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Singh A, Maurer‐Alcalá XX, Solberg T, Häußermann L, Gisler S, Ignarski M, Swart EC, Nowacki M. Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium. EMBO J 2022; 41:e111839. [PMID: 36221862 PMCID: PMC9670198 DOI: 10.15252/embj.2022111839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 01/13/2023] Open
Abstract
Small RNAs mediate the silencing of transposable elements and other genomic loci, increasing nucleosome density and preventing undesirable gene expression. The unicellular ciliate Paramecium is a model to study dynamic genome organization in eukaryotic cells, given its unique feature of nuclear dimorphism. Here, the formation of the somatic macronucleus during sexual reproduction requires eliminating thousands of transposon remnants (IESs) and transposable elements scattered throughout the germline micronuclear genome. The elimination process is guided by Piwi-associated small RNAs and leads to precise cleavage at IES boundaries. Here we show that IES recognition and precise excision are facilitated by recruiting ISWI1, a Paramecium homolog of the chromatin remodeler ISWI. ISWI1 knockdown substantially inhibits DNA elimination, quantitatively similar to development-specific sRNA gene knockdowns but with much greater aberrant IES excision at alternative boundaries. We also identify key development-specific sRNA biogenesis and transport proteins, Ptiwi01 and Ptiwi09, as ISWI1 cofactors in our co-immunoprecipitation studies. Nucleosome profiling indicates that increased nucleosome density correlates with the requirement for ISWI1 and other proteins necessary for IES excision. We propose that chromatin remodeling together with small RNAs is essential for efficient and precise DNA elimination in Paramecium.
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Affiliation(s)
- Aditi Singh
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland,Max Planck Institute for BiologyTubingenGermany
| | | | - Therese Solberg
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland
| | | | - Silvan Gisler
- Institute of Cell BiologyUniversity of BernBernSwitzerland
| | | | - Estienne C Swart
- Institute of Cell BiologyUniversity of BernBernSwitzerland,Max Planck Institute for BiologyTubingenGermany
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2
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Gopinathan G, Diekwisch TGH. Epigenetics and Early Development. J Dev Biol 2022; 10:jdb10020026. [PMID: 35735917 PMCID: PMC9225096 DOI: 10.3390/jdb10020026] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
The epigenome controls all aspect of eukaryotic development as the packaging of DNA greatly affects gene expression. Epigenetic changes are reversible and do not affect the DNA sequence itself but rather control levels of gene expression. As a result, the science of epigenetics focuses on the physical configuration of chromatin in the proximity of gene promoters rather than on the mechanistic effects of gene sequences on transcription and translation. In the present review we discuss three prominent epigenetic modifications, DNA methylation, histone methylation/acetylation, and the effects of chromatin remodeling complexes. Specifically, we introduce changes to the methylated state of DNA through DNA methyltransferases and DNA demethylases, discuss the effects of histone tail modifications such as histone acetylation and methylation on gene expression and present the functions of major ATPase subunit containing chromatin remodeling complexes. We also introduce examples of how changes in these epigenetic factors affect early development in humans and mice. In summary, this review provides an overview over the most important epigenetic mechanisms and provides examples of the dramatic effects of epigenetic changes in early mammalian development.
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Li Y, Gong H, Wang P, Zhu Y, Peng H, Cui Y, Li H, Liu J, Wang Z. The emerging role of ISWI chromatin remodeling complexes in cancer. J Exp Clin Cancer Res 2021; 40:346. [PMID: 34736517 PMCID: PMC8567610 DOI: 10.1186/s13046-021-02151-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Disordered chromatin remodeling regulation has emerged as an essential driving factor for cancers. Imitation switch (ISWI) family are evolutionarily conserved ATP-dependent chromatin remodeling complexes, which are essential for cellular survival and function through multiple genetic and epigenetic mechanisms. Omics sequencing and a growing number of basic and clinical studies found that ISWI family members displayed widespread gene expression and genetic status abnormalities in human cancer. Their aberrant expression is closely linked to patient outcome and drug response. Functional or componential alteration in ISWI-containing complexes is critical for tumor initiation and development. Furthermore, ISWI-non-coding RNA regulatory networks and some non-coding RNAs derived from exons of ISWI member genes play important roles in tumor progression. Therefore, unveiling the transcriptional regulation mechanism underlying ISWI family sparked a booming interest in finding ISWI-based therapies in cancer. This review aims at describing the current state-of-the-art in the role of ISWI subunits and complexes in tumorigenesis, tumor progression, immunity and drug response, and presenting deep insight into the physiological and pathological implications of the ISWI transcription machinery in cancers.
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Affiliation(s)
- Yanan Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Han Gong
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Pan Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yajuan Cui
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Heng Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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Niri F, Terpstra A, Lim KRQ, McDermid H. Chromatin remodeling factor CECR2 forms tissue-specific complexes with CCAR2 and LUZP1. Biochem Cell Biol 2021; 99:759-765. [PMID: 34197713 DOI: 10.1139/bcb-2021-0019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatin remodeling complexes alter chromatin structure to control access to DNA and therefore control cellular processes such as transcription, DNA replication, and DNA repair. CECR2 is a chromatin remodeling factor that plays an important role in neural tube closure and reproduction. Loss-of-function mutations in Cecr2 result primarily in the perinatal lethal neural tube defect exencephaly, with non-penetrant mice that survive to adulthood exhibiting subfertility. CECR2 forms a complex with ISWI proteins SMARCA5 and/or SMARCA1, but further information on the structure and function of the complex is not known. We therefore have identified candidate components of the CECR2-containing remodeling factor (CERF) complex in embryonic stem (ES) cells through mass spectroscopy. Both SMARCA5 and SMARCA1 were confirmed to be present in CERF complexes in ES cells and testis. However, novel proteins CCAR2 and LUZP1 are CERF components in ES cells but not testis. This tissue specificity in mice suggests these complexes may also have functional differences. Furthermore, LUZP1, loss of which is also associated with exencephaly, appears to play a role in stabilizing the CERF complex in ES cells. Keywords: CECR2, LUZP1, CCAR2, Chromatin remodeling factor, Neural tube defects.
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Affiliation(s)
- Farshad Niri
- University of Alberta, 3158, Edmonton, Alberta, Canada, T6G 2R3.,Edmonton, Alberta, Canada, T6E 1V3;
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Dual Regulatory Role of Chromatin Remodeler ISW1 in Coordinating Cellulase and Secondary Metabolite Biosynthesis in Trichoderma reesei. mBio 2021; 13:e0345621. [PMID: 35130719 PMCID: PMC8822348 DOI: 10.1128/mbio.03456-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The saprophytic filamentous fungus Trichoderma reesei represents one of the most prolific cellulase producers isolated from nature. T. reesei also produces a typical yellow pigment identified as sorbicillinoids during cultivation. Here, we identified an evolutionarily conserved histone remodeling factor, ISW1, in T. reesei that simultaneously participates in regulating cellulase and the yellow pigment biosynthesis. Trisw1 deletion almost abolished vegetable growth, asexual spore formation, and cellulase gene expression. However, its absence significantly enhanced the production of the yellow pigment. The observed dual regulatory role of TrISW1 was dependent on its ATPase activity. We demonstrated that Trisw1 disruption elevated the transcription of ypr1 coding for the transcriptional activator of sor genes encoding the polyketide synthases catalyzing the biosynthesis of sorbicillinoids but compromised that of xyr1 encoding the key transcriptional activator of cellulase genes. Discrete T. reesei homologous ISW1 accessory factors were also found to exert differential effects on the expression of these two types of genes. Further analyses showed that TrISW1 was recruited to cellulase gene promoters, and its absence interfered with loss of histone H4 at the cbh1 and eg1 promoters upon cellulose induction. To the contrary, Trisw1 deletion facilitated loss of H4 at the sor locus. These data indicate that TrISW1 represents an important chromatin remodeler with a dual role in coordinating the cellulolytic response and biosynthesis of the major secondary metabolite in T. reesei. IMPORTANCE Microorganisms, including Trichoderma reesei, constantly face the challenge to outcompete other species to ensure efficient colonization in their natural habitat. They achieve this usually by adopting two alternative strategies by either maintaining fast growth on limited nutrient resources or producing a versatile array of secondary metabolites to fight against competitors. These two strategies, however, have to be subtly controlled to balance the assignment of and thus make the best use of cellular resources. Here, we identified a chromatin remodeling factor, TrISW1, with a dual role in coordinating the cellulolytic response and biosynthesis of the major secondary metabolite in T. reesei. The data also provide a novel insight into how T. reesei takes advantage of a chromatin remodeler to exquisitely balance two different adaptive strategies to ensure an efficient allocation of cellular resources to achieve efficient colonization in a specific environment.
