1
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Giudice J, Jiang H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat Rev Mol Cell Biol 2024; 25:683-700. [PMID: 38773325 DOI: 10.1038/s41580-024-00739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Biomolecular condensates, sometimes also known as membraneless organelles (MLOs), can form through weak multivalent intermolecular interactions of proteins and nucleic acids, a process often associated with liquid-liquid phase separation. Biomolecular condensates are emerging as sites and regulatory platforms of vital cellular functions, including transcription and RNA processing. In the first part of this Review, we comprehensively discuss how alternative splicing regulates the formation and properties of condensates, and conversely the roles of biomolecular condensates in splicing regulation. In the second part, we focus on the spatial connection between splicing regulation and nuclear MLOs such as transcriptional condensates, splicing condensates and nuclear speckles. We then discuss key studies showing how splicing regulation through biomolecular condensates is implicated in human pathologies such as neurodegenerative diseases, different types of cancer, developmental disorders and cardiomyopathies, and conclude with a discussion of outstanding questions pertaining to the roles of condensates and MLOs in splicing regulation and how to experimentally study them.
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Affiliation(s)
- Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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2
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Xiao MS, Damodaran AP, Kumari B, Dickson E, Xing K, On TA, Parab N, King HE, Perez AR, Guiblet WM, Duncan G, Che A, Chari R, Andresson T, Vidigal JA, Weatheritt RJ, Aregger M, Gonatopoulos-Pournatzis T. Genome-scale exon perturbation screens uncover exons critical for cell fitness. Mol Cell 2024; 84:2553-2572.e19. [PMID: 38917794 PMCID: PMC11246229 DOI: 10.1016/j.molcel.2024.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 04/04/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.
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Affiliation(s)
- Mei-Sheng Xiao
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Arun Prasath Damodaran
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Bandana Kumari
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Ethan Dickson
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Kun Xing
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Tyler A On
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Nikhil Parab
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Helen E King
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alexendar R Perez
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wilfried M Guiblet
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Gerard Duncan
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Anney Che
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2010, Australia
| | - Michael Aregger
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Thomas Gonatopoulos-Pournatzis
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
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3
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Zhao A, Xu W, Han R, Wei J, Yu Q, Wang M, Li H, Li M, Chi G. Role of histone modifications in neurogenesis and neurodegenerative disease development. Ageing Res Rev 2024; 98:102324. [PMID: 38762100 DOI: 10.1016/j.arr.2024.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Progressive neuronal dysfunction and death are key features of neurodegenerative diseases; therefore, promoting neurogenesis in neurodegenerative diseases is crucial. With advancements in proteomics and high-throughput sequencing technology, it has been demonstrated that histone post-transcriptional modifications (PTMs) are often altered during neurogenesis when the brain is affected by disease or external stimuli and that the degree of histone modification is closely associated with the development of neurodegenerative diseases. This review aimed to show the regulatory role of histone modifications in neurogenesis and neurodegenerative diseases by discussing the changing patterns and functional significance of histone modifications, including histone methylation, acetylation, ubiquitination, phosphorylation, and lactylation. Finally, we explored the control of neurogenesis and the development of neurodegenerative diseases by artificially modulating histone modifications.
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Affiliation(s)
- Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Rui Han
- Department of Neurovascular Surgery, First Hospital of Jilin University, Changchun, 130021, China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Haokun Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
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4
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Carvalho LML, Jorge AADL, Bertola DR, Krepischi ACV, Rosenberg C. A Comprehensive Review of Syndromic Forms of Obesity: Genetic Etiology, Clinical Features and Molecular Diagnosis. Curr Obes Rep 2024; 13:313-337. [PMID: 38277088 DOI: 10.1007/s13679-023-00543-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 01/27/2024]
Abstract
Syndromic obesity refers to obesity occurring with additional clinical findings, such as intellectual disability/developmental delay, dysmorphic features, and congenital malformations. PURPOSE OF REVIEW: To present a narrative review regarding the genetic etiology, clinical description, and molecular diagnosis of syndromic obesity, which is a rare condition with high phenotypic variability and genetic heterogeneity. The following syndromes are presented in this review: Prader-Willi, Bardet-Biedl, Pseudohypoparathyroidism, Alström, Smith-Magenis, Cohen, Temple, 1p36 deletion, 16p11.2 microdeletion, Kleefstra, SIM1-related, Börjeson-Forssman-Lehmann, WAGRO, Carpenter, MORM, and MYT1L-related syndromes. RECENT FINDINGS: There are three main groups of mechanisms for syndromic obesity: imprinting, transcriptional activity regulation, and cellular cilia function. For molecular diagnostic, methods of genome-wide investigation should be prioritized over sequencing of panels of syndromic obesity genes. In addition, we present novel syndromic conditions that need further delineation, but evidences suggest they have a higher frequency of obesity. The etiology of syndromic obesity tends to be linked to disrupted neurodevelopment (central) and is associated with a diversity of genes and biological pathways. In the genetic investigation of individuals with syndromic obesity, the possibility that the etiology of the syndromic condition is independent of obesity should be considered. The accurate genetic diagnosis impacts medical management, treatment, and prognosis, and allows proper genetic counseling.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Alexander Augusto de Lima Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory (LIM/25), Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
- Genetics Unit of Instituto da Criança, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil.
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5
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Abbas G, Vyas R, Noble JC, Lin B, Lane RP. Transformation of an olfactory placode-derived cell into one with stem cell characteristics by disrupting epigenetic barriers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592460. [PMID: 38746208 PMCID: PMC11092772 DOI: 10.1101/2024.05.03.592460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The mammalian olfactory neuronal lineage is regenerative, and accordingly, maintains a population of pluripotent cells that replenish olfactory sensory neurons and other olfactory cell types during the life of the animal. Moreover, in response to acute injury, the early transit amplifying cells along the olfactory sensory neuronal lineage are able to de-differentiate to shift resources in support of tissue restoration. In order to further explore plasticity of various cellular stages along the olfactory sensory neuronal lineage, we challenged the epigenetic stability of two olfactory placode-derived cell lines that model immature olfactory sensory neuronal stages. We found that perturbation of the Ehmt2 chromatin modifier transformed the growth properties, morphology, and gene expression profiles towards states with several stem cell characteristics. This transformation was dependent on continued expression of the large T-antigen, and was enhanced by Sox2 over-expression. These findings may provide momentum for exploring inherent cellular plasticity within early cell types of the olfactory lineage, as well as potentially add to our knowledge of cellular reprogramming. SUMMARY STATEMENT Discovering how epigenetic modifications influence olfactory neuronal lineage plasticity offers insights into regenerative potential and cellular reprogramming.
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6
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Koryakov DE. Diversity and functional specialization of H3K9-specific histone methyltransferases. Bioessays 2024; 46:e2300163. [PMID: 38058121 DOI: 10.1002/bies.202300163] [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: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact with one another. Thus arises a complex system of interchangeability, "division of labor," and contacts with each other and with diverse proteins. Histone methyltransferases specialize in the number of methyl groups that they attach and have different intracellular localizations as well as different distributions on chromosomes. Each also shows distinct binding to different types of sequences and has a specific set of nonhistone substrates.
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Affiliation(s)
- Dmitry E Koryakov
- Lab of Molecular Cytogenetics, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
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7
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Porter RS, Nagai M, An S, Gavilan MC, Murata-Nakamura Y, Bonefas KM, Zhou B, Dionne O, Manuel JM, St-Germain J, Browning L, Laurent B, Cho US, Iwase S. A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563357. [PMID: 37904995 PMCID: PMC10614952 DOI: 10.1101/2023.10.20.563357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A -n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.
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8
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Vini R, Lekshmi A, Ravindran S, Thulaseedharan JV, Sujathan K, Rajavelu A, Sreeja S. 27-Hydroxycholesterol represses G9a expression via oestrogen receptor alpha in breast cancer. J Cell Mol Med 2023; 27:2744-2755. [PMID: 37614064 PMCID: PMC10494299 DOI: 10.1111/jcmm.17882] [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: 11/16/2022] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
27-hydroxycholesterol (27-HC) is a cholesterol metabolite and the first discovered endogenous selective estrogen receptor modulator (SERM) that has been shown to have proliferative and metastatic activity in breast cancer. However, whether 27-HC metabolite modulates the epigenetic signatures in breast cancer and its progression remains unclear. The current study, reports that 27-HC represses the expression of euchromatic histone lysine methyltransferase G9a, further reducing di-methylation at H3K9 in a subset of genes. We also observed reduced occupancy of ERα at the G9a promoter, indicating that 27-HC negatively regulates the ERα occupancy on the G9a promoter and functions as a transcriptional repressor. Further, ChIP-sequencing for the H3K9me2 mark has demonstrated that 27-HC treatment reduces the H3K9me2 mark on subset of genes linked to cancer progression, proliferation, and metastasis. We observed upregulation of these genes following 27-HC treatment which further confirms the loss of methylation at these genes. Immunohistochemical analysis with breast cancer patient tissues indicated a positive correlation between G9a expression and CYP7B1, a key enzyme of 27-HC catabolism. Overall, this study reports that 27-HC represses G9a expression via ERα and reduces the levels of H3K9me2 on a subset of genes, including the genes that aid in breast tumorigenesis and invasion further, increasing its expression in the breast cancer cells.
