment of molecules involved in various signaling pathways are of prime importance for temporal and spatial gene regulation that eventually contribute towards cell type and specificity. Poly (ADP-ribose) polymerase-1 (PARP-1), a 116-kDa nuclear multitasking protein is involved in modulation of chromatin condensation leading to altered gene expression. In response to activation signals, it adds ADP-ribose units to various target proteins including itself, thus regulating various key cellular processes like DNA repair, cell death, transcription, mRNA splicing etc. This review provides insights into the role of PARP-1 in gene regulation, cell differentiation and multicellular morphogenesis. In addition, the review also explores involvement of PARP-1 in immune cells development and therapeutic possibilities to treat various human diseases.
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Affiliation(s)
- Tina Jubin
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Ashlesha Kadam
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Amina Rafath Gani
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India; Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 Telangana, India
| | - Mala Singh
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Mitesh Dwivedi
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India; C.G. Bhakta Institute of Biotechnology, Faculty of Science, Uka Tarsadia University, Surat, Gujarat 394350, India
| | - Rasheedunnisa Begum
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India.
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21
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Xing Y, Zhao X, Yu T, Liang D, Li J, Wei G, Liu G, Cui X, Zhao H, Cai L. MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs. PLoS One 2016; 11:e0155443. [PMID: 27167218 PMCID: PMC4864242 DOI: 10.1371/journal.pone.0155443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/28/2016] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood. Although numerous databases have been built to describe AS, molecular interaction databases associated with AS have only recently emerged. In this study, we present a new database, MiasDB, that provides a description of molecular interactions associated with human AS events. This database covers 938 interactions between human splicing factors, RNA elements, transcription factors, kinases and modified histones for 173 human AS events. Every entry includes the interaction partners, interaction type, experimental methods, AS type, tissue specificity or disease-relevant information, a simple description of the functionally tested interaction in the AS event and references. The database can be queried easily using a web server (http://47.88.84.236/Miasdb). We display some interaction figures for several genes. With this database, users can view the regulation network describing AS events for 12 given genes.
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Affiliation(s)
- Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xiujuan Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Tao Yu
- School of Science, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Dong Liang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jun Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Guanyun Wei
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xiangjun Cui
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- * E-mail:
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22
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Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing. Proc Natl Acad Sci U S A 2015; 112:14840-5. [PMID: 26578803 DOI: 10.1073/pnas.1506760112] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA polymerase II (RNAPII) transcription elongation is a highly regulated process that greatly influences mRNA levels as well as pre-mRNA splicing. Despite many studies in vitro, how chromatin modulates RNAPII elongation in vivo is still unclear. Here, we show that a decrease in the level of available canonical histones leads to more accessible chromatin with decreased levels of canonical histones and variants H2A.X and H2A.Z and increased levels of H3.3. With this altered chromatin structure, the RNAPII elongation rate increases, and the kinetics of pre-mRNA splicing is delayed with respect to RNAPII elongation. Consistent with the kinetic model of cotranscriptional splicing, the rapid RNAPII elongation induced by histone depletion promotes the skipping of variable exons in the CD44 gene. Indeed, a slowly elongating mutant of RNAPII was able to rescue this defect, indicating that the defective splicing induced by histone depletion is a direct consequence of the increased elongation rate. In addition, genome-wide analysis evidenced that histone reduction promotes widespread alterations in pre-mRNA processing, including intron retention and changes in alternative splicing. Our data demonstrate that pre-mRNA splicing may be regulated by chromatin structure through the modulation of the RNAPII elongation rate.
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23
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Shkreta L, Chabot B. The RNA Splicing Response to DNA Damage. Biomolecules 2015; 5:2935-77. [PMID: 26529031 PMCID: PMC4693264 DOI: 10.3390/biom5042935] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/20/2015] [Accepted: 10/16/2015] [Indexed: 12/29/2022] Open
Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
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Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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Nalabothula N, Al-jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN. Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation. PLoS One 2015; 10:e0135410. [PMID: 26305327 PMCID: PMC4549251 DOI: 10.1371/journal.pone.0135410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/21/2015] [Indexed: 12/22/2022] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1’s role in gene regulation.