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Gu BW, Tan LM, Zhang CJ, Hou XM, Cai XW, Chen S, He XJ. FHA2 is a plant-specific ISWI subunit responsible for stamen development and plant fertility. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1703-1716. [PMID: 32396248 DOI: 10.1111/jipb.12945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Imitation Switch (ISWI) chromatin remodelers are known to function in diverse multi-subunit complexes in yeast and animals. However, the constitution and function of ISWI complexes in Arabidopsis thaliana remain unclear. In this study, we identified forkhead-associated domain 2 (FHA2) as a plant-specific subunit of an ISWI chromatin-remodeling complex in Arabidopsis. By in vivo and in vitro analyses, we demonstrated that FHA2 directly binds to RLT1 and RLT2, two redundant subunits of the ISWI complex in Arabidopsis. The stamen filament is shorter in the fha2 and rlt1/2 mutants than in the wild type, whereas their pistil lengths are comparable. The shorter filament, which is due to reduced cell size, results in insufficient pollination and reduced fertility. The rlt1/2 mutant shows an early-flowering phenotype, whereas the phenotype is not shared by the fha2 mutant. Consistent with the functional specificity of FHA2, our RNA-seq analysis indicated that the fha2 mutant affects a subset of RLT1/2-regulated genes that does not include genes involved in the regulation of flowering time. This study demonstrates that FHA2 functions as a previously uncharacterized subunit of the Arabidopsis ISWI complex and is exclusively involved in regulating stamen development and plant fertility.
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Affiliation(s)
- Bo-Wen Gu
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lian-Mei Tan
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xiao-Mei Hou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 10084, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 10084, China
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Xu X, Zhang J, Tian Y, Gao Y, Dong X, Chen W, Yuan X, Yin W, Xu J, Chen K, He C, Wei L. CircRNA inhibits DNA damage repair by interacting with host gene. Mol Cancer 2020; 19:128. [PMID: 32838810 PMCID: PMC7446195 DOI: 10.1186/s12943-020-01246-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/12/2020] [Indexed: 01/01/2023] Open
Abstract
Background Deregulated circular RNAs (circRNAs) are associated with the development of cancer and therapy resistance. However, functional research of circRNAs mostly focus on potential miRNA or protein binding and more potential regulation of circRNA on host gene DNA in cancers are yet to be inspected. Method We performed total RNA sequencing on clinical breast cancer samples and identified the expression patterns of circRNAs and corresponding host genes in patient blood, tumor and adjacent normal tissues. qPCR, northern blot and in situ hybridization were used to validate the dysregulation of circRNA circSMARCA5. A series of procedures including R-loop dot-blotting, DNA-RNA immunoprecipitation and mass spectrum, etc. were conducted to explore the regulation of circSMARCA5 on the transcription of exon 15 of SMARCA5. Moreover, immunofluorescence and in vivo experiments were executed to investigate the overexpression of circSMARCA5 with drug sensitivities. Results We found that circRNAs has average higher expression over its host linear genes in peripheral blood. Compared to adjacent normal tissues, circSMARCA5 is decreased in breast cancer tissues, contrary to host gene SMARCA5. The enforced expression of circSMARCA5 induced drug sensitivity of breast cancer cell lines in vitro and in vivo. Furthermore, we demonstrated that circSMARCA5 can bind to its parent gene locus, forming an R-loop, which results in transcriptional pausing at exon 15 of SMARCA5. CircSMARCA5 expression resulted in the downregulation of SMARCA5 and the production of a truncated nonfunctional protein, and the overexpression of circSMARCA5 was sufficient to improve sensitivity to cytotoxic drugs. Conclusion Our results revealed a new regulatory mechanism for circRNA on its host gene and provided evidence that circSMARCA5 may serve as a therapeutic target for drug-resistant breast cancer patients.
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Affiliation(s)
- Xiaolong Xu
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Jingwei Zhang
- Hubei Key Laboratory of Tumor Biological Behaviors, Department of Breast and Thyroid Surgery, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yihao Tian
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yang Gao
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Xin Dong
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Wenbo Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Xiaoning Yuan
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Weinan Yin
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Jinjing Xu
- Hubei Key Laboratory of Tumor Biological Behaviors, Department of Breast and Thyroid Surgery, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China. .,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lei Wei
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China. .,Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, 430071, Hubei, China.
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8
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Díaz-Olmos Y, Batista M, Ludwig A, Marchini FK. Characterising ISWI chromatin remodeler in Trypanosoma cruzi. Mem Inst Oswaldo Cruz 2020; 115:e190457. [PMID: 32428081 PMCID: PMC7233268 DOI: 10.1590/0074-02760190457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/23/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Imitation SWItch (ISWI) ATPase is the catalytic subunit in diverse chromatin remodeling complexes. These complexes modify histone-DNA interactions and therefore play a pivotal role in different DNA-dependent processes. In Trypanosoma cruzi, a protozoan that controls gene expression principally post-transcriptionally, the transcriptional regulation mechanisms mediated by chromatin remodeling are poorly understood. OBJECTIVE To characterise the ISWI remodeler in T. cruzi (TcISWI). METHODS A new version of pTcGW vectors was constructed to express green fluorescent protein (GFP)-tagged TcISWI. CRISPR-Cas9 system was used to obtain parasites with inactivated TcISWI gene and we determined TcISWI partners by cryomilling-affinity purification-mass spectrometry (MS) assay as an approximation to start to unravel the function of this protein. FINDINGS Our approach identified known ISWI partners [nucleoplasmin-like protein (NLP), regulator of chromosome condensation 1-like protein (RCCP) and phenylalanine/tyrosine-rich protein (FYRP)], previously characterised in T. brucei, and new components in TcISWI complex [DRBD2, DHH1 and proteins containing a domain characteristic of structural maintenance of chromosomes (SMC) proteins]. Data are available via ProteomeXchange with identifier PXD017869. MAIN CONCLUSIONS In addition to its participation in transcriptional silencing, as it was reported in T. brucei, the data generated here provide a framework that suggests a role for TcISWI chromatin remodeler in different nuclear processes in T. cruzi, including mRNA nuclear export control and chromatin compaction. Further work is necessary to clarify the TcISWI functional diversity that arises from this protein interaction study.
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Affiliation(s)
- Yirys Díaz-Olmos
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Michel Batista
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Fabricio K Marchini
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
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9
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Ji JH, Min S, Chae S, Ha GH, Kim Y, Park YJ, Lee CW, Cho H. De novo phosphorylation of H2AX by WSTF regulates transcription-coupled homologous recombination repair. Nucleic Acids Res 2020; 47:6299-6314. [PMID: 31045206 PMCID: PMC6614800 DOI: 10.1093/nar/gkz309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/25/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Histone H2AX undergoes a phosphorylation switch from pTyr142 (H2AX-pY142) to pSer139 (γH2AX) in the DNA damage response (DDR); however, the functional role of H2AX-pY142 remains elusive. Here, we report a new layer of regulation involving transcription-coupled H2AX-pY142 in the DDR. We found that constitutive H2AX-pY142 generated by Williams-Beuren syndrome transcription factor (WSTF) interacts with RNA polymerase II (RNAPII) and is associated with RNAPII-mediated active transcription in proliferating cells. Also, removal of pre-existing H2AX-pY142 by ATM-dependent EYA1/3 phosphatases disrupts this association and requires for transcriptional silencing at transcribed active damage sites. The following recovery of H2AX-pY142 via translocation of WSTF to DNA lesions facilitates transcription-coupled homologous recombination (TC-HR) in the G1 phase, whereby RAD51 loading, but not RPA32, utilizes RNAPII-dependent active RNA transcripts as donor templates. We propose that the WSTF-H2AX-RNAPII axis regulates transcription and TC-HR repair to maintain genome integrity.
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Affiliation(s)
- Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, South Korea
| | - Sunwoo Min
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, South Korea
| | - Geun-Hyoung Ha
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Yonghyeon Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Yeon-Ji Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Hyeseong Cho
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, South Korea.,Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
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10
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Zaware N, Zhou MM. Bromodomain biology and drug discovery. Nat Struct Mol Biol 2019; 26:870-879. [PMID: 31582847 DOI: 10.1038/s41594-019-0309-8] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
The bromodomain (BrD) is a conserved structural module found in chromatin- and transcription-associated proteins that acts as the primary reader for acetylated lysine residues. This basic activity endows BrD proteins with versatile functions in the regulation of protein-protein interactions mediating chromatin-templated gene transcription, DNA recombination, replication and repair. Consequently, BrD proteins are involved in the pathogenesis of numerous human diseases. In this Review, we highlight our current understanding of BrD biology, and discuss the latest development of small-molecule inhibitors targeting BrDs as emerging epigenetic therapies for cancer and inflammatory disorders.