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Affiliation(s)
- Ravindran Vini
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology (RGCB)ThiruvananthapuramIndia
- Research CentreUniversity of KeralaThiruvananthapuramIndia
| | - Asha Lekshmi
- Laboratory of Cytogenetics and Molecular DiagnosticsDivision of Cancer Research, Regional Cancer CentreThiruvananthapuramIndia
| | - Swathy Ravindran
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology (RGCB)ThiruvananthapuramIndia
| | - Jissa Vinoda Thulaseedharan
- Achutha Menon Centre for Health Science Studies (AMCHSS)Sree Chitra Tirunal Institute for Medical Sciences and TechnologyThiruvananthapuramIndia
| | - Kunjuraman Sujathan
- Laboratory of Cytogenetics and Molecular DiagnosticsDivision of Cancer Research, Regional Cancer CentreThiruvananthapuramIndia
- Health Software Technology Group, Centre for Development of Advanced Computing (CDAC)ThiruvananthapuramIndia
| | - Arumugam Rajavelu
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology (RGCB)ThiruvananthapuramIndia
- Department of Biotechnology, Bhupat & Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiIndia
| | - Sreeharshan Sreeja
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology (RGCB)ThiruvananthapuramIndia
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9
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Uriostegui-Arcos M, Mick ST, Shi Z, Rahman R, Fiszbein A. Splicing activates transcription from weak promoters upstream of alternative exons. Nat Commun 2023; 14:3435. [PMID: 37301863 PMCID: PMC10256964 DOI: 10.1038/s41467-023-39200-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Transcription and splicing are intrinsically coupled. Alternative splicing of internal exons can fine-tune gene expression through a recently described phenomenon called exon-mediated activation of transcription starts (EMATS). However, the association of this phenomenon with human diseases remains unknown. Here, we develop a strategy to activate gene expression through EMATS and demonstrate its potential for treatment of genetic diseases caused by loss of expression of essential genes. We first identified a catalog of human EMATS genes and provide a list of their pathological variants. To test if EMATS can be used to activate gene expression, we constructed stable cell lines expressing a splicing reporter based on the alternative splicing of motor neuron 2 (SMN2) gene. Using small molecules and antisense oligonucleotides (ASOs) currently used for treatment of spinal muscular atrophy, we demonstrated that increase of inclusion of alternative exons can trigger an activation of gene expression up to 45-fold by enhancing transcription in EMATS-like genes. We observed the strongest effects in genes under the regulation of weak human promoters located proximal to highly included skipped exons.
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Affiliation(s)
| | - Steven T Mick
- Biology Department, Boston University, Boston, 02215, USA
| | - Zhuo Shi
- Biology Department, Massachusetts Institute of Technology, Cambridge, 02139, USA
| | - Rufuto Rahman
- Biology Department, Boston University, Boston, 02215, USA
| | - Ana Fiszbein
- Biology Department, Boston University, Boston, 02215, USA.
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10
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Marasco LE, Kornblihtt AR. The physiology of alternative splicing. Nat Rev Mol Cell Biol 2023; 24:242-254. [PMID: 36229538 DOI: 10.1038/s41580-022-00545-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
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11
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Agosto LM, Mallory MJ, Ferretti MB, Blake D, Krick KS, Gazzara MR, Garcia BA, Lynch KW. Alternative splicing of HDAC7 regulates its interaction with 14-3-3 proteins to alter histone marks and target gene expression. Cell Rep 2023; 42:112273. [PMID: 36933216 PMCID: PMC10113009 DOI: 10.1016/j.celrep.2023.112273] [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: 08/31/2022] [Revised: 01/28/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Chromatin regulation and alternative splicing are both critical mechanisms guiding gene expression. Studies have demonstrated that histone modifications can influence alternative splicing decisions, but less is known about how alternative splicing may impact chromatin. Here, we demonstrate that several genes encoding histone-modifying enzymes are alternatively spliced downstream of T cell signaling pathways, including HDAC7, a gene previously implicated in controlling gene expression and differentiation in T cells. Using CRISPR-Cas9 gene editing and cDNA expression, we show that differential inclusion of HDAC7 exon 9 controls the interaction of HDAC7 with protein chaperones, resulting in changes to histone modifications and gene expression. Notably, the long isoform, which is induced by the RNA-binding protein CELF2, promotes expression of several critical T cell surface proteins including CD3, CD28, and CD69. Thus, we demonstrate that alternative splicing of HDAC7 has a global impact on histone modification and gene expression that contributes to T cell development.
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Affiliation(s)
- Laura M Agosto
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael J Mallory
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Max B Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Davia Blake
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keegan S Krick
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Genomic and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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Yang H, Chen Z, Gao W. EHMT2 affects microglia polarization and aggravates neuronal damage and inflammatory response via regulating HMOX1. Transl Neurosci 2023; 14:20220276. [PMID: 37529171 PMCID: PMC10388136 DOI: 10.1515/tnsci-2022-0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 08/03/2023] Open
Abstract
Objective This research was designed to ascertain the function of euchromatic histone lysine methyltransferase 2 (EHMT2) in ischemic stroke-induced neuronal damage and inflammatory response and its regulatory mechanism. Methods Mouse microglia (BV-2 cells) were induced by oxygen glucose deprivation/reoxygenation (OGD/R) to establish a cellular model, and then co-cultured with HT22 hippocampal neurons. After that, HT22 cell viability and apoptosis were evaluated, followed by the measurement of apoptosis-related factors (B-cell lymphoma-2, Bcl-2 associated X, and cleaved-Caspase 3). Meanwhile, the expression of inducible nitric oxide synthase (M1 microglia polarization marker) and arginase 1 (M2 microglia polarization marker) in BV-2 cells was detected, as well as the levels of inflammatory factors (tumor necrosis factor-α, interleukin [IL]-6, IL-10, IL-1β, and IL-4). Additionally, the expression of EHMT2 and heme oxygenase 1 (HMOX1) in BV-2 cells was assessed by quantitative reverse transcription polymerase chain reaction and western blot, and the binding between EHMT2 and HMOX1 was predicted and verified. Results OGD/R treatment led to decreased cell viability and increased cell apoptosis in HT22 cells, and aggravated inflammatory response in BV-2 cells. In OGD/R-induced BV-2 cells, EHMT2 and HMOX1 were increasingly expressed, and knockdown of EHMT2 or HMOX1 in BV-2 cells could inhibit neuronal damage and inflammatory response. Moreover, EHMT2 promoted HMOX1 transcription level by histone methylation. Conclusion Collected evidence showed that down-regulation of EHMT2 relieved neuronal damage and inflammatory response by inhibiting HMOX1 expression.
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Affiliation(s)
- Huaitao Yang
- Department of Neurosurgery, Jingzhou Hospital Affiliated to Yangtze University, No. 26, Chuyuan Ave, Jingzhou District, Jingzhou, Hubei 434020, P.R. China
| | - Zhifang Chen
- Department of Obstetrics and Gynecology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Wenhong Gao
- Department of Neurosurgery, Jingzhou Hospital Affiliated to Yangtze University, No. 26, Chuyuan Ave, Jingzhou District, Jingzhou, Hubei 434020, P.R. China
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14
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Levinsky AJ, McEdwards G, Sethna N, Currie MA. Targets of histone H3 lysine 9 methyltransferases. Front Cell Dev Biol 2022; 10:1026406. [PMID: 36568972 PMCID: PMC9768651 DOI: 10.3389/fcell.2022.1026406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Histone H3 lysine 9 di- and trimethylation are well-established marks of constitutively silenced heterochromatin domains found at repetitive DNA elements including pericentromeres, telomeres, and transposons. Loss of heterochromatin at these sites causes genomic instability in the form of aberrant DNA repair, chromosome segregation defects, replication stress, and transposition. H3K9 di- and trimethylation also regulate cell type-specific gene expression during development and form a barrier to cellular reprogramming. However, the role of H3K9 methyltransferases extends beyond histone methylation. There is a growing list of non-histone targets of H3K9 methyltransferases including transcription factors, steroid hormone receptors, histone modifying enzymes, and other chromatin regulatory proteins. Additionally, two classes of H3K9 methyltransferases modulate their own function through automethylation. Here we summarize the structure and function of mammalian H3K9 methyltransferases, their roles in genome regulation and constitutive heterochromatin, as well as the current repertoire of non-histone methylation targets including cases of automethylation.