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Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Taha Al-jumaily
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Abdallah M. Eteleeb
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Robert M. Flight
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Shao Xiaorong
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Hunter Moseley
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
| | - Yvonne N. Fondufe-Mittendorf
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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25
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Primary microRNA processing is functionally coupled to RNAP II transcription in vitro. Sci Rep 2015; 5:11992. [PMID: 26149087 PMCID: PMC4493704 DOI: 10.1038/srep11992] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/15/2015] [Indexed: 12/13/2022] Open
Abstract
Previous studies in vivo reported that processing of primary microRNA (pri-miRNA) is coupled to transcription by RNA polymerase II (RNAP II) and can occur co-transcriptionally. Here we have established a robust in vivo system in which pri-miRNA is transcribed by RNAP II and processed to pre-miRNA in HeLa cell nuclear extracts. We show that both the kinetics and efficiency of pri-miRNA processing are dramatically enhanced in this system compared to that of the corresponding naked pri-miRNA. Moreover, this enhancement is general as it occurs with multiple pri-miRNAs. We also show that nascent pri-miRNA is efficiently processed before it is released from the DNA template. Together, our work directly demonstrates that transcription and pri-miRNA processing are functionally coupled and establishes the first in vivo model systems for this functional coupling and for co-transcriptional processing.
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FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP. Proc Natl Acad Sci U S A 2015; 112:8608-13. [PMID: 26124092 DOI: 10.1073/pnas.1506282112] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Pre-mRNA splicing is coupled to transcription by RNA polymerase II (RNAP II). We previously showed that U1 small nuclear ribonucleoprotein (snRNP) associates with RNAP II, and both RNAP II and U1 snRNP are also the most abundant factors associated with the protein fused-in-sarcoma (FUS), which is mutated to cause the neurodegenerative disease amyotrophic lateral sclerosis. Here, we show that an antisense morpholino that base-pairs to the 5' end of U1 snRNA blocks splicing in the coupled system and completely disrupts the association between U1 snRNP and both FUS and RNAP II, but has no effect on the association between FUS and RNAP II. Conversely, we found that U1 snRNP does not interact with RNAP II in FUS knockdown extracts. Moreover, using these extracts, we found that FUS must be present during the transcription reaction in order for splicing to occur. Together, our data lead to a model that FUS functions in coupling transcription to splicing via mediating an interaction between RNAP II and U1 snRNP.
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27
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Tejedor JR, Tilgner H, Iannone C, Guigó R, Valcárcel J. Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing. RNA (NEW YORK, N.Y.) 2015; 21:1187-1202. [PMID: 25904137 PMCID: PMC4436670 DOI: 10.1261/rna.049890.115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
The OLR1 gene encodes the oxidized low-density lipoprotein receptor (LOX-1), which is responsible for the cellular uptake of oxidized LDL (Ox-LDL), foam cell formation in atheroma plaques and atherosclerotic plaque rupture. Alternative splicing (AS) of OLR1 exon 5 generates two protein isoforms with antagonistic functions in Ox-LDL uptake. Previous work identified six single nucleotide polymorphisms (SNPs) in linkage disequilibrium that influence the inclusion levels of OLR1 exon 5 and correlate with the risk of cardiovascular disease. Here we use minigenes to recapitulate the effects of two allelic series (Low- and High-Risk) on OLR1 AS and identify one SNP in intron 4 (rs3736234) as the main contributor to the differences in exon 5 inclusion, while the other SNPs in the allelic series attenuate the drastic effects of this key SNP. Bioinformatic, proteomic, mutational and functional high-throughput analyses allowed us to define regulatory sequence motifs and identify SR protein family members (SRSF1, SRSF2) and HMGA1 as factors involved in the regulation of OLR1 AS. Our results suggest that antagonism between SRSF1 and SRSF2/HMGA1, and differential recognition of their regulatory motifs depending on the identity of the rs3736234 polymorphism, influence OLR1 exon 5 inclusion and the efficiency of Ox-LDL uptake, with potential implications for atherosclerosis and coronary disease.
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Affiliation(s)
- J Ramón Tejedor
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Hagen Tilgner
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Camilla Iannone
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Roderic Guigó
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, 08020 Barcelona, Spain
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28
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Acetylation of intragenic histones on HPV16 correlates with enhanced HPV16 gene expression. Virology 2015; 482:244-59. [PMID: 25900886 DOI: 10.1016/j.virol.2015.02.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/23/2015] [Accepted: 02/25/2015] [Indexed: 11/21/2022]
Abstract
We report that many histone modifications are unevenly distributed over the HPV16 genome in cervical cancer cells as well as in HPV16-immortalized keratinocytes. For example, H3K36me3 and H3K9Ac that are common in highly expressed cellular genes and over exons, were more common in the early than in the late region of the HPV16 genome. In contrast, H3K9me3, H4K20me3, H2BK5me1 and H4K16Ac were more frequent in the HPV16 late region. Furthermore, a region encompassing the HPV16 early polyadenylation signal pAE displayed high levels of histone H3 acetylation. Histone deacetylase (HDAC) inhibitors caused a 2- to 8-fold induction of HPV16 early and late mRNAs in cervical cancer cells and in immortalized keratinocytes, while at the same time increasing the levels of acetylated histones in the cells and on the HPV16 genome specifically. We concluded that increased histone acetylation on the HPV16 genome correlates with increased HPV16 gene expression.