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Affiliation(s)
- Nilesh Zaware
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Sokpor G, Castro-Hernandez R, Rosenbusch J, Staiger JF, Tuoc T. ATP-Dependent Chromatin Remodeling During Cortical Neurogenesis. Front Neurosci 2018; 12:226. [PMID: 29686607 PMCID: PMC5900035 DOI: 10.3389/fnins.2018.00226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly. ATP-dependent chromatin remodeling complexes regulate gene expression through utilization of energy from ATP hydrolysis to reorganize chromatin structure. These chromatin remodeling complexes are characteristically multimeric, with some capable of adopting functionally distinct conformations via subunit reconstitution to perform specific roles in major aspects of cortical neurogenesis. In this review, we highlight the functions of such chromatin remodelers during cortical development. We also bring together various proposed mechanisms by which ATP-dependent chromatin remodelers function individually or in concert, to specifically modulate vital steps in cortical neurogenesis.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Ricardo Castro-Hernandez
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
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12
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Loss of ISWI Function in Drosophila Nuclear Bodies Drives Cytoplasmic Redistribution of Drosophila TDP-43. Int J Mol Sci 2018; 19:ijms19041082. [PMID: 29617352 PMCID: PMC5979594 DOI: 10.3390/ijms19041082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022] Open
Abstract
Over the past decade, evidence has identified a link between protein aggregation, RNA biology, and a subset of degenerative diseases. An important feature of these disorders is the cytoplasmic or nuclear aggregation of RNA-binding proteins (RBPs). Redistribution of RBPs, such as the human TAR DNA-binding 43 protein (TDP-43) from the nucleus to cytoplasmic inclusions is a pathological feature of several diseases. Indeed, sporadic and familial forms of amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration share as hallmarks ubiquitin-positive inclusions. Recently, the wide spectrum of neurodegenerative diseases characterized by RBPs functions’ alteration and loss was collectively named proteinopathies. Here, we show that TBPH (TAR DNA-binding protein-43 homolog), the Drosophila ortholog of human TDP-43 TAR DNA-binding protein-43, interacts with the arcRNA hsrω and with hsrω-associated hnRNPs. Additionally, we found that the loss of the omega speckles remodeler ISWI (Imitation SWI) changes the TBPH sub-cellular localization to drive a TBPH cytoplasmic accumulation. Our results, hence, identify TBPH as a new component of omega speckles and highlight a role of chromatin remodelers in hnRNPs nuclear compartmentalization.
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Brandão F, Esher SK, Ost KS, Pianalto K, Nichols CB, Fernandes L, Bocca AL, Poças-Fonseca MJ, Alspaugh JA. HDAC genes play distinct and redundant roles in Cryptococcus neoformans virulence. Sci Rep 2018; 8:5209. [PMID: 29581526 PMCID: PMC5979944 DOI: 10.1038/s41598-018-21965-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/14/2018] [Indexed: 01/01/2023] Open
Abstract
The human fungal pathogen Cryptococcus neoformans undergoes many phenotypic changes to promote its survival in specific ecological niches and inside the host. To explore the role of chromatin remodeling on the expression of virulence-related traits, we identified and deleted seven genes encoding predicted class I/II histone deacetylases (HDACs) in the C. neoformans genome. These studies demonstrated that individual HDACs control non-identical but overlapping cellular processes associated with virulence, including thermotolerance, capsule formation, melanin synthesis, protease activity and cell wall integrity. We also determined the HDAC genes necessary for C. neoformans survival during in vitro macrophage infection and in animal models of cryptococcosis. Our results identified the HDA1 HDAC gene as a central mediator controlling several cellular processes, including mating and virulence. Finally, a global gene expression profile comparing the hda1Δ mutant versus wild-type revealed altered transcription of specific genes associated with the most prominent virulence attributes in this fungal pathogen. This study directly correlates the effects of Class I/II HDAC-mediated chromatin remodeling on the marked phenotypic plasticity and virulence potential of this microorganism. Furthermore, our results provide insights into regulatory mechanisms involved in virulence gene expression that are likely shared with other microbial pathogens.
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Affiliation(s)
- Fabiana Brandão
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Shannon K Esher
- Department of Medicine/Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Kyla S Ost
- Department of Medicine/Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Kaila Pianalto
- Department of Medicine/Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Connie B Nichols
- Department of Medicine/Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Larissa Fernandes
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Anamélia L Bocca
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Marcio José Poças-Fonseca
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - J Andrew Alspaugh
- Department of Medicine/Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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14
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Abstract
Recent studies from a number of model organisms have indicated chromatin structure and its remodeling as a major contributory agent for aging. Few recent experiments also demonstrate that modulation in the chromatin modifying agents also affect the life span of an organism and even in some cases the change is inherited epigenetically to subsequent generations. Hence, in the present report we discuss the chromatin organization and its changes during aging.
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Affiliation(s)
- Pramod C. Rath
- School of Life Sciences, Molecular Biology Laboratory, Jawaharlal Nehru University, New Delhi, Delhi India
| | - Ramesh Sharma
- Department of Biochemistry, North Eastern Hill University, Shillong, Megalaya India
| | - S. Prasad
- Biochemistry & Molecular Biology Lab, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh India
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15
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Sugimoto N, Fujita M. Molecular Mechanism for Chromatin Regulation During MCM Loading in Mammalian Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:61-78. [PMID: 29357053 DOI: 10.1007/978-981-10-6955-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA replication is a fundamental process required for the accurate and timely duplication of chromosomes. During late mitosis to G1 phase, the MCM2-7 complex is loaded onto chromatin in a manner dependent on ORC, CDC6, and Cdt1, and chromatin becomes licensed for replication. Although every eukaryotic organism shares common features in replication control, there are also some differences among species. For example, in higher eukaryotic cells including human cells, no strict sequence specificity has been observed for replication origins, unlike budding yeast or bacterial replication origins. Therefore, elements other than beyond DNA sequences are important for regulating replication. For example, the stability and precise positioning of nucleosomes affects replication control. However, little is known about how nucleosome structure is regulated when replication licensing occurs. During the last decade, histone acetylation enzyme HBO1, chromatin remodeler SNF2H, and histone chaperone GRWD1 have been identified as chromatin-handling factors involved in the promotion of replication licensing. In this review, we discuss how the rearrangement of nucleosome formation by these factors affects replication licensing.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
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16
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Lee B, Duz MB, Sagong B, Koparir A, Lee KY, Choi JY, Seven M, Yuksel A, Kim UK, Ozen M. Revealing the function of a novel splice-site mutation of CHD7 in CHARGE syndrome. Gene 2015; 576:776-81. [PMID: 26551301 DOI: 10.1016/j.gene.2015.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/24/2015] [Accepted: 11/04/2015] [Indexed: 11/27/2022]
Abstract
Most cases of CHARGE syndrome are sporadic and autosomal dominant. CHD7 is a major causative gene of CHARGE syndrome. In this study, we screened CHD7 in two Turkish patients demonstrating symptoms of CHARGE syndrome such as coloboma, heart defect, choanal atresia, retarded growth, genital abnomalities and ear anomalies. Two mutations of CHD7 were identified including a novel splice-site mutation (c.2443-2A>G) and a previously known frameshift mutation (c.2504_2508delATCTT). We performed exon trapping analysis to determine the effect of the c.2443-2A>G mutation at the transcriptional level, and found that it caused a complete skip of exon 7 and splicing at a cryptic splice acceptor site. Our current study is the second study demonstrating an exon 7 deficit in CHD7. Results of previous studies suggest that the c.2443-2A>G mutation affects the formation of nasal tissues and the neural retina during early development, resulting in choanal atresia and coloboma, respectively. The findings of the present study will improve our understanding of the genetic causes of CHARGE syndrome.
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Affiliation(s)
- Byeonghyeon Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Mehmet Bugrahan Duz
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Asuman Koparir
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, South Korea
| | - Mehmet Seven
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Adnan Yuksel
- Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea.
| | - Mustafa Ozen
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey; Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey; Department of Pathology & Immunology, Baylor College of Medicine, Michael E. DeBakey VAMC, Houston, TX, United States.
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17
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Singh AK, Lakhotia SC. The hnRNP A1 homolog Hrb87F/Hrp36 is important for telomere maintenance in Drosophila melanogaster. Chromosoma 2015; 125:373-88. [PMID: 26373285 DOI: 10.1007/s00412-015-0540-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/25/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
Abstract
Unlike the telomerase-dependent mammalian telomeres, HeT-A, TART, and TAHRE (HTT) retroposon arrays regulate Drosophila telomere length. Cap prevents telomeric associations (TAs) and telomeric fusions (TFs). Our results suggest important roles of Hrb87F in telomeric HTT array and cap maintenance in Drosophila. All chromosome arms, except 2L, in Df(3R)Hrb87F homozygotes (Hrb87F-null) displayed significantly elongated telomeres with amplified HTT arrays and high TAs, all of which resolved without damage. Presence of FLAG-tagged Hrb87F (FLAG-Hrb87F) on cap and subtelomeric regions following hsFLAG-Hrb87F transgene expression in Df(3R)Hrb87F homozygotes suppressed TAs without affecting telomere length. A normal X-chromosome telomere expanded within five generations in Hrb87F-null background and displayed high TAs, but not when hsFLAG-Hrb87F was co-expressed. Tel (1) /Gaiano line or HP1 loss-of-function mutant-derived expanded telomeres carry Hrb87F on cap and HTT arrays while Hrb87F-null telomeres have HP1 and HOAP on caps and expanded HTT arrays. ISWI, seen only on cap on normal telomeres, was abundant on Hrb87F-null expanded HTT arrays. Extended telomeres derived from Tel (1) (Gaiano) or HP1-null mutation background interact with those from Hrb87F-null, since while the end association frequency was negligible in Df(3R)Hrb87F/+ nuclei, it increased significantly in co-presence of Tel (1) or HP1-null-based expanded telomere/s. Together, these suggest complex interactions between members of the proteome of telomere so that absence of any key member leads to telomere expansion and/or enhanced TAs/TFs. HTT expansion in Hrb87F-null condition is not developmental but a germline event presumably because absence of Hrb87F in germline may deregulate HTT retroposition/replication leading to telomere elongation.