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Affiliation(s)
- Aidan J. Levinsky
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Gregor McEdwards
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nasha Sethna
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Mark A. Currie
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada,*Correspondence: Mark A. Currie,
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15
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The RNA helicase DDX5 cooperates with EHMT2 to sustain alveolar rhabdomyosarcoma growth. Cell Rep 2022; 40:111267. [PMID: 36044855 DOI: 10.1016/j.celrep.2022.111267] [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: 05/05/2021] [Revised: 06/14/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood characterized by the inability to exit the proliferative myoblast-like stage. The alveolar fusion positive subtype (FP-RMS) is the most aggressive and is mainly caused by the expression of PAX3/7-FOXO1 oncoproteins, which are challenging pharmacological targets. Here, we show that the DEAD box RNA helicase 5 (DDX5) is overexpressed in alveolar RMS cells and that its depletion and pharmacological inhibition decrease FP-RMS viability and slow tumor growth in xenograft models. Mechanistically, we provide evidence that DDX5 functions upstream of the EHMT2/AKT survival signaling pathway, by directly interacting with EHMT2 mRNA, modulating its stability and consequent protein expression. We show that EHMT2 in turns regulates PAX3-FOXO1 activity in a methylation-dependent manner, thus sustaining FP-RMS myoblastic state. Together, our findings identify another survival-promoting loop in FP-RMS and highlight DDX5 as a potential therapeutic target to arrest RMS growth.
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16
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Fan M, Shi H, Yao H, Wang W, Zhang Y, Jiang C, Lin R. Glutamate regulates gliosis of BMSCs to promote ENS regeneration through α-KG and H3K9/H3K27 demethylation. Stem Cell Res Ther 2022; 13:255. [PMID: 35715822 PMCID: PMC9205030 DOI: 10.1186/s13287-022-02936-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background There is a lack of effective therapies for enteric nervous system (ENS) injury. Our previous study showed that transplanted bone marrow-derived mesenchymal stem cells (BMSCs) play a “glia-like cells” role in initiating ENS regeneration in denervated mice. Cellular energy metabolism is an important factor in maintaining the biological characteristics of stem cells. However, how cellular energy metabolism regulates the fate of BMSCs in the ENS-injured microenvironment is unclear. Methods The biological characteristics, energy metabolism, and histone methylation levels of BMSCs following ENS injury were determined. Then, glutamate dehydrogenase 1 (Glud1) which catalyzes the oxidative deamination of glutamate to α-KG was overexpressed (OE) in BMSCs. Further, OE-Glud1 BMSCs were targeted–transplanted into the ENS injury site of denervated mice to determine their effects on ENS regeneration. Results In vitro, in the ENS-injured high-glutamate microenvironment, the ratio of α-ketoglutarate (α-KG) to succinate (P < 0.05), the histone demethylation level (P < 0.05), the protein expression of glial cell markers (P < 0.05), and the gene expression of Glud1 (P < 0.05) were significantly increased. And the binding of H3K9me3 to the GFAP, S100B, and GDNF promoter was enhanced (P < 0.05). Moreover, α-KG treatment increased the monomethylation and decreased the trimethylation on H3K9 (P < 0.01) and H3K27 (P < 0.05) in BMSCs and significantly upregulated the protein expression of glial cell markers (P < 0.01), which was reversed by the α-KG competitive inhibitor D-2-hydroxyglutarate (P < 0.05). Besides, overexpression of Glud1 in BMSCs exhibited increases in monomethylation and decreases in trimethylation on H3K9 (P < 0.05) and H3K27 (P < 0.05), and upregulated protein expression of glial cell markers (P < 0.01). In vivo, BMSCs overexpressing Glud1 had a strong promotion effect on ENS regeneration in denervated mice through H3K9/H3K27 demethylation (P < 0.05), and upregulating the expression of glial cell protein (P < 0.05). Conclusions BMSCs overexpressing Glud1 promote the expression of glial cell markers and ENS remodeling in denervated mice through regulating intracellular α-KG and H3K9/H3K27 demethylation. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02936-7.
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Affiliation(s)
- Mengke Fan
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Huiying Shi
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hailing Yao
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weijun Wang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yurui Zhang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chen Jiang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Rong Lin
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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17
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Marasco LE, Dujardin G, Sousa-Luís R, Liu YH, Stigliano JN, Nomakuchi T, Proudfoot NJ, Krainer AR, Kornblihtt AR. Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell 2022; 185:2057-2070.e15. [PMID: 35688133 DOI: 10.1016/j.cell.2022.04.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/17/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022]
Abstract
Spinal muscular atrophy (SMA) is a motor-neuron disease caused by mutations of the SMN1 gene. The human paralog SMN2, whose exon 7 (E7) is predominantly skipped, cannot compensate for the lack of SMN1. Nusinersen is an antisense oligonucleotide (ASO) that upregulates E7 inclusion and SMN protein levels by displacing the splicing repressors hnRNPA1/A2 from their target site in intron 7. We show that by promoting transcriptional elongation, the histone deacetylase inhibitor VPA cooperates with a nusinersen-like ASO to promote E7 inclusion. Surprisingly, the ASO promotes the deployment of the silencing histone mark H3K9me2 on the SMN2 gene, creating a roadblock to RNA polymerase II elongation that inhibits E7 inclusion. By removing the roadblock, VPA counteracts the chromatin effects of the ASO, resulting in higher E7 inclusion without large pleiotropic effects. Combined administration of the nusinersen-like ASO and VPA in SMA mice strongly synergizes SMN expression, growth, survival, and neuromuscular function.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Gwendal Dujardin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Rui Sousa-Luís
- Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jose N Stigliano
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina.
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18
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol 2022; 23:623-640. [PMID: 35562425 PMCID: PMC9099300 DOI: 10.1038/s41580-022-00483-w] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/14/2022]
Abstract
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, G9A and G9A-like protein (GLP) — and the ‘readers’ of H3K9me2 or H3K9me3 are highly conserved and show considerable redundancy. Despite their redundancy, genetic ablation or mistargeting of an individual H3K9 methyltransferase can correlate with impaired cell differentiation, loss of tissue identity, premature aging and/or cancer. In this Review, we discuss recent advances in understanding the roles of the known H3K9-specific HMTs in ensuring transcriptional homeostasis during tissue differentiation in mammals. We examine the effects of H3K9-methylation-dependent gene repression in haematopoiesis, muscle differentiation and neurogenesis in mammals, and compare them with mechanistic insights obtained from the study of model organisms, notably Caenorhabditis elegans and Drosophila melanogaster. In all these organisms, H3K9-specific HMTs have both unique and redundant roles that ensure the maintenance of tissue integrity by restricting the binding of transcription factors to lineage-specific promoters and enhancer elements. Histone H3 Lys9 (H3K9)-methylated heterochromatin ensures transcriptional silencing of repetitive elements and genes, and its deregulation leads to impaired cell and tissue identity, premature aging and cancer. Recent studies in mammals clarified the roles H3K9-specific histone methyltransferases in ensuring transcriptional homeostasis during tissue differentiation.
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19
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Nothof SA, Magdinier F, Van-Gils J. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication. Genes (Basel) 2022; 13:genes13040639. [PMID: 35456445 PMCID: PMC9029427 DOI: 10.3390/genes13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Chromatin structure is an essential regulator of gene expression. Its state of compaction contributes to the regulation of genetic programs, in particular during differentiation. Epigenetic processes, which include post-translational modifications of histones, DNA methylation and implication of non-coding RNA, are powerful regulators of gene expression. Neurogenesis and neuronal differentiation are spatio-temporally regulated events that allow the formation of the central nervous system components. Here, we review the chromatin structure and post-translational histone modifications associated with neuronal differentiation. Studying the impact of histone modifications on neuronal differentiation improves our understanding of the pathophysiological mechanisms of chromatinopathies and opens up new therapeutic avenues. In addition, we will discuss techniques for the analysis of histone modifications on a genome-wide scale and the pathologies associated with the dysregulation of the epigenetic machinery.