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29
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Abstract
Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA-protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.
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Affiliation(s)
- Yeon Lee
- Center for RNA Systems Biology; Division of Biochemistry, Biophysics, and Structural Biology; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204;
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30
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Mayor R, Izquierdo-Bouldstridge A, Millán-Ariño L, Bustillos A, Sampaio C, Luque N, Jordan A. Genome distribution of replication-independent histone H1 variants shows H1.0 associated with nucleolar domains and H1X associated with RNA polymerase II-enriched regions. J Biol Chem 2015; 290:7474-91. [PMID: 25645921 DOI: 10.1074/jbc.m114.617324] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unlike core histones, the linker histone H1 family is more evolutionarily diverse, and many organisms have multiple H1 variants or subtypes. In mammals, the H1 family includes seven somatic H1 variants; H1.1 to H1.5 are expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. Using ChIP-sequencing data and cell fractionation, we have compared the genomic distribution of H1.0 and H1X in human breast cancer cells, in which we previously observed differential distribution of H1.2 compared with the other subtypes. We have found H1.0 to be enriched at nucleolus-associated DNA repeats and chromatin domains, whereas H1X is associated with coding regions, RNA polymerase II-enriched regions, and hypomethylated CpG islands. Further, H1X accumulates within constitutive or included exons and retained introns and toward the 3' end of expressed genes. Inducible H1X knockdown does not affect cell proliferation but dysregulates a subset of genes related to cell movement and transport. In H1X-depleted cells, the promoters of up-regulated genes are not occupied specifically by this variant, have a lower than average H1 content, and, unexpectedly, do not form an H1 valley upon induction. We conclude that H1 variants are not distributed evenly across the genome and may participate with some specificity in chromatin domain organization or gene regulation.
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Affiliation(s)
- Regina Mayor
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Andrea Izquierdo-Bouldstridge
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Lluís Millán-Ariño
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Alberto Bustillos
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Cristina Sampaio
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Neus Luque
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Albert Jordan
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
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31
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Wang Y, Liu J, Huang BO, Xu YM, Li J, Huang LF, Lin J, Zhang J, Min QH, Yang WM, Wang XZ. Mechanism of alternative splicing and its regulation. Biomed Rep 2014; 3:152-158. [PMID: 25798239 DOI: 10.3892/br.2014.407] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/10/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing of precursor mRNA is an essential mechanism to increase the complexity of gene expression, and it plays an important role in cellular differentiation and organism development. Regulation of alternative splicing is a complicated process in which numerous interacting components are at work, including cis-acting elements and trans-acting factors, and is further guided by the functional coupling between transcription and splicing. Additional molecular features, such as chromatin structure, RNA structure and alternative transcription initiation or alternative transcription termination, collaborate with these basic components to generate the protein diversity due to alternative splicing. All these factors contributing to this one fundamental biological process add up to a mechanism that is critical to the proper functioning of cells. Any corruption of the process may lead to disruption of normal cellular function and the eventuality of disease. Cancer is one of those diseases, where alternative splicing may be the basis for the identification of novel diagnostic and prognostic biomarkers, as well as new strategies for therapy. Thus, an in-depth understanding of alternative splicing regulation has the potential not only to elucidate fundamental biological principles, but to provide solutions for various diseases.