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Affiliation(s)
- Anand K Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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18
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Stanne T, Narayanan MS, Ridewood S, Ling A, Witmer K, Kushwaha M, Wiesler S, Wickstead B, Wood J, Rudenko G. Identification of the ISWI Chromatin Remodeling Complex of the Early Branching Eukaryote Trypanosoma brucei. J Biol Chem 2015; 290:26954-26967. [PMID: 26378228 PMCID: PMC4646403 DOI: 10.1074/jbc.m115.679019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 12/25/2022] Open
Abstract
ISWI chromatin remodelers are highly conserved in eukaryotes and are important for the assembly and spacing of nucleosomes, thereby controlling transcription initiation and elongation. ISWI is typically associated with different subunits, forming specialized complexes with discrete functions. In the unicellular parasite Trypanosoma brucei, which causes African sleeping sickness, TbISWI down-regulates RNA polymerase I (Pol I)-transcribed variant surface glycoprotein (VSG) gene expression sites (ESs), which are monoallelically expressed. Here, we use tandem affinity purification to determine the interacting partners of TbISWI. We identify three proteins that do not show significant homology with known ISWI-associated partners. Surprisingly, one of these is nucleoplasmin-like protein (NLP), which we had previously shown to play a role in ES control. In addition, we identify two novel ISWI partners, regulator of chromosome condensation 1-like protein (RCCP) and phenylalanine/tyrosine-rich protein (FYRP), both containing protein motifs typically found on chromatin proteins. Knockdown of RCCP or FYRP in bloodstream form T. brucei results in derepression of silent variant surface glycoprotein ESs, as had previously been shown for TbISWI and NLP. All four proteins are expressed and interact with each other in both major life cycle stages and show similar distributions at Pol I-transcribed loci. They are also found at Pol II strand switch regions as determined with ChIP. ISWI, NLP, RCCP, and FYRP therefore appear to form a single major ISWI complex in T. brucei (TbIC). This reduced complexity of ISWI regulation and the presence of novel ISWI partners highlights the early divergence of trypanosomes in evolution.
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Affiliation(s)
- Tara Stanne
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Mani Shankar Narayanan
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Sophie Ridewood
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Alexandra Ling
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Kathrin Witmer
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Manish Kushwaha
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Simone Wiesler
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Bill Wickstead
- the School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Jennifer Wood
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Gloria Rudenko
- Division of Cell and Molecular Biology, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and.
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19
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Regulation of ISWI chromatin remodelling activity. Chromosoma 2014; 123:91-102. [PMID: 24414837 DOI: 10.1007/s00412-013-0447-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 12/22/2022]
Abstract
The packaging of the eukaryotic genome into chromatin facilitates the storage of the genetic information within the nucleus, but prevents the access to the underlying DNA sequences. Structural changes in chromatin are mediated by several mechanisms. Among them, ATP-dependent remodelling complexes belonging to ISWI family provides one of the best examples that eukaryotic cells evolved to finely regulate these changes. ISWI-containing complexes use the energy derived from ATP hydrolysis to rearrange nucleosomes on chromatin in order to favour specific nuclear reactions. The combination of regulatory nuclear factors associated with the ATPase subunit as well as its modulation by specific histone modifications, specializes the nuclear function of each ISWI-containing complex. Here we review the different ways by which ISWI enzymatic activity can be modulated and regulated in the nucleus of eukaryotic cells.
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20
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Coppola A, Romito A, Borel C, Gehrig C, Gagnebin M, Falconnet E, Izzo A, Altucci L, Banfi S, Antonarakis SE, Minchiotti G, Cobellis G. Cardiomyogenesis is controlled by the miR-99a/let-7c cluster and epigenetic modifications. Stem Cell Res 2013; 12:323-37. [PMID: 24365598 DOI: 10.1016/j.scr.2013.11.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 01/24/2023] Open
Abstract
Understanding the molecular basis of cardiomyocyte development is critical for understanding the pathogenesis of pre- and post-natal cardiac disease. MicroRNAs (miRNAs) are post-transcriptional modulators of gene expression that play an important role in many developmental processes. Here, we show that the miR-99a/let-7c cluster, mapping on human chromosome 21, is involved in the control of cardiomyogenesis by altering epigenetic factors. By perturbing miRNA expression in mouse embryonic stem cells, we find that let-7c promotes cardiomyogenesis by upregulating genes involved in mesoderm specification (T/Bra and Nodal) and cardiac differentiation (Mesp1, Nkx2.5 and Tbx5). The action of let-7c is restricted to the early phase of mesoderm formation at the expense of endoderm and its late activation redirects cells toward other mesodermal derivatives. The Polycomb complex group protein Ezh2 is a direct target of let-7c, which promotes cardiac differentiation by modifying the H3K27me3 marks from the promoters of crucial cardiac transcription factors (Nkx2.5, Mef2c, Tbx5). In contrast, miR-99a represses cardiac differentiation via the nucleosome-remodeling factor Smarca5, attenuating the Nodal/Smad2 signaling. We demonstrated that the identified targets are underexpressed in human Down syndrome fetal heart specimens. By perturbing the expression levels of these miRNAs in embryonic stem cells, we were able to demonstrate that these miRNAs control lineage- and stage-specific transcription factors, working in concert with chromatin modifiers to direct cardiomyogenesis.
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Affiliation(s)
- Antonietta Coppola
- Department of Biophysics, Biochemistry and General Pathology, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Antonio Romito
- Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Maryline Gagnebin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Antonella Izzo
- Department of Molecular Medicine and Biotechnology, Università Federico II, 80131 Napoli, Italy
| | - Lucia Altucci
- Department of Biophysics, Biochemistry and General Pathology, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Sandro Banfi
- Department of Biophysics, Biochemistry and General Pathology, Seconda Università di Napoli, 80138 Napoli, Italy; Telethon Institute of Genetics and Medicine (TIGEM), 80131 Napoli, Italy
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Gabriella Minchiotti
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Napoli, Italy
| | - Gilda Cobellis
- Department of Biophysics, Biochemistry and General Pathology, Seconda Università di Napoli, 80138 Napoli, Italy.
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21
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Liu B, Yip RK, Zhou Z. Chromatin remodeling, DNA damage repair and aging. Curr Genomics 2013; 13:533-47. [PMID: 23633913 PMCID: PMC3468886 DOI: 10.2174/138920212803251373] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 06/19/2012] [Accepted: 07/25/2012] [Indexed: 01/26/2023] Open
Abstract
Cells are constantly exposed to a variety of environmental and endogenous conditions causing DNA damage, which is detected and repaired by conserved DNA repair pathways to maintain genomic integrity. Chromatin remodeling is critical in this process, as the organization of eukaryotic DNA into compact chromatin presents a natural barrier to all DNA-related events. Studies on human premature aging syndromes together with normal aging have suggested that accumulated damages might lead to exhaustion of resources that are required for physiological functions and thus accelerate aging. In this manuscript, combining the present understandings and latest findings, we focus mainly on discussing the role of chromatin remodeling in the repair of DNA double-strand breaks (DSBs) and regulation of aging.
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Affiliation(s)
- Baohua Liu
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China ; Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
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22
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Polyakova O, Borman S, Grimley R, Vamathevan J, Hayes B, Solari R. Identification of novel interacting partners of Sirtuin6. PLoS One 2012; 7:e51555. [PMID: 23240041 PMCID: PMC3519869 DOI: 10.1371/journal.pone.0051555] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/01/2012] [Indexed: 02/01/2023] Open
Abstract
SIRT6 is a member of the Sirtuin family of histone deacetylases that has been implicated in inflammatory, aging and metabolic pathways. Some of its actions have been suggested to be via physical interaction with NFκB and HIF1α and transcriptional regulation through its histone deacetylase activity. Our previous studies have investigated the histone deacetylase activity of SIRT6 and explored its ability to regulate the transcriptional responses to an inflammatory stimulus such as TNFα. In order to develop a greater understanding of SIRT6 function we have sought to identify SIRT6 interacting proteins by both yeast-2-hybrid and co-immunoprecipitation studies. We report a number of interacting partners which strengthen previous findings that SIRT6 functions in base excision repair (BER), and novel interactors which suggest a role in nucleosome and chromatin remodeling, the cell cycle and NFκB biology.