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Affiliation(s)
- Sophie A. Nothof
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Frédérique Magdinier
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Julien Van-Gils
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
- Reference Center AD SOOR, AnDDI-RARE, Inserm U 1211, Medical Genetics Department, Bordeaux University, Center Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France
- Correspondence:
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20
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Baker M, Petasny M, Taqatqa N, Bentata M, Kay G, Engal E, Nevo Y, Siam A, Dahan S, Salton M. KDM3A regulates alternative splicing of cell-cycle genes following DNA damage. RNA (NEW YORK, N.Y.) 2021; 27:1353-1362. [PMID: 34321328 PMCID: PMC8522690 DOI: 10.1261/rna.078796.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Changes in the cellular environment result in chromatin structure alteration, which in turn regulates gene expression. To learn about the effect of the cellular environment on the transcriptome, we studied the H3K9 demethylase KDM3A. Using RNA-seq, we found that KDM3A regulates the transcription and alternative splicing of genes associated with cell cycle and DNA damage. We showed that KDM3A undergoes phosphorylation by PKA at serine 265 following DNA damage, and that the phosphorylation is important for proper cell-cycle regulation. We demonstrated that SAT1 alternative splicing, regulated by KDM3A, plays a role in cell-cycle regulation. Furthermore we found that KDM3A's demethylase activity is not needed for SAT1 alternative splicing regulation. In addition, we identified KDM3A's protein partner ARID1A, the SWI/SNF subunit, and SRSF3 as regulators of SAT1 alternative splicing and showed that KDM3A is essential for SRSF3 binding to SAT1 pre-mRNA. These results suggest that KDM3A serves as a sensor of the environment and an adaptor for splicing factor binding. Our work reveals chromatin sensing of the environment in the regulation of alternative splicing.
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Affiliation(s)
- Mai Baker
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mayra Petasny
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Nadeen Taqatqa
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mercedes Bentata
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Eden Engal
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Yuval Nevo
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ahmad Siam
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Sara Dahan
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
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21
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Poulard C, Noureddine LM, Pruvost L, Le Romancer M. Structure, Activity, and Function of the Protein Lysine Methyltransferase G9a. Life (Basel) 2021; 11:life11101082. [PMID: 34685453 PMCID: PMC8541646 DOI: 10.3390/life11101082] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/17/2022] Open
Abstract
G9a is a lysine methyltransferase catalyzing the majority of histone H3 mono- and dimethylation at Lys-9 (H3K9), responsible for transcriptional repression events in euchromatin. G9a has been shown to methylate various lysine residues of non-histone proteins and acts as a coactivator for several transcription factors. This review will provide an overview of the structural features of G9a and its paralog called G9a-like protein (GLP), explore the biochemical features of G9a, and describe its post-translational modifications and the specific inhibitors available to target its catalytic activity. Aside from its role on histone substrates, the review will highlight some non-histone targets of G9a, in order gain insight into their role in specific cellular mechanisms. Indeed, G9a was largely described to be involved in embryonic development, hypoxia, and DNA repair. Finally, the involvement of G9a in cancer biology will be presented.
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Affiliation(s)
- Coralie Poulard
- Cancer Research Cancer of Lyon, Université de Lyon, F-69000 Lyon, France; (L.M.N.); (L.P.); (M.L.R.)
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Correspondence:
| | - Lara M. Noureddine
- Cancer Research Cancer of Lyon, Université de Lyon, F-69000 Lyon, France; (L.M.N.); (L.P.); (M.L.R.)
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences, Lebanese University, Hadat-Beirut 90565, Lebanon
| | - Ludivine Pruvost
- Cancer Research Cancer of Lyon, Université de Lyon, F-69000 Lyon, France; (L.M.N.); (L.P.); (M.L.R.)
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Muriel Le Romancer
- Cancer Research Cancer of Lyon, Université de Lyon, F-69000 Lyon, France; (L.M.N.); (L.P.); (M.L.R.)
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
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22
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Li T, Li H, Li Y, Dong SA, Yi M, Zhang QX, Feng B, Yang L, Shi FD, Yang CS. Multi-Level Analyses of Genome-Wide Association Study to Reveal Significant Risk Genes and Pathways in Neuromyelitis Optica Spectrum Disorder. Front Genet 2021; 12:690537. [PMID: 34367251 PMCID: PMC8335167 DOI: 10.3389/fgene.2021.690537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Neuromyelitis optica spectrum disorder (NMOSD) is an inflammatory disease of the central nervous system and it is understandable that environmental and genetic factors underlie the etiology of NMOSD. However, the susceptibility genes and associated pathways of NMOSD patients who are AQP4-Ab positive and negative have not been elucidated. Methods Secondary analysis from a NMOSD Genome-wide association study (GWAS) dataset originally published in 2018 (215 NMOSD cases and 1244 controls) was conducted to identify potential susceptibility genes and associated pathways in AQP4-positive and negative NMOSD patients, respectively (132 AQP4-positive and 83 AQP4-negative). Results In AQP4-positive NMOSD cases, five shared risk genes were obtained at chromosome 6 in AQP4-positive NMOSD cases by using more stringent p-Values in both methods (p < 0.05/16,532), comprising CFB, EHMT2, HLA-DQA1, MSH5, and SLC44A4. Fifty potential susceptibility gene sets were determined and 12 significant KEGG pathways were identified. Sixty-seven biological process pathways, 32 cellular-component pathways, and 29 molecular-function pathways with a p-Value of <0.05 were obtained from the GO annotations of the 128 pathways identified. In the AQP4 negative NMOSD group, no significant genes were obtained by using more stringent p-Values in both methods (p < 0.05/16,485). The 22 potential susceptibility gene sets were determined. There were no shared potential susceptibility genes between the AQP4-positive and negative groups, furthermore, four significant KEGG pathways were also identified. Of the GO annotations of the 165 pathways identified, 99 biological process pathways, 37 cellular-component pathways, and 29 molecular-function pathways with a p-Value of <0.05 were obtained. Conclusion The potential molecular mechanism underlying NMOSD may be related to proteins encoded by these novel genes in complements, antigen presentation, and immune regulation. The new results may represent an improved comprehension of the genetic and molecular mechanisms underlying NMOSD.
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Affiliation(s)
- Ting Li
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - He Li
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Yue Li
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Shu-An Dong
- Department of Anesthesiology, Tianjin Hospital of Integrated Traditional Chinese and Western Medicine, Tianjin, China
| | - Ming Yi
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Qiu-Xia Zhang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Feng
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Li Yang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Fu-Dong Shi
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, United States
| | - Chun-Sheng Yang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
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23
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Batsché E, Yi J, Mauger O, Kornobis E, Hopkins B, Hanmer-Lloyd C, Muchardt C. CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms. Nucleic Acids Res 2021; 49:6213-6237. [PMID: 34086943 PMCID: PMC8216461 DOI: 10.1093/nar/gkab437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (meDNA) is a modulator of alternative splicing, and splicing perturbations are involved in tumorigenesis nearly as frequently as DNA mutations. However, the impact of meDNA on tumorigenesis via splicing-mediated mechanisms has not been thoroughly explored. Here, we found that HCT116 colon carcinoma cells inactivated for the DNA methylases DNMT1/3b undergo a partial epithelial to mesenchymal transition associated with increased CD44 variant exon skipping. These skipping events are directly mediated by the loss of intragenic meDNA and the chromatin factors MBD1/2/3 and HP1γ and are also linked to phosphorylation changes in elongating RNA polymerase II. The role of meDNA in alternative splicing was confirmed by using the dCas9/DNMT3b tool. We further tested whether the meDNA level could have predictive value in the MCF10A model for breast cancer progression and in patients with acute lymphoblastic leukemia (B ALL). We found that a small number of differentially spliced genes, mostly involved in splicing and signal transduction, are correlated with the local modulation of meDNA. Our observations suggest that, although DNA methylation has multiple avenues to affect alternative splicing, its indirect effect may also be mediated through alternative splicing isoforms of these meDNA sensors.