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Affiliation(s)
- Yan Wang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Liu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - B O Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Yan-Mei Xu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Lin-Feng Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jin Lin
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Zhang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Qing-Hua Min
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Wei-Ming Yang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Xiao-Zhong Wang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
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32
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Woods BA, Levine RL. The role of mutations in epigenetic regulators in myeloid malignancies. Immunol Rev 2014; 263:22-35. [DOI: 10.1111/imr.12246] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Brittany A. Woods
- Louis V. Gerstner Sloan Kettering Graduate School of Biomedical Sciences; Memorial Sloan Kettering Cancer Center; New York NY USA
- Human Oncology and Pathogenesis Program; Memorial Sloan Kettering Cancer Center; New York NY USA
| | - Ross L. Levine
- Louis V. Gerstner Sloan Kettering Graduate School of Biomedical Sciences; Memorial Sloan Kettering Cancer Center; New York NY USA
- Human Oncology and Pathogenesis Program; Memorial Sloan Kettering Cancer Center; New York NY USA
- Leukemia Service; Department of Medicine; Memorial Sloan Kettering Cancer Center; New York NY USA
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33
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Siala O, Rebai A, Fakhfakh F. Slight variations in the SC35 ESE sequence motif among human chromosomes: a computational approach. Gene 2014; 545:102-10. [PMID: 24792892 DOI: 10.1016/j.gene.2014.04.075] [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: 02/17/2014] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 11/26/2022]
Abstract
Gene expression is initiated by the binding of transcription factors to cis-regulatory modules such as enhancer elements binding to the Serine/Arginine proteins. Recently, we noticed an increased ability to identify the location as well as the motifs of enhancers using genome-wide information on spliceosomal factor occupancy, cofactor recruitment and chromatin modifications. In this study, we have undertaken a large-scale genomic analysis in an attempt to uncover if the exonic splicing enhancer motif binding to the SC35 and the SRp40 SR proteins is conserved among several groups of human genes. For the SRp40, the results showed that the ESE consensus is conserved among human genes. Concerning the SC35 SR protein, results showed an ESE motif conserved among human tissues and between different levels of muscular cell differentiation and within the same chromosome. However, this motif displays subtle discrepancies between genes localized in different chromosomes. These results emphasize the presence of different translational isoforms of the SFRS2 gene encoding for the SC35, or different post-translational protein maturations in different chromosomes, confirming that chromatin structure is another layer of gene regulation. These links between chromatin pattern and splicing give further mechanistic support to functional interconnections between splicing, transcription and chromatin structure, and raise the intriguing possibility of the existence of a memory for splicing patterns to be inherited through epigenetic modifications.
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Affiliation(s)
- Olfa Siala
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Avenue Majida Boulila, 3029 Sfax, Tunisia.
| | - Ahmed Rebai
- Unit of Bioinformatics and Biostatistics, Centre of Biotechnology of Sfax, Sfax 3038, Tunisia.
| | - Faiza Fakhfakh
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Avenue Majida Boulila, 3029 Sfax, Tunisia.
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34
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Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet 2014; 15:163-75. [PMID: 24514444 DOI: 10.1038/nrg3662] [Citation(s) in RCA: 546] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maturation of mRNA precursors often occurs simultaneously with their synthesis by RNA polymerase II (Pol II). The co-transcriptional nature of mRNA processing has permitted the evolution of coupling mechanisms that coordinate transcription with mRNA capping, splicing, editing and 3' end formation. Recent experiments using sophisticated new methods for analysis of nascent RNA have provided important insights into the relative amount of co-transcriptional and post-transcriptional processing, the relationship between mRNA elongation and processing, and the role of the Pol II carboxy-terminal domain (CTD) in regulating these processes.
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Affiliation(s)
- David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, MS8101, PO BOX 6511, Aurora, Colorado 80045, USA
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35
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Itzykson R, Kosmider O, Fenaux P. Somatic mutations and epigenetic abnormalities in myelodysplastic syndromes. Best Pract Res Clin Haematol 2014; 26:355-64. [PMID: 24507812 DOI: 10.1016/j.beha.2014.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During many years, very limited data had been available on specific gene mutations in MDS in particular due to the fact that balanced chromosomal translocations (which have allowed to discover many "leukemia" genes) are very rare in MDS, while chromosomal deletions are generally very large, making it difficult to identify genes of interest. Recently, the advent of next generation sequencing (NGS) techniques has helped identify somatic gene mutations in 75-80% of MDS, that cluster mainly in four functional groups, i.e. cytokine signaling (RAS genes), DNA methylation, (TET2, IDH1/2, DNMT3a genes) histone modifications (ASXL1 and EZH2 genes), and spliceosome (SF3B1 and SRSF2 genes) along with mutations of RUNX1 and TP 53 genes. Most of those mutations, except SF3B1 and TET2 mutations, are associated with an overall poorer prognosis, while some gene mutations (mainly TET2 mutation), may be associated to better response to hypomethylating agents. The frequent mutations of epigenetic modulators in MDS appear to largely contribute to the importance of epigenetic deregulation (in particular gene hypermethylation and histone deacetylation) in MDS progression, and may account at least partially for the efficacy of hypomethylating agents in the treatment of MDS.