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Affiliation(s)
- Oxana Polyakova
- Platform Technology Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
| | - Satty Borman
- Platform Technology Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
| | - Rachel Grimley
- Platform Technology Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
| | - Jessica Vamathevan
- Computational Biology, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
| | - Brian Hayes
- Allergic Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
| | - Roberto Solari
- Allergic Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, Hertfordshire, United Kingdom
- * E-mail:
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23
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Yip DJ, Corcoran CP, Alvarez-Saavedra M, DeMaria A, Rennick S, Mears AJ, Rudnicki MA, Messier C, Picketts DJ. Snf2l regulates Foxg1-dependent progenitor cell expansion in the developing brain. Dev Cell 2012; 22:871-8. [PMID: 22516202 DOI: 10.1016/j.devcel.2012.01.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 01/11/2012] [Accepted: 01/26/2012] [Indexed: 01/21/2023]
Abstract
Balancing progenitor cell self-renewal and differentiation is essential for brain development and is regulated by the activity of chromatin remodeling complexes. Nevertheless, linking chromatin changes to specific pathways that control cortical histogenesis remains a challenge. Here we identify a genetic interaction between the chromatin remodeler Snf2l and Foxg1, a key regulator of neurogenesis. Snf2l mutant mice exhibit forebrain hypercellularity arising from increased Foxg1 expression, increased progenitor cell expansion, and delayed differentiation. We demonstrate that Snf2l binds to the Foxg1 locus at midneurogenesis and that the phenotype is rescued by reducing Foxg1 dosage, thus revealing that Snf2l and Foxg1 function antagonistically to regulate brain size.
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Affiliation(s)
- Darren J Yip
- Regenerative Medicine Program, Ottawa Hospital Research Institute, and Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
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24
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ATP-independent cooperative binding of yeast Isw1a to bare and nucleosomal DNA. PLoS One 2012; 7:e31845. [PMID: 22359636 PMCID: PMC3281020 DOI: 10.1371/journal.pone.0031845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 01/13/2012] [Indexed: 12/26/2022] Open
Abstract
Among chromatin remodeling factors, the ISWI family displays a nucleosome-enhanced ATPase activity coupled to DNA translocation. While these enzymes are known to bind to DNA, their activity has not been fully characterized. Here we use TEM imaging and single molecule manipulation to investigate the interaction between DNA and yeast Isw1a. We show that Isw1a displays a highly cooperative ATP-independent binding to and bridging between DNA segments. Under appropriate tension, rare single nucleation events can sometimes be observed and loop DNA with a regular step. These nucleation events are often followed by binding of successive complexes bridging between nearby DNA segments in a zipper-like fashion, as confirmed by TEM observations. On nucleosomal substrates, we show that the specific ATP-dependent remodeling activity occurs in the context of cooperative Isw1a complexes bridging extranucleosomal DNA. Our results are interpreted in the context of the recently published partial structure of Isw1a and support its acting as a “protein ruler” (with possibly more than one tick).
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25
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Abstract
One of the best studied systems for mammalian chromatin remodeling is transcriptional regulation during T cell development. The variety of these studies have led to important findings in T cell gene regulation and cell fate determination. Importantly, these findings have also advanced our knowledge of the function of remodeling enzymes in mammalian gene regulation. First we briefly present biochemical and cell-free analysis of 3 types of ATP dependent remodeling enzymes (SWI/SNF, Mi2, and ISWI) to construct an intellectual framework to understand how these enzymes might be working. Second, we compare and contrast the function of these enzymes during early (thymic) and late (peripheral) T cell development. Finally, we examine some of the gaps in our present understanding.
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Affiliation(s)
- Andrea L. Wurster
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, USA
| | - Michael J. Pazin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, USA
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26
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Abstract
The cardiovascular system is broadly composed of the heart, which pumps blood, and the blood vessels, which carry blood to and from tissues of the body. Heart malformations are the most serious common birth defect, affecting at least 2% of newborns and leading to significant morbidity and mortality. Severe heart malformations cause heart failure in fetuses, infants, and children, whereas milder heart defects may not trigger significant heart dysfunction until early or midadulthood. Severe vasculogenesis or angiogenesis defects in embryos are incompatible with life, and anomalous arterial patterning may cause vascular aberrancies that often require surgical treatment. It is therefore important to understand the underlying mechanisms that control cardiovascular development. Understanding developmental mechanisms will also help us design better strategies to regenerate cardiovascular tissues for therapeutic purposes. An important mechanism regulating genes involves the modification of chromatin, the higher-order structure in which DNA is packaged. Recent studies have greatly expanded our understanding of the regulation of cardiovascular development at the chromatin level, including the remodeling of chromatin and the modification of histones. Chromatin-level regulation integrates multiple inputs and coordinates broad gene expression programs. Thus, understanding chromatin-level regulation will allow for a better appreciation of gene regulation as a whole and may set a fundamental basis for cardiovascular disease. This review focuses on how chromatin-remodeling and histone-modifying factors regulate gene expression to control cardiovascular development.
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Affiliation(s)
- Ching-Pin Chang
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.
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27
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Sugimoto N, Yugawa T, Iizuka M, Kiyono T, Fujita M. Chromatin remodeler sucrose nonfermenting 2 homolog (SNF2H) is recruited onto DNA replication origins through interaction with Cdc10 protein-dependent transcript 1 (Cdt1) and promotes pre-replication complex formation. J Biol Chem 2011; 286:39200-10. [PMID: 21937426 DOI: 10.1074/jbc.m111.256123] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
From late mitosis to the G(1) phase of the cell cycle, ORC, CDC6, and Cdt1 form the machinery necessary to load MCM2-7 complexes onto DNA. Here, we show that SNF2H, a member of the ATP-dependent chromatin-remodeling complex, is recruited onto DNA replication origins in human cells in a Cdt1-dependent manner and positively regulates MCM loading. SNF2H physically interacted with Cdt1. ChIP assays indicated that SNF2H associates with replication origins specifically during the G(1) phase. Binding of SNF2H at origins was decreased by Cdt1 silencing and, conversely, enhanced by Cdt1 overexpression. Furthermore, SNF2H silencing prevented MCM loading at origins and moderately inhibited S phase progression. Although neither SNF2H overexpression nor SNF2H silencing appeared to impact rereplication induced by Cdt1 overexpression, Cdt1-induced checkpoint activation was inhibited by SNF2H silencing. Collectively, these data suggest that SNF2H may promote MCM loading at DNA replication origins via interaction with Cdt1 in human cells. Because efficient loading of excess MCM complexes is thought to be required for cells to tolerate replication stress, Cdt1- and SNF2H-mediated promotion of MCM loading may be biologically relevant for the regulation of DNA replication.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
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Onorati MC, Lazzaro S, Mallik M, Ingrassia AMR, Carreca AP, Singh AK, Chaturvedi DP, Lakhotia SC, Corona DFV. The ISWI chromatin remodeler organizes the hsrω ncRNA-containing omega speckle nuclear compartments. PLoS Genet 2011; 7:e1002096. [PMID: 21637796 PMCID: PMC3102753 DOI: 10.1371/journal.pgen.1002096] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/06/2011] [Indexed: 12/23/2022] Open
Abstract
The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA) essential, among other functions, for the assembly and organization of the omega speckles. The nucleoplasmic omega speckles play important functions in RNA metabolism, in normal and stressed cells, by regulating availability of hnRNPs and some other RNA processing proteins. Chromatin remodelers, as well as nuclear speckles and their associated ncRNAs, are emerging as important components of gene regulatory networks, although their functional connections have remained poorly defined. Here we provide multiple lines of evidence showing that the hsrω ncRNA interacts in vivo and in vitro with ISWI, regulating its ATPase activity. Remarkably, we found that the organization of nucleoplasmic omega speckles depends on ISWI function. Our findings highlight a novel role for chromatin remodelers in organization of nucleoplasmic compartments, providing the first example of interaction between an ATP-dependent chromatin remodeler and a large ncRNA. Chromatin structure and function are regulated by the concerted activity of covalent modifiers of chromatin, nucleosome remodeling factors, and several emerging classes of non-coding RNAs. ISWI is an evolutionarily conserved ATP-dependent chromatin remodeler playing essential roles in chromosome condensation, gene expression, and DNA replication. ISWI activity has been involved in a variety of nuclear functions including telomere silencing, stem cell renewal, neural morphogenesis, and epigenetic reprogramming. Using an in vivo assay to identify factors regulating ISWI activity in the model system Drosophila melanogaster, we recovered a genetic interaction between ISWI and hsrω. The hsrω gene encodes multiple non-coding RNAs (ncRNAs), of which the >10 kb nuclear hsrω-n RNA, with functional homolog in mammals, is essential for the assembly and organization of hnRNP-containing nucleoplasmic omega speckles. These special nuclear compartments play essential roles in the storage/sequestration of hnRNP family and other proteins, thus playing important roles in mRNA maturation and other regulatory processes. Here we show that the hsrω-n ncRNA interacts in vivo and in vitro with ISWI to directly regulate its ATPase activity. We also provide in vivo data showing that omega speckle nuclear organization depends on ISWI function, highlighting a novel role for chromatin remodelers in nuclear speckles organization.