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Affiliation(s)
- Eric Batsché
- Epigenetics and RNA metabolism in human diseases. CNRS UMR8256 - Biological Adaptation and Ageing. Institut de Biologie Paris-Seine. Sciences Sorbonne Université. 7–9 Quai Saint Bernard, 75005 Paris, France
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
| | - Jia Yi
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Ecole Doctorale Complexite du Vivant (ED515), Sorbonne Université, Paris, France
| | - Oriane Mauger
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Ecole Doctorale Complexite du Vivant (ED515), Sorbonne Université, Paris, France
| | - Etienne Kornobis
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
| | - Benjamin Hopkins
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Keele University, Keele, Staffordshire ST5 5BG UK
| | - Charlotte Hanmer-Lloyd
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Keele University, Keele, Staffordshire ST5 5BG UK
| | - Christian Muchardt
- Epigenetics and RNA metabolism in human diseases. CNRS UMR8256 - Biological Adaptation and Ageing. Institut de Biologie Paris-Seine. Sciences Sorbonne Université. 7–9 Quai Saint Bernard, 75005 Paris, France
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
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24
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Li D, McIntosh CS, Mastaglia FL, Wilton SD, Aung-Htut MT. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener 2021; 10:16. [PMID: 34016162 PMCID: PMC8136212 DOI: 10.1186/s40035-021-00240-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is a fundamental step in eukaryotic gene expression that systematically removes non-coding regions (introns) and ligates coding regions (exons) into a continuous message (mature mRNA). This process is highly regulated and can be highly flexible through a process known as alternative splicing, which allows for several transcripts to arise from a single gene, thereby greatly increasing genetic plasticity and the diversity of proteome. Alternative splicing is particularly prevalent in neuronal cells, where the splicing patterns are continuously changing to maintain cellular homeostasis and promote neurogenesis, migration and synaptic function. The continuous changes in splicing patterns and a high demand on many cis- and trans-splicing factors contribute to the susceptibility of neuronal tissues to splicing defects. The resultant neurodegenerative diseases are a large group of disorders defined by a gradual loss of neurons and a progressive impairment in neuronal function. Several of the most common neurodegenerative diseases involve some form of splicing defect(s), such as Alzheimer's disease, Parkinson's disease and spinal muscular atrophy. Our growing understanding of RNA splicing has led to the explosion of research in the field of splice-switching antisense oligonucleotide therapeutics. Here we review our current understanding of the effects alternative splicing has on neuronal differentiation, neuronal migration, synaptic maturation and regulation, as well as the impact on neurodegenerative diseases. We will also review the current landscape of splice-switching antisense oligonucleotides as a therapeutic strategy for a number of common neurodegenerative disorders.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Craig Stewart McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Frank Louis Mastaglia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Steve Donald Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia. .,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia.
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25
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Wilson C, Giono LE, Rozés-Salvador V, Fiszbein A, Kornblihtt AR, Cáceres A. The Histone Methyltransferase G9a Controls Axon Growth by Targeting the RhoA Signaling Pathway. Cell Rep 2021; 31:107639. [PMID: 32402271 DOI: 10.1016/j.celrep.2020.107639] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/18/2020] [Accepted: 04/21/2020] [Indexed: 12/19/2022] Open
Abstract
The generation of axonal and dendritic domains is critical for brain circuitry assembly and physiology. Negative players, such as the RhoA-Rho coiled-coil-associated protein kinase (ROCK) signaling pathway, restrain axon development and polarization. Surprisingly, the genetic control of neuronal polarity has remained largely unexplored. Here, we report that, in primary cultured neurons, expression of the histone methyltransferase G9a and nuclear translocation of its major splicing isoform (G9a/E10+) peak at the time of axon formation. RNAi suppression of G9a/E10+ or pharmacological blockade of G9a constrains neuronal migration, axon initiation, and the establishment of neuronal polarity in situ and in vitro. Inhibition of G9a function upregulates RhoA-ROCK activity by increasing the expression of Lfc, a guanine nucleotide exchange factor (GEF) for RhoA. Together, these results identify G9a as a player in neuronal polarization.
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Affiliation(s)
- Carlos Wilson
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC-CONICET-UNC) Friuli 2434, 5016 Córdoba, Argentina; Universidad Nacional de Córdoba (UNC), Av. Haya de la Torre s/n, 5000 Córdoba, Argentina; Centro de Investigación en Medicina Traslacional "Severo R Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Av. Friuli 2786, 5016 Córdoba, Argentina
| | - Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Victoria Rozés-Salvador
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC-CONICET-UNC) Friuli 2434, 5016 Córdoba, Argentina; Universidad Nacional de Córdoba (UNC), Av. Haya de la Torre s/n, 5000 Córdoba, Argentina
| | - Ana Fiszbein
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alfredo Cáceres
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC-CONICET-UNC) Friuli 2434, 5016 Córdoba, Argentina; Universidad Nacional de Córdoba (UNC), Av. Haya de la Torre s/n, 5000 Córdoba, Argentina; Centro de Investigación en Medicina Traslacional "Severo R Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Av. Friuli 2786, 5016 Córdoba, Argentina.
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26
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Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
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27
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Jan S, Dar MI, Wani R, Sandey J, Mushtaq I, Lateef S, Syed SH. Targeting EHMT2/ G9a for cancer therapy: Progress and perspective. Eur J Pharmacol 2020; 893:173827. [PMID: 33347828 DOI: 10.1016/j.ejphar.2020.173827] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
Euchromatic histone lysine methyltransferase-2, also known as G9a, is a ubiquitously expressed SET domain-containing histone lysine methyltransferase linked with both facultative and constitutive heterochromatin formation and transcriptional repression. It is an essential developmental gene and reported to play role in embryonic development, establishment of proviral silencing in ES cells, tumor cell growth, metastasis, T-cell immune response, cocaine induced neural plasticity and cognition and adaptive behavior. It is mainly responsible for carrying out mono, di and tri methylation of histone H3K9 in euchromatin. G9a levels are elevated in many cancers and its selective inhibition is known to reduce the cell growth and induce autophagy, apoptosis and senescence. We carried out a thorough search of online literature databases including Pubmed, Scopus, Journal websites, Clinical trials etc to gather the maximum possible information related to the G9a. The main messages from the cited papers are presented in a systematic manner. Chemical structures were drawn by Chemdraw software. In this review, we shed light on current understanding of structure and biological activity of G9a, the molecular events directing its targeting to genomic regions and its post-translational modification. Finally, we discuss the current strategies to target G9a in different cancers and evaluate the available compounds and agents used to inhibit G9a functions. The review provides the present status and future directions of research in targeting G9a and provides the basis to persuade the development of novel strategies to target G9a -related effects in cancer cells.
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Affiliation(s)
- Suraya Jan
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohd Ishaq Dar
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rubiada Wani
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jagjeet Sandey
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Iqra Mushtaq
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sammar Lateef
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sajad Hussain Syed
- CSIR, Indian Institute of Integrative Medicine, Sanatnagar, 190005, Srinagar, Kashmir, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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28
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Wilson C, Cáceres A. New insights on epigenetic mechanisms supporting axonal development: histone marks and miRNAs. FEBS J 2020; 288:6353-6364. [PMID: 33332753 DOI: 10.1111/febs.15673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/21/2020] [Accepted: 12/15/2020] [Indexed: 11/27/2022]
Abstract
Mechanisms supporting axon growth and the establishment of neuronal polarity have remained largely disconnected from their genetic and epigenetic fundamentals. Recently, post-transcriptional modifications of histones involved in chromatin folding and transcription, and microRNAs controlling translation have emerged as regulators of axonal specification, growth, and guidance. In this article, we review novel evidence supporting the concept that epigenetic mechanisms work at both transcriptional and post-transcriptional levels to shape axons. We also discuss the role of splicing on axonal growth, as one of the most (if not the most) powerful post-transcriptional mechanism to diversify genetic information. Overall, we think exploring the gap between epigenetics and axonal growth raises new questions and perspectives to the development of axons in physiological and pathological contexts.
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Affiliation(s)
- Carlos Wilson
- Centro de Investigación en Medicina Traslacional "Severo R Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Córdoba, Argentina.,Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC-CONICET-UNC), Córdoba, Argentina.,Universidad Nacional de Córdoba (UNC), Argentina
| | - Alfredo Cáceres
- Centro de Investigación en Medicina Traslacional "Severo R Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Córdoba, Argentina
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29
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Fiszbein A, Krick KS, Begg BE, Burge CB. Exon-Mediated Activation of Transcription Starts. Cell 2019; 179:1551-1565.e17. [PMID: 31787377 DOI: 10.1016/j.cell.2019.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/20/2019] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
Abstract
The processing of RNA transcripts from mammalian genes occurs in proximity to their transcription. Here, we describe a phenomenon affecting thousands of genes that we call exon-mediated activation of transcription starts (EMATS), in which the splicing of internal exons impacts promoter choice and the expression level of the gene. We observed that evolutionary gain of internal exons is associated with gain of new transcription start sites (TSSs) nearby and increased gene expression. Inhibiting exon splicing reduced transcription from nearby promoters, and creation of new spliced exons activated transcription from cryptic promoters. The strongest effects occurred for weak promoters located proximal and upstream of efficiently spliced exons. Together, our findings support a model in which splicing recruits transcription machinery locally to influence TSS choice and identify exon gain, loss, and regulatory change as major contributors to the evolution of alternative promoters and gene expression in mammals.