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Affiliation(s)
- Raphael Itzykson
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM Unit U944, Hôpital St Louis, Paris, France
| | - Olivier Kosmider
- Laboratoire d'hématologie, Hôpital Cochin, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 5, France
| | - Pierre Fenaux
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM UMR-S-940, Hôpital St Louis, Paris, France.
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36
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Gruber AJ, Zavolan M. Modulation of epigenetic regulators and cell fate decisions by miRNAs. Epigenomics 2013; 5:671-83. [DOI: 10.2217/epi.13.65] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mammalian gene expression is controlled at multiple levels by a variety of regulators, including chromatin modifiers, transcription factors and miRNAs. The latter are small, ncRNAs that inhibit the expression of target mRNAs by reducing both their stability and translation rate. In this review, we summarize the recent work towards characterizing miRNA targets that are themselves involved in the regulation of gene expression at the epigenetic level. Epigenetic regulators are strongly enriched among the predicted targets of miRNAs, which may contribute to the documented importance of miRNAs for pluripotency, organism development and somatic cell reprogramming.
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Affiliation(s)
- Andreas J Gruber
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Mihaela Zavolan
- Swiss Institute of Bioinformatics, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
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37
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Itzykson R, Fenaux P. Epigenetics of myelodysplastic syndromes. Leukemia 2013; 28:497-506. [DOI: 10.1038/leu.2013.343] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/27/2013] [Accepted: 10/30/2013] [Indexed: 12/23/2022]
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38
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Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
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Affiliation(s)
- Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
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39
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Role of pseudoexons and pseudointrons in human cancer. Int J Cell Biol 2013; 2013:810572. [PMID: 24204383 PMCID: PMC3800588 DOI: 10.1155/2013/810572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/09/2013] [Indexed: 11/18/2022] Open
Abstract
In all eukaryotic organisms, pre-mRNA splicing and alternative splicing processes play an essential role in regulating the flow of information required to drive complex developmental and metabolic pathways. As a result, eukaryotic cells have developed a very efficient macromolecular machinery, called the spliceosome, to correctly recognize the pre-mRNA sequences that need to be inserted in a mature mRNA (exons) from those that should be removed (introns). In healthy individuals, alternative and constitutive splicing processes function with a high degree of precision and fidelity in order to ensure the correct working of this machinery. In recent years, however, medical research has shown that alterations at the splicing level play an increasingly important role in many human hereditary diseases, neurodegenerative processes, and especially in cancer origin and progression. In this minireview, we will focus on several genes whose association with cancer has been well established in previous studies, such as ATM, BRCA1/A2, and NF1. In particular, our objective will be to provide an overview of the known mechanisms underlying activation/repression of pseudoexons and pseudointrons; the possible utilization of these events as biomarkers of tumor staging/grading; and finally, the treatment options for reversing pathologic splicing events.
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Hnilicová J, Hozeifi S, Stejskalová E, Dušková E, Poser I, Humpolíčková J, Hof M, Staněk D. The C-terminal domain of Brd2 is important for chromatin interaction and regulation of transcription and alternative splicing. Mol Biol Cell 2013; 24:3557-68. [PMID: 24048450 PMCID: PMC3826993 DOI: 10.1091/mbc.e13-06-0303] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This study determines genes that are regulated by Brd2 and finds that, in addition to expression control, Brd2 modulates the alternative splicing of several hundred genes. The in vivo interaction of Brd2 with chromatin is analyzed, and the contributions of individual Brd2 domains to the chromatin interaction are determined. Brd2 is a member of the bromodomain extra terminal (BET) protein family, which consists of four chromatin-interacting proteins that regulate gene expression. Each BET protein contains two N-terminal bromodomains, which recognize acetylated histones, and the C-terminal protein–protein interaction domain. Using a genome-wide screen, we identify 1450 genes whose transcription is regulated by Brd2. In addition, almost 290 genes change their alternative splicing pattern upon Brd2 depletion. Brd2 is specifically localized at promoters of target genes, and our data show that Brd2 interaction with chromatin cannot be explained solely by histone acetylation. Using coimmunoprecipitation and live-cell imaging, we show that the C-terminal part is crucial for Brd2 association with chromatin. Live-cell microscopy also allows us to map the average binding time of Brd2 to chromatin and quantify the contributions of individual Brd2 domains to the interaction with chromatin. Finally, we show that bromodomains and the C-terminal domain are equally important for transcription and splicing regulation, which correlates with the role of these domains in Brd2 binding to chromatin.