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Affiliation(s)
- Maria C. Onorati
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Sandra Lazzaro
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Moushami Mallik
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Antonia M. R. Ingrassia
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Anna P. Carreca
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
| | - Anand K. Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Deo Prakash Chaturvedi
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Subhash C. Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Davide F. V. Corona
- Dulbecco Telethon Institute, Università degli Studi di Palermo, Dipartimento STEMBIO – Sezione Biologia Cellulare, Palermo, Italy
- * E-mail:
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Abstract
Chromatin regulation provides an important means for controlling cardiac gene expression under different physiological and pathological conditions. Processes that direct the development of normal embryonic hearts and pathology of stressed adult hearts may share general mechanisms that govern cardiac gene expression by chromatin-regulating factors. These common mechanisms may provide a framework for us to investigate the interactions among diverse chromatin remodelers/modifiers and various transcription factors in the fine regulation of gene expression, essential for all aspects of cardiovascular biology. Aberrant cardiac gene expression, triggered by a variety of pathological insults, can cause heart diseases in both animals and humans. The severity of cardiomyopathy and heart failure correlates strongly with abnormal cardiac gene expression. Therefore, controlling cardiac gene expression presents a promising approach to the treatment of human cardiomyopathy. This review focuses on the roles of ATP-dependent chromatin-remodeling factors and chromatin-modifying enzymes in the control of gene expression during cardiovascular development and disease.
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Affiliation(s)
- Pei Han
- CCSR Building, Room 3115-C, 269 Campus Dr, Stanford, CA 94305-5169, USA
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30
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Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI. EMBO J 2011; 30:1766-77. [PMID: 21448136 DOI: 10.1038/emboj.2011.98] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 02/25/2011] [Indexed: 12/22/2022] Open
Abstract
The evolutionarily conserved ATP-dependent nucleosome remodelling factor ISWI can space nucleosomes affecting a variety of nuclear processes. In Drosophila, loss of ISWI leads to global transcriptional defects and to dramatic alterations in higher-order chromatin structure, especially on the male X chromosome. In order to understand if chromatin condensation and gene expression defects, observed in ISWI mutants, are directly correlated with ISWI nucleosome spacing activity, we conducted a genome-wide survey of ISWI binding and nucleosome positioning in wild-type and ISWI mutant chromatin. Our analysis revealed that ISWI binds both genic and intergenic regions. Remarkably, we found that ISWI binds genes near their promoters causing specific alterations in nucleosome positioning at the level of the Transcription Start Site, providing an important insights in understanding ISWI role in higher eukaryote transcriptional regulation. Interestingly, differences in nucleosome spacing, between wild-type and ISWI mutant chromatin, tend to accumulate on the X chromosome for all ISWI-bound genes analysed. Our study shows how in higher eukaryotes the activity of the evolutionarily conserved nucleosome remodelling factor ISWI regulates gene expression and chromosome organization genome-wide.
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Barnett C, Krebs JE. WSTF does it all: a multifunctional protein in transcription, repair, and replication. Biochem Cell Biol 2011; 89:12-23. [PMID: 21326359 PMCID: PMC3251257 DOI: 10.1139/o10-114] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Williams syndrome transcription factor (WSTF) has emerged as an incredibly versatile nuclear protein. WSTF and the ATP-dependent chromatin remodeling complexes in which it exists, WINAC, WICH, and B-WICH, have been studied in a variety of organisms. This research has revealed roles for WSTF in a number of diverse molecular events. WSTF function includes chromatin assembly, RNA polymerase I and III gene regulation, vitamin D metabolism, and DNA repair. In addition to functioning as a subunit of several ATP-dependent chromatin remodeling complexes, WSTF binds specifically to acetylated histones and is itself a histone kinase as well as a target of phosphorylation. This review will describe the three known WSTF-containing complexes and discuss their various roles as well as mechanisms of regulating WSTF activity.
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Affiliation(s)
- Chris Barnett
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508
| | - Jocelyn E. Krebs
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508
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Abstract
Sequence-specific transcription factors (TFs) play a central role in regulating transcription initiation by directing the recruitment and activity of the general transcription machinery and accessory factors. It is now well established that many of the effects exerted by TFs in eukaryotes are mediated through interactions with a host of coregulators that modify the chromatin state, resulting in a more open (in case of activation) or closed conformation (in case of repression). The relationship between TFs and chromatin is a two-way street, however, as chromatin can in turn influence the recognition and binding of target sequences by TFs. The aim of this chapter is to highlight how this dynamic interplay between TF-directed remodelling of chromatin and chromatin-adjusted targeting of TF binding determines where and how transcription is initiated, and to what degree it is productive.
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Insights into how chromatin remodeling factors find their target in the nucleus. Proc Natl Acad Sci U S A 2010; 107:19611-2. [PMID: 21059914 DOI: 10.1073/pnas.1014956107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Biedermann S, Hellmann H. The DDB1a interacting proteins ATCSA-1 and DDB2 are critical factors for UV-B tolerance and genomic integrity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:404-15. [PMID: 20128879 DOI: 10.1111/j.1365-313x.2010.04157.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The integrity of the genome is a fundamental prerequisite for the well-being of all living organisms. Critical for the genomic integrity are effective DNA damage detection mechanisms that enable the cell to rapidly activate the necessary repair machinery. Here, we describe Arabidopsis thaliana ATCSA-1, which is an ortholog of the mammalian Cockayne Syndrome type-A protein involved in transcription-coupled DNA repair processes. ATCSA-1 is a critical component for initiating the repair of UV-B-induced DNA lesions, and, together with the damage-specific DNA binding protein 2 (DDB2), is necessary for light-independent repair processes in Arabidopsis. The transcriptional profile of both genes revealed that ATCSA-1 is strongly expressed in most tissues, whereas DDB2 is only weakly expressed, predominantly in the root tips and anthers of flowers. In contrast to ATCSA-1, DDB2 expression is rapidly inducible by UV treatment. Like DDB2, ATCSA-1 is localized to the nucleus, and assembles with DDB1 and CUL4 proteins into a complex. ATCSA-1 is an unstable protein that is degraded in a 26S proteasome-dependent manner. Overall, the results presented here form a functional description of a plant Cockayne syndrome factor A (CSA) ortholog, and demonstrate the importance of ATCSA-1 for UV-B tolerance.
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Affiliation(s)
- Sascha Biedermann
- School of Biological Sciences, Washington State University, Pullman, 99164, WA, USA
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35
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The nucleosome remodeling factor ISWI functionally interacts with an evolutionarily conserved network of cellular factors. Genetics 2010; 185:129-40. [PMID: 20194965 DOI: 10.1534/genetics.110.114256] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ISWI is an evolutionarily conserved ATP-dependent chromatin remodeling factor playing central roles in DNA replication, RNA transcription, and chromosome organization. The variety of biological functions dependent on ISWI suggests that its activity could be highly regulated. Our group has previously isolated and characterized new cellular activities that positively regulate ISWI in Drosophila melanogaster. To identify factors that antagonize ISWI activity we developed a novel in vivo eye-based assay to screen for genetic suppressors of ISWI. Our screen revealed that ISWI interacts with an evolutionarily conserved network of cellular and nuclear factors that escaped previous genetic and biochemical analyses.
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36
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Abstract
New methods for the genome-wide analysis of chromatin are providing insight into its roles in development and their underlying mechanisms. Current studies indicate that chromatin is dynamic, with its structure and its histone modifications undergoing global changes during transitions in development and in response to extracellular cues. In addition to DNA methylation and histone modification, ATP-dependent enzymes that remodel chromatin are important controllers of chromatin structure and assembly, and are major contributors to the dynamic nature of chromatin. Evidence is emerging that these chromatin-remodelling enzymes have instructive and programmatic roles during development. Particularly intriguing are the findings that specialized assemblies of ATP-dependent remodellers are essential for establishing and maintaining pluripotent and multipotent states in cells.