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Affiliation(s)
- Ana Fiszbein
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Keegan S Krick
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Bridget E Begg
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
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30
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Neural progenitor cells mediated by H2A.Z.2 regulate microglial development via Cxcl14 in the embryonic brain. Proc Natl Acad Sci U S A 2019; 116:24122-24132. [PMID: 31712428 DOI: 10.1073/pnas.1913978116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Microglia, the resident immune cells of the central nervous system, play an important role in the brain. Microglia have a special spatiotemporal distribution during the development of the cerebral cortex. Neural progenitor cells (NPCs) are the main source of neural-specific cells in the early brain. It is unclear whether NPCs affect microglial development and what molecular mechanisms control early microglial localization. H2A.Z.2, a histone variant of H2A, has a key role in gene expression regulation, genomic stability, and chromatin remodeling, but its function in brain development is not fully understood. Here, we found that the specific deletion of H2A.Z.2 in neural progenitor cells led to an abnormal increase in microglia in the ventricular zone/subventricular zone (VZ/SVZ) of the embryonic cortex. Mechanistically, H2A.Z.2 regulated microglial development by incorporating G9a into the promoter region of Cxcl14 and promoted H3k9me2 modification to inhibit the transcription of Cxcl14 in neural progenitor cells. Meanwhile, we found that the deletion of H2A.Z.2 in microglia itself had no significant effect on microglial development in the early cerebral cortex. Our findings demonstrate a key role of H2A.Z.2 in neural progenitor cells in controlling microglial development and broaden our knowledge of 2 different types of cells that may affect each other through crosstalk in the central nervous system.
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31
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Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW. Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Genome Res 2019; 29:2046-2055. [PMID: 31727681 PMCID: PMC6886501 DOI: 10.1101/gr.248435.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 09/16/2019] [Indexed: 02/05/2023]
Abstract
Alternative pre-mRNA splicing has long been proposed to contribute greatly to proteome complexity. However, the extent to which mature mRNA isoforms are successfully translated into protein remains controversial. Here, we used high-throughput RNA sequencing and mass spectrometry (MS)–based proteomics to better evaluate the translation of alternatively spliced mRNAs. To increase proteome coverage and improve protein quantitation, we optimized cell fractionation and sample processing steps at both the protein and peptide level. Furthermore, we generated a custom peptide database trained on analysis of RNA-seq data with MAJIQ, an algorithm optimized to detect and quantify differential and unannotated splice junction usage. We matched tandem mass spectra acquired by data-dependent acquisition (DDA) against our custom RNA-seq based database, as well as SWISS-PROT and RefSeq databases to improve identification of splicing-derived proteoforms by 28% compared with use of the SWISS-PROT database alone. Altogether, we identified peptide evidence for 554 alternate proteoforms corresponding to 274 genes. Our increased depth and detection of proteins also allowed us to track changes in the transcriptome and proteome induced by T-cell stimulation, as well as fluctuations in protein subcellular localization. In sum, our data here confirm that use of generic databases in proteomic studies underestimates the number of spliced mRNA isoforms that are translated into protein and provides a workflow that improves isoform detection in large-scale proteomic experiments.
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Affiliation(s)
- Laura M Agosto
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Caleb M Radens
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Genetics and Epigenetics, Cell & Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josue Baeza
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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32
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Malekzadeh A, Leurs C, van Wieringen W, Steenwijk MD, Schoonheim MM, Amann M, Naegelin Y, Kuhle J, Killestein J, Teunissen CE. Plasma proteome in multiple sclerosis disease progression. Ann Clin Transl Neurol 2019; 6:1582-1594. [PMID: 31364818 PMCID: PMC7651845 DOI: 10.1002/acn3.771] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023] Open
Abstract
Background The pathophysiology of multiple sclerosis disease progression remains undetermined. The aim of this study was to identify differences in plasma proteome during different stages of MS disease progression. Methods We used a multiplex aptamer proteomics platform (Somalogic) for sensitive detection of 1129 proteins in plasma. MS patients were selected and categorized based on baseline and a 4‐year follow‐up EDSS (delta EDSS) scores; relapse‐onset (RO) slow progression (n = 31), RO with rapid progression (n = 29), primary progressive (n = 30), and healthy controls (n = 20). The relation of baseline plasma protein levels with delta EDSS and different MRI progression parameters were assessed using linear regression models. Results Regression analyses of plasma proteins with delta EDSS showed six significant associations. Strong associations were found for the proteins LGLAS8 (P = 7.64 × 10−5, q = 0.06), CCL3 (P = 0.0001, q = 0.06), and RGMA (P = 0.0005, q = 0.09). In addition, associations of plasma proteins were found with percentage brain volume for C3 (P = 2,08 × 10−9, q = 1,70 × 10−6), FGF9 (P = 3,42 × 10−9, q = 1,70 × 10−6), and EHMT2 (P = 0.0007, q = 0.01). Most of the significant markers were associated with cell‐cell and cell‐extracellular matrix adhesion, immune system communication, immune system activation, and complement pathways. Conclusions Our results revealed eight novel biomarkers related to clinical and radiological progression in MS. These results indicate that changes in immune system, complement pathway and ECM remodeling proteins contribute to MS progression and may therefore be further explored for use in prognosis of MS.
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Affiliation(s)
- Arjan Malekzadeh
- Department of Clinical Chemistry, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Cyra Leurs
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Wessel van Wieringen
- Department of Mathematics, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Martijn D Steenwijk
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, MS Center Amsterdam, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Menno M Schoonheim
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, MS Center Amsterdam, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Michael Amann
- Division of Diagnostic and Interventional Neuroradiology, Department of Radiology and Nuclear Medicine, University Hospital Basel, Basel, Switzerland.,Medical Image Analysis Center (MIAC AG), Basel, Switzerland
| | - Yvonne Naegelin
- Department of Biomedicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Jens Kuhle
- Department of Biomedicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Joep Killestein
- Department of Neurology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Department of Clinical Chemistry, Amsterdam University Medical Centre, Amsterdam, The Netherlands
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33
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Karl M, Sommer C, Gabriel CH, Hecklau K, Venzke M, Hennig AF, Radbruch A, Selbach M, Baumgrass R. Recruitment of Histone Methyltransferase Ehmt1 to Foxp3 TSDR Counteracts Differentiation of Induced Regulatory T Cells. J Mol Biol 2019; 431:3606-3625. [PMID: 31362003 DOI: 10.1016/j.jmb.2019.07.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022]
Abstract
Differentiation toward CD4+ regulatory T (Treg) cells is essentially dependent on an epigenetic program at Treg signature genes, which involves remodeling of the Treg-specific demethylated regions (TSDRs). In particular, the epigenetic status of the conserved non-coding sequence 2 of Foxp3 (Foxp3 TSDR) determines expression stability of the master transcription factor and thus Treg lineage identity. However, the molecular mechanisms controlling the epigenetic remodeling at TSDRs in Treg and conventional T cells are largely unknown. Using a combined approach of DNA pull-down and mass spectrometric analysis, we report a novel regulatory mechanism in which transcription factor Wiz recruits the histone methyltransferase Ehmt1 to Foxp3 TSDR. We show that both Wiz and Ehmt1 are crucial for shaping the region with the repressive histone modification H3K9me2 in conventional T cells. Consistently, knocking out either Ehmt1 or Wiz by CRISPR/Cas resulted in the loss of H3K9me2 and enhanced Foxp3 expression during iTreg differentiation. Moreover, the essential role of the Wiz-Ehmt1 interaction as observed at several TSDRs indicates a global function of Ehmt1 in the Treg differentiation program.
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Affiliation(s)
- Martin Karl
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Sommer
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christian H Gabriel
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Katharina Hecklau
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Melanie Venzke
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Anna Floriane Hennig
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Andreas Radbruch
- Cell Biology, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany; Charité-University Medicine, Charitéplatz 1, 10117 Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Ria Baumgrass
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany.
