1
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Weissman JD, Kotekar A, Barbash Z, Mu J, Singer DS. CCAAT Promoter element regulates transgenerational expression of the MHC class I gene. Chromosoma 2024; 133:203-216. [PMID: 38922437 PMCID: PMC11266202 DOI: 10.1007/s00412-024-00820-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Transgenerational gene expression depends on both underlying DNA sequences and epigenetic modifications. The latter, which can result in transmission of variegated gene expression patterns across multiple generations without DNA alterations, has been termed epigenetic inheritance and has been documented in plants, worms, flies and mammals. Whereas transcription factors binding to cognate DNA sequence elements regulate gene expression, the molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. Here we report that mutation of the CCAAT box promoter element abrogates NF-Y binding and disrupts the stable transgenerational expression of an MHC class I transgene. Transgenic mice with a mutated CCAAT box in the MHC class I transgene display variegated expression of the transgene among littermates and progeny in multiple independently derived transgenic lines. After 4 generations, CCAAT mutant transgenic lines derived from a single founder stably displayed distinct patterns of expression. Histone modifications and RNA polymerase II binding correlate with expression of CCAAT mutant transgenic lines, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box also results in changes to CTCF binding and DNA looping patterns across the transgene that correlate with expression status. These studies identify the CCAAT promoter element as a regulator of stable transgenerational gene expression such that mutation of the CCAAT box results in variegated transgenerational inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study provides insights into how fidelity of gene expression patterns is maintained through multiple generations.
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Affiliation(s)
- Jocelyn D Weissman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA
| | - Aparna Kotekar
- NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI), National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | | | - Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA
| | - Dinah S Singer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA.
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2
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Goes CP, Botezelli VS, De La Cruz SM, Cruz MC, Azambuja AP, Simoes-Costa M, Yan CYI. ASCL1 promotes Scrt2 expression in the neural tube. Front Cell Dev Biol 2024; 12:1324584. [PMID: 38655067 PMCID: PMC11036302 DOI: 10.3389/fcell.2024.1324584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
ASCL1 is a transcription factor that directs neural progenitors towards lineage differentiation. Although many of the molecular mechanisms underlying its action have been described, several of its targets remain unidentified. We identified in the chick genome a putative enhancer (cE1) upstream of the transcription factor Scratch2 (Scrt2) locus with a predicted heterodimerization motif for ASCL1 and POU3F2. In this study, we investigated the role of ASCL1 and this enhancer in regulating the expression of the Scrt2 in the embryonic spinal cord. We confirmed that cE1 region interacted with the Scrt2 promoter. cE1 was sufficient to mediate ASCL1-driven expression in the neural tube through the heterodimerization sites. Moreover, Scrt2 expression was inhibited when we removed cE1 from the genome. These findings strongly indicate that ASCL1 regulates Scrt2 transcription in the neural tube through cE1.
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Affiliation(s)
- Carolina Purcell Goes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Vitória Samartin Botezelli
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Shirley Mirna De La Cruz
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Mário Costa Cruz
- Core Research Facilities (CEFAP), Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Ana Paula Azambuja
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
- Department of Systems Biology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
- Department of Systems Biology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Chao Yun Irene Yan
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
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3
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Wang Z, Luo M, Liang Q, Zhao K, Hu Y, Wang W, Feng X, Hu B, Teng J, You T, Li R, Bao Z, Pan W, Yang T, Zhang C, Li T, Dong X, Yi X, Liu B, Zhao L, Li M, Chen K, Song W, Yang J, Li MJ. Landscape of enhancer disruption and functional screen in melanoma cells. Genome Biol 2023; 24:248. [PMID: 37904237 PMCID: PMC10614365 DOI: 10.1186/s13059-023-03087-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/12/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those in enhancers, can shape tumor evolution, thereby emphasizing the importance in systematically deciphering enhancer disruptions in melanoma. RESULTS Here, we leveraged 297 melanoma whole-genome sequencing samples to prioritize highly recurrent regions. By performing a genome-scale CRISPR interference (CRISPRi) screen on highly recurrent region-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers reveal many known and hidden mechanisms underlying melanoma growth. Utilizing extensive functional validation experiments, we demonstrate that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A, and another distal enhancer is able to sustain PTEN tumor-suppressive potential via long-range interactions. CONCLUSIONS Our study establishes a catalogue of crucial enhancers and their target genes in melanoma growth and progression, and illuminates the identification of novel mechanisms of dysregulation for melanoma driver genes and new therapeutic targeting strategies.