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Affiliation(s)
- Lena Ho
- Stanford University Medical School, Room B211, Beckman Center, 279 Campus Drive, Stanford, California 94305, USA
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37
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Pham CD, He X, Schnitzler GR. Divergent human remodeling complexes remove nucleosomes from strong positioning sequences. Nucleic Acids Res 2009; 38:400-13. [PMID: 19906705 PMCID: PMC2811002 DOI: 10.1093/nar/gkp1030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nucleosome positioning plays a major role in controlling the accessibility of DNA to transcription factors and other nuclear processes. Nucleosome positions after assembly are at least partially determined by the relative affinity of DNA sequences for the histone octamer. Nucleosomes can be moved, however, by a class of ATP dependent chromatin remodeling complexes. We recently showed that the human SWI/SNF remodeling complex moves nucleosomes in a sequence specific manner, away from nucleosome positioning sequences (NPSes). Here, we compare the repositioning specificity of five remodelers of diverse biological functions (hSWI/SNF, the SNF2h ATPase and the hACF, CHRAC and WICH complexes than each contain SNF2h) on 5S rDNA, MMTV and 601 NPS polynucleosomal templates. We find that all five remodelers act similarly to reduce nucleosome occupancy over the strongest NPSes, an effect that could directly contribute to the function of WICH in activating 5S rDNA transcription. While some differences were observed between complexes, all five remodelers were found to result in surprisingly similar nucleosome distributions. This suggests that remodeling complexes may share a conserved repositioning specificity, and that their divergent biological functions may largely arise from other properties conferred by complex-specific subunits.
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Affiliation(s)
- Chuong D Pham
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
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38
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Biochemical analyses of nuclear receptor-dependent transcription with chromatin templates. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:137-92. [PMID: 20374704 DOI: 10.1016/s1877-1173(09)87005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Chromatin, the physiological template for transcription, plays important roles in gene regulation by nuclear receptors (NRs). It can (1) restrict the binding of NRs or the transcriptional machinery to their genomic targets, (2) serve as a target of regulatory posttranslational modifications by NR coregulator proteins with histone-directed enzymatic activities, and (3) function as a binding scaffold for a variety of transcription-related proteins. The advent of in vitro or "cell-free" systems that accurately recapitulate ligand-dependent transcription by NRs with chromatin templates has allowed detailed analyses of these processes. Biochemical studies have advanced our understanding of the mechanisms of gene regulation, including the role of ligands, coregulators, and nucleosome remodeling. In addition, they have provided new insights about the dynamics of NR-mediated transcription. This chapter reviews the current methodologies for assembling, transcribing, and analyzing chromatin in vitro, as well as the new information that has been gained from these studies.
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39
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Walker P, Doenecke D, Kahle J. Importin 13 mediates nuclear import of histone fold-containing chromatin accessibility complex heterodimers. J Biol Chem 2009; 284:11652-62. [PMID: 19218565 DOI: 10.1074/jbc.m806820200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The histone fold is a structural element that facilitates heterodimerization, and histone fold heterodimers play crucial roles in gene regulation. Here, we investigated the nuclear import of two human histone fold pairs, which belong to the H2A/H2B family: CHRAC-15/CHRAC-17 and p12/CHRAC-17. Our results from in vitro nuclear import assays with permeabilized cells and in vivo cotransfection experiments reveal that importin 13 facilitates nuclear import of both histone fold heterodimers. Using glutathione S-transferase pulldown experiments, we provide evidence that heterodimers are required for efficient binding of importin 13 because the monomers alone do not significantly interact. Mutational analysis shows that stepwise substitution of basic amino acid residues conserved among the histone fold subunits leads to a progressive loss of importin 13 binding and nuclear accumulation of CHRAC-15/CHRAC-17 and p12/CHRAC-17. The distribution of basic amino acid residues among the histone fold subunits essential for nuclear uptake suggests that heterodimerization of the histone fold motif-containing proteins forms an importin 13-specific binding platform.
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Affiliation(s)
- Patrick Walker
- Institut für Biochemie und Molekulare Zellbiologie, Abteilung Molekularbiologie, Universität Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
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40
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Sala A, La Rocca G, Burgio G, Kotova E, Di Gesù D, Collesano M, Ingrassia AMR, Tulin AV, Corona DFV. The nucleosome-remodeling ATPase ISWI is regulated by poly-ADP-ribosylation. PLoS Biol 2009; 6:e252. [PMID: 18922045 PMCID: PMC2567001 DOI: 10.1371/journal.pbio.0060252] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 09/09/2008] [Indexed: 12/22/2022] Open
Abstract
ATP-dependent nucleosome-remodeling enzymes and covalent modifiers of chromatin
set the functional state of chromatin. However, how these enzymatic activities
are coordinated in the nucleus is largely unknown. We found that the
evolutionary conserved nucleosome-remodeling ATPase ISWI and the poly-ADP-ribose
polymerase PARP genetically interact. We present evidence showing that ISWI is
target of poly-ADP-ribosylation. Poly-ADP-ribosylation counteracts ISWI function
in vitro and in vivo. Our work suggests that ISWI is a physiological target of
PARP and that poly-ADP-ribosylation can be a new, important post-translational
modification regulating the activity of ATP-dependent nucleosome remodelers. The ISWI protein is a highly conserved nucleosome remodeler that plays essential
roles in regulating chromosome structure, DNA replication, and gene expression.
The variety of functions associated with ISWI activity are probably connected to
the ability of other cellular factors to regulate its ATP-dependent
nucleosome-remodeling activity. We identified one factor—the poly-ADP-ribose
polymerase, PARP—that can counteract ISWI function. PARP is an abundant nuclear
protein that catalyzes the transfer of ADP-ribose units to specific proteins
involved in DNA repair, transcription, and chromatin structure. Our work
suggests that the activity of an ATP-dependent remodeler can be modulated by
poly-ADP-ribosylation in order to regulate chromatin function in vivo. Enzymes that mediate nucleosome remodeling and poly-ADP-ribosylation play
essential roles in the eukaryotic cell. A new study suggests a mechanism to
explain how two nuclear enzymes can coordinate their activities to regulate
chromatin structure and function.
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Affiliation(s)
- Anna Sala
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
| | - Gaspare La Rocca
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
| | - Giosalba Burgio
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di
Palermo, Palermo, Italy
| | - Elena Kotova
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
of America
| | - Dario Di Gesù
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di
Palermo, Palermo, Italy
| | - Marianna Collesano
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
| | | | - Alexei V Tulin
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
of America
| | - Davide F. V Corona
- Istituto Telethon Dulbecco, Universita' degli Studi di Palermo,
Palermo, Italy
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di
Palermo, Palermo, Italy
- * To whom correspondence should be addressed. E-mail:
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Meagher RB, Kandasamy MK, McKinney EC, Roy E. Chapter 5. Nuclear actin-related proteins in epigenetic control. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 277:157-215. [PMID: 19766970 PMCID: PMC2800988 DOI: 10.1016/s1937-6448(09)77005-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The nuclear actin-related proteins (ARPs) share overall structure and low-level sequence homology with conventional actin. They are indispensable subunits of macromolecular machines that control chromatin remodeling and modification leading to dynamic changes in DNA structure, transcription, and DNA repair. Cellular, genetic, and biochemical studies suggest that the nuclear ARPs are essential to the epigenetic control of the cell cycle and cell proliferation in all eukaryotes, while in plants and animals they also exert epigenetic controls over most stages of multicellular development including organ initiation, the switch to reproductive development, and senescence and programmed cell death. A theme emerging from plants and animals is that in addition to their role in controlling the general compaction of DNA and gene silencing, isoforms of nuclear ARP-containing chromatin complexes have evolved to exert dynamic epigenetic control over gene expression and different phases of multicellular development. Herein, we explore this theme by examining nuclear ARP phylogeny, activities of ARP-containing chromatin remodeling complexes that lead to epigenetic control, expanding developmental roles assigned to several animal and plant ARP-containing complexes, the evidence that thousands of ARP complex isoforms may have evolved in concert with multicellular development, and ARPs in human disease.
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Affiliation(s)
- Richard B Meagher
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, GA 30602, USA
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42
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Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X. Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Structure 2008; 16:1417-27. [PMID: 18786404 DOI: 10.1016/j.str.2008.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Revised: 06/11/2008] [Accepted: 06/30/2008] [Indexed: 11/30/2022]
Abstract
RapA, as abundant as sigma70 in the cell, is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein with ATPase activity. It stimulates RNAP recycling during transcription. We report a structure of RapA that is also a full-length structure for the entire Swi2/Snf2 family. RapA contains seven domains, two of which exhibit novel protein folds. Our model of RapA in complex with ATP and double-stranded DNA (dsDNA) suggests that RapA may bind to and translocate on dsDNA. Our kinetic template-switching assay shows that RapA facilitates the release of sequestered RNAP from a posttranscrption/posttermination complex for transcription reinitiation. Our in vitro competition experiment indicates that RapA binds to core RNAP only but is readily displaceable by sigma70. RapA is likely another general transcription factor, the structure of which provides a framework for future studies of this bacterial Swi2/Snf2 protein and its important roles in RNAP recycling during transcription.