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34
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Abstract
The epigenetic control of gene expression could be affected by addition and/or removal of post-translational modifications such as phosphorylation, acetylation and methylation of histone proteins, as well as methylation of DNA (5-methylation on cytosines). Misregulation of these modifications is associated with altered gene expression, resulting in various disease conditions. G9a belongs to the protein lysine methyltransferases that specifically methylates the K9 residue of histone H3, leading to suppression of several tumor suppressor genes. In this review, G9a functions, role in various diseases, structural biology aspects for inhibitor design, structure-activity relationship among the reported inhibitors are discussed which could aid in the design and development of potent G9a inhibitors for cancer treatment in the future.
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35
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DDX5 plays essential transcriptional and post-transcriptional roles in the maintenance and function of spermatogonia. Nat Commun 2019; 10:2278. [PMID: 31123254 PMCID: PMC6533336 DOI: 10.1038/s41467-019-09972-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/02/2019] [Indexed: 02/07/2023] Open
Abstract
Mammalian spermatogenesis is sustained by mitotic germ cells with self-renewal potential known as undifferentiated spermatogonia. Maintenance of undifferentiated spermatogonia and spermatogenesis is dependent on tightly co-ordinated transcriptional and post-transcriptional mechanisms. The RNA helicase DDX5 is expressed by spermatogonia but roles in spermatogenesis are unexplored. Using an inducible knockout mouse model, we characterise an essential role for DDX5 in spermatogonial maintenance and show that Ddx5 is indispensable for male fertility. We demonstrate that DDX5 regulates appropriate splicing of key genes necessary for spermatogenesis. Moreover, DDX5 regulates expression of cell cycle genes in undifferentiated spermatogonia post-transcriptionally and is required for cell proliferation and survival. DDX5 can also act as a transcriptional co-activator and we demonstrate that DDX5 interacts with PLZF, a transcription factor required for germline maintenance, to co-regulate select target genes. Combined, our data reveal a critical multifunctional role for DDX5 in regulating gene expression programmes and activity of undifferentiated spermatogonia. Sustained sperm production is dependent on activity of undifferentiated spermatogonia. Here, the authors demonstrate an essential role for RNA helicase DDX5 in maintenance of spermatogonia in adults through control of gene transcription plus RNA processing and export.
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36
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Maslon MM, Braunschweig U, Aitken S, Mann AR, Kilanowski F, Hunter CJ, Blencowe BJ, Kornblihtt AR, Adams IR, Cáceres JF. A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes. EMBO J 2019; 38:embj.2018101244. [PMID: 30988016 PMCID: PMC6484407 DOI: 10.15252/embj.2018101244] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
The rate of RNA polymerase II (RNAPII) elongation has an important role in the control of alternative splicing (AS); however, the in vivo consequences of an altered elongation rate are unknown. Here, we generated mouse embryonic stem cells (ESCs) knocked in for a slow elongating form of RNAPII We show that a reduced transcriptional elongation rate results in early embryonic lethality in mice. Focusing on neuronal differentiation as a model, we observed that slow elongation impairs development of the neural lineage from ESCs, which is accompanied by changes in AS and in gene expression along this pathway. In particular, we found a crucial role for RNAPII elongation rate in transcription and splicing of long neuronal genes involved in synapse signaling. The impact of the kinetic coupling of RNAPII elongation rate with AS is greater in ESC-differentiated neurons than in pluripotent cells. Our results demonstrate the requirement for an appropriate transcriptional elongation rate to ensure proper gene expression and to regulate AS during development.
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Affiliation(s)
- Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ulrich Braunschweig
- Donnelly Centre, Department of Molecular Genetics University of Toronto, Toronto, ON, Canada
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Abigail R Mann
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Fiona Kilanowski
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Chris J Hunter
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Benjamin J Blencowe
- Donnelly Centre, Department of Molecular Genetics University of Toronto, Toronto, ON, Canada
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ian R Adams
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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37
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Abstract
Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Recent approaches are now providing more wide-ranging surveys of the extent of alternative splicing; some indicate that alternative splicing is less widespread than in other model eukaryotes, whereas others suggest levels comparable to those of previously studied groups. In many cases, apicomplexan alternative splicing events appear not to generate multiple alternative proteins but instead produce aberrant or noncoding transcripts. Nonetheless, appropriate regulation of alternative splicing is clearly essential in Plasmodium and Toxoplasma parasites, suggesting a biological role for at least some of the alternative splicing observed. Several studies have now disrupted conserved regulators of alternative splicing and demonstrated lethal effects in apicomplexans. This minireview discusses methods to accurately determine the extent of alternative splicing in Apicomplexa and discuss potential biological roles for this conserved process in a phylum of parasites with compact genomes.
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38
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Lipscombe D, Lopez Soto EJ. Alternative splicing of neuronal genes: new mechanisms and new therapies. Curr Opin Neurobiol 2019; 57:26-31. [PMID: 30703685 DOI: 10.1016/j.conb.2018.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 12/27/2018] [Indexed: 12/22/2022]
Abstract
Dynamic changes in alternative splicing during the life cycle of neurons support development and plasticity, and are implicated in disease pathology. Cell-specific alternative splicing programs coordinate exon selection across networks of functionally connected genes. In this opinion piece, we highlight recent publications that identify some of the molecular mechanisms-RNA and DNA binding proteins and epigenetic modifications-which direct cell-specific exon selection during pre-mRNA splicing. Aberrant splicing patterns are signature features of a growing number of diseases of the nervous system. Recent publications demonstrate the value of delineating basic mechanisms that dictate exon choice to inform the development of new therapeutic strategies that correct or compensate for damaging deficits in alternative splicing.
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Affiliation(s)
- Diane Lipscombe
- Robert J and Nancy D Carney Institute for Brain Science, Department of Neuroscience, Brown University, Providence, RI 02912, USA.
| | - Eduardo Javier Lopez Soto
- Robert J and Nancy D Carney Institute for Brain Science, Department of Neuroscience, Brown University, Providence, RI 02912, USA
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39
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Godoy Herz MA, Kornblihtt AR. Alternative Splicing and Transcription Elongation in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:309. [PMID: 30972082 PMCID: PMC6443983 DOI: 10.3389/fpls.2019.00309] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/26/2019] [Indexed: 05/19/2023]
Abstract
Alternative splicing and transcription elongation by RNA polymerase II (RNAPII) are two processes which are tightly connected. Splicing is a co-transcriptional process, and different experimental approaches show that splicing is coupled to transcription in Drosophila, yeast and mammals. However, little is known about coupling of transcription and alternative splicing in plants. The kinetic coupling explains how changes in RNAPII elongation rate influence alternative splicing choices. Recent work in Arabidopsis shows that expression of a dominant negative transcription elongation factor, TFIIS, enhances exon inclusion. Furthermore, the Arabidopsis transcription elongation complex has been recently described, providing new information about elongation factors that interact with elongating RNAPII. Light regulates alternative splicing in plants through a chloroplast retrograde signaling. We have recently shown that light promotes RNAPII elongation in the affected genes, while in darkness elongation is lower. These changes in transcription are consistent with elongation causing the observed changes in alternative splicing. Altogether, these findings provide evidence that coupling between transcription and alternative splicing is an important layer of gene expression regulation in plants.
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Affiliation(s)
- Micaela A. Godoy Herz
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Alberto R. Kornblihtt
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
- *Correspondence: Alberto R. Kornblihtt,
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40
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Su CH, D D, Tarn WY. Alternative Splicing in Neurogenesis and Brain Development. Front Mol Biosci 2018; 5:12. [PMID: 29484299 PMCID: PMC5816070 DOI: 10.3389/fmolb.2018.00012] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing of precursor mRNA is an important mechanism that increases transcriptomic and proteomic diversity and also post-transcriptionally regulates mRNA levels. Alternative splicing occurs at high frequency in brain tissues and contributes to every step of nervous system development, including cell-fate decisions, neuronal migration, axon guidance, and synaptogenesis. Genetic manipulation and RNA sequencing have provided insights into the molecular mechanisms underlying the effects of alternative splicing in stem cell self-renewal and neuronal fate specification. Timely expression and perhaps post-translational modification of neuron-specific splicing regulators play important roles in neuronal development. Alternative splicing of many key transcription regulators or epigenetic factors reprograms the transcriptome and hence contributes to stem cell fate determination. During neuronal differentiation, alternative splicing also modulates signaling activity, centriolar dynamics, and metabolic pathways. Moreover, alternative splicing impacts cortical lamination and neuronal development and function. In this review, we focus on recent progress toward understanding the contributions of alternative splicing to neurogenesis and brain development, which has shed light on how splicing defects may cause brain disorders and diseases.