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Affiliation(s)
- Jarmila Hnilicová
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic Max Planck Institute for Molecular Cell Biology and Genetics, Dresden 01307, Germany J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 182 23, Czech Republic
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Zhang Z, Jones A, Joo HY, Zhou D, Cao Y, Chen S, Erdjument-Bromage H, Renfrow M, He H, Tempst P, Townes TM, Giles KE, Ma L, Wang H. USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing. Genes Dev 2013; 27:1581-95. [PMID: 23824326 DOI: 10.1101/gad.211037.112] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-translational histone modifications play important roles in regulating chromatin structure and function. Histone H2B ubiquitination and deubiquitination have been implicated in transcriptional regulation, but the function of H2B deubiquitination is not well defined, particularly in higher eukaryotes. Here we report the purification of ubiquitin-specific peptidase 49 (USP49) as a histone H2B-specific deubiquitinase and demonstrate that H2B deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons. USP49 forms a complex with RuvB-like1 (RVB1) and SUG1 and specifically deubiquitinates histone H2B in vitro and in vivo. USP49 knockdown results in small changes in gene expression but affects the abundance of >9000 isoforms. Exons down-regulated in USP49 knockdown cells show both elevated levels of alternative splicing and a general decrease in splicing efficiency. Importantly, USP49 is relatively enriched at this set of exons. USP49 knockdown increased H2B ubiquitination (uH2B) levels at these exons as well as upstream 3' and downstream 5' intronic splicing elements. Change in H2B ubiquitination level, as modulated by USP49, regulates U1A and U2B association with chromatin and binding to nascent pre-mRNA. Although H3 levels are relatively stable after USP49 depletion, H2B levels at these exons are dramatically increased, suggesting that uH2B may enhance nucleosome stability. Therefore, this study identifies USP49 as a histone H2B-specific deubiquitinase and uncovers a critical role for H2B deubiquitination in cotranscriptional pre-mRNA processing events.
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Affiliation(s)
- Zhuo Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Brugiolo M, Herzel L, Neugebauer KM. Counting on co-transcriptional splicing. F1000PRIME REPORTS 2013; 5:9. [PMID: 23638305 PMCID: PMC3619158 DOI: 10.12703/p5-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Splicing is the removal of intron sequences from pre-mRNA by the spliceosome. Researchers working in multiple model organisms – notably yeast, insects and mammalian cells – have shown that pre-mRNA can be spliced during the process of transcription (i.e. co-transcriptionally), as well as after transcription termination (i.e. post-transcriptionally). Co-transcriptional splicing does not assume that transcription and splicing machineries are mechanistically coupled, yet it raises this possibility. Early studies were based on a limited number of genes, which were often chosen because of their experimental accessibility. Since 2010, eight studies have used global datasets as counting tools, in order to quantify co-transcriptional intron removal. The consensus view, based on four organisms, is that the majority of splicing events take place co-transcriptionally in most cells and tissues. Here, we discuss the nature of the various global datasets and how bioinformatic analyses were conducted. Considering the broad differences in experimental approach and analysis, the level of agreement on the prevalence of co-transcriptional splicing is remarkable.
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Lee KM, Tarn WY. Coupling pre-mRNA processing to transcription on the RNA factory assembly line. RNA Biol 2013; 10:380-90. [PMID: 23392244 DOI: 10.4161/rna.23697] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
It has been well-documented that nuclear processing of primary transcripts of RNA polymerase II occurs co-transcriptionally and is functionally coupled to transcription. Moreover, increasing evidence indicates that transcription influences pre-mRNA splicing and even several post-splicing RNA processing events. In this review, we discuss the issues of how RNA polymerase II modulates co-transcriptional RNA processing events via its carboxyl terminal domain, and the protein domains involved in coupling of transcription and RNA processing events. In addition, we describe how transcription influences the expression or stability of mRNAs through the formation of distinct mRNP complexes. Finally, we delineate emerging findings that chromatin modifications function in the regulation of RNA processing steps, especially splicing, in addition to transcription. Overall, we provide a comprehensive view that transcription could integrate different control systems, from epigenetic to post-transcriptional control, for efficient gene expression.
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Affiliation(s)
- Kuo-Ming Lee
- Institute of Biomedical Sciences; Academia Sinica; Taipei, Taiwan
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