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Affiliation(s)
- Gary Shaw
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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43
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Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. PLoS Genet 2008; 4:e1000241. [PMID: 18974875 PMCID: PMC2570622 DOI: 10.1371/journal.pgen.1000241] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Accepted: 09/29/2008] [Indexed: 12/22/2022] Open
Abstract
We have characterized the biological functions of the chromatin remodeling protein Bptf (Bromodomain PHD-finger Transcription Factor), the largest subunit of NURF (Nucleosome Remodeling Factor) in a mammal. Bptf mutants manifest growth defects at the post-implantation stage and are reabsorbed by E8.5. Histological analyses of lineage markers show that Bptf−/− embryos implant but fail to establish a functional distal visceral endoderm. Microarray analysis at early stages of differentiation has identified Bptf-dependent gene targets including homeobox transcriptions factors and genes essential for the development of ectoderm, mesoderm, and both definitive and visceral endoderm. Differentiation of Bptf−/− embryonic stem cell lines into embryoid bodies revealed its requirement for development of mesoderm, endoderm, and ectoderm tissue lineages, and uncovered many genes whose activation or repression are Bptf-dependent. We also provide functional and physical links between the Bptf-containing NURF complex and the Smad transcription factors. These results suggest that Bptf may co-regulate some gene targets of this pathway, which is essential for establishment of the visceral endoderm. We conclude that Bptf likely regulates genes and signaling pathways essential for the development of key tissues of the early mouse embryo. While the chromatin of eukaryotes provides an efficient means to compact large amounts of DNA into a small nucleus, it renders the DNA relatively inaccessible. ATP-dependent chromatin remodeling complexes mobilize nucleosomes and provide a means to gain access to DNA in chromatin. While the biochemical functions of chromatin remodeling complexes is well-characterized, less is known of their biological functions. In this manuscript, we elucidate the biological functions of Bptf, a subunit of the NURF chromatin remodeling complex. Our studies show that Bptf is required for the establishment of the anterior–posterior axis of the mouse embryo during the earliest stages of development. To understand its functions in tissue differentiation, we generated and characterized Bptf-mutant ES cells. Mutant embryonic stem cells show significant defects in the differentiation of ectoderm, endoderm, and mesoderm. Genome-wide analysis of gene expression defects during differentiation has identified many Bptf-dependent pathways including key regulators of ectoderm, endoderm, and mesoderm differentiation. Moreover, we have identified critical functions for Bptf during the TGFβ/Smad-induced expression of visceral endoderm and mesoderm markers, an important signaling pathway in the early embryo. These results suggest that chromatin remodeling by Bptf regulates key signaling pathways in the early mouse embryo.
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Burgio G, La Rocca G, Sala A, Arancio W, Di Gesù D, Collesano M, Sperling AS, Armstrong JA, van Heeringen SJ, Logie C, Tamkun JW, Corona DFV. Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI. PLoS Genet 2008; 4:e1000089. [PMID: 18535655 PMCID: PMC2390755 DOI: 10.1371/journal.pgen.1000089] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Accepted: 05/02/2008] [Indexed: 02/03/2023] Open
Abstract
Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.
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Affiliation(s)
- Giosalba Burgio
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di Palermo, Palermo, Italy
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Pandey SP, Baldwin IT. Silencing RNA-directed RNA polymerase 2 increases the susceptibility of Nicotiana attenuata to UV in the field and in the glasshouse. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 54:845-62. [PMID: 18298673 DOI: 10.1111/j.1365-313x.2008.03450.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA-directed RNA-polymerases (RdRs) are essential in small interfering RNA (siRNA) biogenesis and appear to be functionally specialized. We examined the consequences of silencing RdR2 in Nicotiana attenuata with a field release, and transcriptional, two-dimensional proteomic and metabolite analyses. NaRdR2-silenced plants (irRdR2) had large reductions (46% of wild type) in 22-24-nt small RNAs (smRNAs), and smaller reductions (35, 23 and 26% of wild type) in the 19-21, 25-27 and 28-30-nt smRNAs, respectively. When planted into their native habitats in the Great Basin Desert, irRdR2 plants had impaired growth and reproductive output, which were associated with reduced levels of leaf phenolics (rutin and 4'-chlorogenic acid) and MYB and PAL transcripts, but were unaffected in their herbivore resistance. These phenotypes were confirmed in glasshouse experiments, but only when irRdR2 plants were grown with UV-B radiation. irRdR2 plants had wild-type levels of elicited phytohormones and resistance to Manduca sexta attack, but when exposed to UV-B, had reduced growth, fitness, levels of MYB and PAL transcripts, and phenolics. Proteins related to protection against oxidative and physiological stresses, chromatin remodeling and transcription were also downregulated. Silencing the MYB gene by virus-induced gene silencing (VIGS) in wild-type plants reduced levels of PAL transcripts and phenolics, as it did in UV-exposed irRdR2 plants. Bioinformatic analysis revealed that genes involved in phenylpropanoid biosynthesis contained a large number of smRNA binding motives, suggesting that these genes are targets of smRNAs. We conclude that although NaRdR2 transcripts are upregulated in response to both UV-B and herbivore elicitation, the responses they regulate have been tailored to provide protection from UV-B radiation.
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Affiliation(s)
- Shree P Pandey
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena 07745, Germany
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Xia Y, Jiang B, Zou Y, Gao G, Shang L, Chen B, Liu Q, Gong Y. Sp1 and CREB regulate basal transcription of the human SNF2L gene. Biochem Biophys Res Commun 2008; 368:438-44. [PMID: 18243132 DOI: 10.1016/j.bbrc.2008.01.111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Accepted: 01/24/2008] [Indexed: 11/15/2022]
Abstract
Imitation Switch (ISWI) is a member of the SWI2/SNF2 superfamily of ATP-dependent chromatin remodelers, which are involved in multiple nuclear functions, including transcriptional regulation, replication, and chromatin assembly. Mammalian genomes encode two ISWI orthologs, SNF2H and SNF2L. In order to clarify the molecular mechanisms governing the expression of human SNF2L gene, we functionally examined the transcriptional regulation of human SNF2L promoter. Reporter gene assays demonstrated that the minimal SNF2L promoter was located between positions -152 to -86 relative to the transcription start site. In this region we have identified a cAMP-response element (CRE) located at -99 to -92 and a Sp1-binding site at -145 to -135 that play a critical role in regulating basal activity of human SNF2L gene, which were proven by deletion and mutation of specific binding sites, EMSA, and down-regulating Sp1 and CREB via RNAi. This study provides the first insight into the mechanisms that control basal expression of human SNF2L gene.
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Affiliation(s)
- Yu Xia
- Key Laboratory for Experimental Teratology of the Ministry of Education and Institute of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
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Brown E, Malakar S, Krebs JE. How many remodelers does it take to make a brain? Diverse and cooperative roles of ATP-dependent chromatin-remodeling complexes in development. Biochem Cell Biol 2008; 85:444-62. [PMID: 17713580 DOI: 10.1139/o07-059] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The development of a metazoan from a single-celled zygote to a complex multicellular organism requires elaborate and carefully regulated programs of gene expression. However, the tight packaging of genomic DNA into chromatin makes genes inaccessible to the cellular machinery and must be overcome by the processes of chromatin remodeling; in addition, chromatin remodeling can preferentially silence genes when their expression is not required. One class of chromatin remodelers, ATP-dependent chromatin-remodeling enzymes, can slide nucleosomes along the DNA to make specific DNA sequences accessible or inaccessible to regulators at a particular stage of development. While all ATPases in the SWI2/SNF2 superfamily share the fundamental ability to alter DNA accessibility in chromatin, they do not act alone, but rather, are subunits of a large assortment of protein complexes. Recent studies illuminate common themes by which the subunit compositions of chromatin-remodeling complexes specify the developmental roles that chromatin remodelers play in specific tissues and at specific stages of development, in response to specific signaling pathways and transcription factors. In this review, we will discuss the known roles in metazoan development of 3 major subfamilies of chromatin-remodeling complexes: the SNF2, ISWI, and CHD subfamilies.
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Affiliation(s)
- Elvin Brown
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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Affiliation(s)
- J Adam Hall
- Department of Biological Sciences, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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Pal S, Sif S. Interplay between chromatin remodelers and protein arginine methyltransferases. J Cell Physiol 2008; 213:306-15. [PMID: 17708529 DOI: 10.1002/jcp.21180] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chromatin modifying enzymes have emerged as key regulators of all DNA based processes, which control cell growth, development, and differentiation. Recently, it has become clear that different chromatin remodeling and histone-modifying activities are involved in transcriptional activation and repression. Among the enzymes involved in regulating chromatin structure is the family of protein arginine methyltransferases (PRMTs) that specializes in methylating both histones as well as key cellular proteins. There are eleven different PRMT genes (PRMT1-11) whose biological function remains under explored. PRMTs regulate various cellular processes such as DNA repair and transcription, RNA processing, signal transduction, and nucleo-cytoplasmic localization. Like histone lysine methylation, methylation of histone arginine residues can either induce or inhibit transcription depending on the residue being modified and the type of methylation being introduced. In this review, we will focus on the latest findings and biological roles of ATP-dependent chromatin remodeling complexes and PRMT enzymes, and how their aberrant expression is linked to cancer.
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Affiliation(s)
- Sharmistha Pal
- Department of Molecular and Cellular Biochemistry, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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