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Affiliation(s)
- Chun-Hao Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Dhananjaya D
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
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41
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FIH Is an Oxygen Sensor in Ovarian Cancer for G9a/GLP-Driven Epigenetic Regulation of Metastasis-Related Genes. Cancer Res 2017; 78:1184-1199. [DOI: 10.1158/0008-5472.can-17-2506] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/01/2017] [Accepted: 12/15/2017] [Indexed: 11/16/2022]
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42
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Neuron-specific alternative splicing of transcriptional machineries: Implications for neurodevelopmental disorders. Mol Cell Neurosci 2017; 87:35-45. [PMID: 29254826 DOI: 10.1016/j.mcn.2017.10.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 02/07/2023] Open
Abstract
The brain has long been known to display the most complex pattern of alternative splicing, thereby producing diverse protein isoforms compared to other tissues. Recent evidence indicates that many alternative exons are neuron-specific, evolutionarily conserved, and found in regulators of transcription including DNA-binding protein and histone modifying enzymes. This raises a possibility that neurons adopt unique mechanisms of transcription. Given that transcriptional machineries are frequently mutated in neurodevelopmental disorders with cognitive dysfunction, it is important to understand how neuron-specific alternative splicing contributes to proper transcriptional regulation in the brain. In this review, we summarize current knowledge regarding how neuron-specific splicing events alter the function of transcriptional regulators and shape unique gene expression patterns in the brain and the implications of neuronal splicing to the pathophysiology of neurodevelopmental disorders.
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43
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Epigenetic Etiology of Intellectual Disability. J Neurosci 2017; 37:10773-10782. [PMID: 29118205 DOI: 10.1523/jneurosci.1840-17.2017] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022] Open
Abstract
Intellectual disability (ID) is a prevailing neurodevelopmental condition associated with impaired cognitive and adaptive behaviors. Many chromatin-modifying enzymes and other epigenetic regulators have been genetically associated with ID disorders (IDDs). Here we review how alterations in the function of histone modifiers, chromatin remodelers, and methyl-DNA binding proteins contribute to neurodevelopmental defects and altered brain plasticity. We also discuss how progress in human genetics has led to the generation of mouse models that unveil the molecular etiology of ID, and outline the direction in which this field is moving to identify therapeutic strategies for IDDs. Importantly, because the chromatin regulators linked to IDDs often target common downstream genes and cellular processes, the impact of research in individual syndromes goes well beyond each syndrome and can also contribute to the understanding and therapy of other IDDs. Furthermore, the investigation of these disorders helps us to understand the role of chromatin regulators in brain development, plasticity, and gene expression, thereby answering fundamental questions in neurobiology.
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44
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Moriel-Carretero M, Ovejero S, Gérus-Durand M, Vryzas D, Constantinou A. Fanconi anemia FANCD2 and FANCI proteins regulate the nuclear dynamics of splicing factors. J Cell Biol 2017; 216:4007-4026. [PMID: 29030393 PMCID: PMC5716273 DOI: 10.1083/jcb.201702136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 08/02/2017] [Accepted: 08/25/2017] [Indexed: 01/20/2023] Open
Abstract
Moriel-Carretero et al. show that the Fanconi anemia proteins FANCI and FANCD2 associate with the splicing factor SF3B1 and that DNA replication stress induces the FANCI-dependent release of SF3B1 from nuclear speckles. FANCI and FANCD2 prevent accumulation of postcatalytic intron lariats, suggesting that they help coordinate DNA replication and transcription. Proteins disabled in the cancer-prone disorder Fanconi anemia (FA) ensure the maintenance of chromosomal stability during DNA replication. FA proteins regulate replication dynamics, coordinate replication-coupled repair of interstrand DNA cross-links, and mitigate conflicts between replication and transcription. Here we show that FANCI and FANCD2 associate with splicing factor 3B1 (SF3B1), a key spliceosomal protein of the U2 small nuclear ribonucleoprotein (U2 snRNP). FANCI is in close proximity to SF3B1 in the nucleoplasm of interphase and mitotic cells. Furthermore, we find that DNA replication stress induces the release of SF3B1 from nuclear speckles in a manner that depends on FANCI and on the activity of the checkpoint kinase ATR. In chromatin, both FANCD2 and FANCI associate with SF3B1, prevent accumulation of postcatalytic intron lariats, and contribute to the timely eviction of splicing factors. We propose that FANCD2 and FANCI contribute to the organization of functional domains in chromatin, ensuring the coordination of DNA replication and cotranscriptional processes.
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Affiliation(s)
- María Moriel-Carretero
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Sara Ovejero
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Marie Gérus-Durand
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Dimos Vryzas
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
| | - Angelos Constantinou
- Institute of Human Genetics, Centre National de la Recherche Scientifique UMR 9002, Université de Montpellier, Montpellier, France
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45
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Kornblihtt AR. Epigenetics at the base of alternative splicing changes that promote colorectal cancer. J Clin Invest 2017; 127:3281-3283. [PMID: 28825597 DOI: 10.1172/jci96497] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromatin modification influences gene expression by either repressing or activating genes, depending on the specific histone mark. Chromatin structure can also influence alternative splicing of transcripts; however, the mechanisms by which epigenetic marks influence splicing are poorly understood. A report in the current issue of the JCI highlights the biological importance of the coordinated control of alternative pre-mRNA splicing by chromatin structure and transcriptional elongation. Yuan et al. found that mutation of the histone methyl transferase SEDT2 affects alternative splicing fates of several key regulatory genes, including those involved in Wnt signaling. As a consequence, loss of SEDT2 in the intestine aggravated Wnt/β-catenin signaling effects, thereby leading to colorectal cancer.
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46
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Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol 2017; 18:437-451. [PMID: 28488700 DOI: 10.1038/nrm.2017.27] [Citation(s) in RCA: 776] [Impact Index Per Article: 110.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alternative splicing of eukaryotic transcripts is a mechanism that enables cells to generate vast protein diversity from a limited number of genes. The mechanisms and outcomes of alternative splicing of individual transcripts are relatively well understood, and recent efforts have been directed towards studying splicing networks. It has become apparent that coordinated splicing networks regulate tissue and organ development, and that alternative splicing has important physiological functions in different developmental processes in humans.
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47
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Deimling SJ, Olsen JB, Tropepe V. The expanding role of the Ehmt2/G9a complex in neurodevelopment. NEUROGENESIS 2017; 4:e1316888. [PMID: 28596979 DOI: 10.1080/23262133.2017.1316888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/22/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
Abstract
Epigenetic regulators play a crucial role in neurodevelopment. One such epigenetic complex, Ehmt1/2 (G9a/GLP), is essential for repressing gene transcription by methylating H3K9 in a highly tissue- and temporal-specific manner. Recently, data has emerged suggesting that this complex plays additional roles in regulating the activity of numerous other non-histone proteins. While much is known about the downstream effects of Ehmt1/2 function, evidence is only beginning to come to light suggesting the control of Ehmt1/2 function may be, at least in part, due to context-dependent binding partners. Here we review emerging roles for the Ehmt1/2 complex suggesting that it may play a much larger role than previously recognized, and discuss binding partners that we and others have recently characterized which act to coordinate its activity during early neurodevelopment.
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Affiliation(s)
- Steven J Deimling
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Jonathan B Olsen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Vincent Tropepe
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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48
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Abstract
Alternative splicing (AS) greatly expands the coding capacities of genomes by allowing the generation of multiple mature mRNAs from a limited number of genes. Although the massive switch in AS profiles that often accompanies variations in gene expression patterns occurring during cell differentiation has been characterized for a variety of models, their causes and mechanisms remain largely unknown. Here, we integrate foundational and recent studies indicating the AS switches that govern the processes of cell fate determination. We include some distinct AS events in pluripotent cells and somatic reprogramming and discuss new progresses on alternative isoform expression in adipogenesis, myogenic differentiation and stimulation of immune cells. Finally, we cover novel insights on AS mechanisms during neuronal differentiation, paying special attention to the role of chromatin structure.
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Affiliation(s)
- Ana Fiszbein
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
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49
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Casadio M. Alberto Kornblihtt: Coupling alternative splicing with transcription. J Cell Biol 2017; 216:284-285. [PMID: 28104749 PMCID: PMC5294796 DOI: 10.1083/jcb.201701050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Kornblihtt studies how gene expression is controlled in mammals and plants.
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50
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Rusconi F, Grillo B, Toffolo E, Mattevi A, Battaglioli E. NeuroLSD1: Splicing-Generated Epigenetic Enhancer of Neuroplasticity. Trends Neurosci 2017; 40:28-38. [DOI: 10.1016/j.tins.2016.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/18/2016] [Indexed: 12/17/2022]
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