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Affiliation(s)
- Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Menghan Luo
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Scientific Research Center, Wenzhou Medical University, Wenzhou, China
| | - Ke Zhao
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuelin Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bolang Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianjin Teng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianyi You
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ran Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhengkai Bao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wenhao Pan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Tielong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chao Zhang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ting Li
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Li Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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4
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Chang LH, Ghosh S, Papale A, Luppino JM, Miranda M, Piras V, Degrouard J, Edouard J, Poncelet M, Lecouvreur N, Bloyer S, Leforestier A, Joyce EF, Holcman D, Noordermeer D. Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. Nat Commun 2023; 14:5615. [PMID: 37699887 PMCID: PMC10497529 DOI: 10.1038/s41467-023-41265-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.
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Affiliation(s)
- Li-Hsin Chang
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, and National Institute of Health Research, Blood and Transplant Research Unit in Precision Cellular Therapeutics, OX3 9DS, Oxford, UK
| | - Sourav Ghosh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Department of Pathology and Laboratory Medicine, Western University, N6A3K7, London, ON, Canada
| | - Andrea Papale
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
| | - Jennifer M Luppino
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mélanie Miranda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Vincent Piras
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Joanne Edouard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Mallory Poncelet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nathan Lecouvreur
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sébastien Bloyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Amélie Leforestier
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides (LPS), 91405, Orsay, France
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Holcman
- École Normale Supérieure, IBENS, Université PSL, 75005, Paris, France
- Churchill College, University of Cambridge, CB3 0DS, Cambridge, UK
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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5
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Weissman JD, Kotekar A, Barbash Z, Mu J, Singer DS. Transgenerational Epigenetic Inheritance of MHC Class I Gene Expression is Regulated by the CCAAT Promoter Element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536772. [PMID: 37333336 PMCID: PMC10274869 DOI: 10.1101/2023.04.13.536772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Transgenerational epigenetic inheritance is defined as the transmission of traits or gene expression patterns across multiple generations that do not derive from DNA alterations. The effect of multiple stress factors or metabolic changes resulting in such inheritance have been documented in plants, worms and flies and mammals. The molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. In this study, we show that mutation of a promoter element, the CCAAT box, disrupts stable expression of an MHC Class I transgene, resulting in variegated expression among progeny for at least 4 generations in multiple independently derived transgenic lines. Histone modifications and RNA polII binding correlate with expression, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box abrogates NF-Y binding and results in changes to CTCF binding and DNA looping patterns across the gene that correlate with expression status from one generation to the next. These studies identify the CCAAT promoter element as a regulator of stable transgenerational epigenetic inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study could provide important insights into how fidelity of gene expression patterns is maintained through multiple generations.
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Affiliation(s)
- Jocelyn D Weissman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Aparna Kotekar
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Zohar Barbash
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Dinah S Singer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
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6
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An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. Nat Commun 2023; 14:1208. [PMID: 36869052 PMCID: PMC9984425 DOI: 10.1038/s41467-023-36897-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Genetic sharing is extensively observed for autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of autoimmune disease pleiotropic loci, we found most of these shared genetic effects are transmitted from regulatory code. We used an evidence-based strategy to functionally prioritize causal pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, yielded many lines of evidence as being causal. Mechanistically, the rs4728142-containing region interacts with the IRF5 alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific loop to promote IRF5-short transcript expression at the rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between the regulatory variant and fine-scale molecular phenotype underlying the dysfunction of pleiotropic genes in human autoimmunity.
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7
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Trangle SS, Rosenberg T, Parnas H, Levy G, Bar E, Marco A, Barak B. In individuals with Williams syndrome, dysregulation of methylation in non-coding regions of neuronal and oligodendrocyte DNA is associated with pathology and cortical development. Mol Psychiatry 2023; 28:1112-1127. [PMID: 36577841 DOI: 10.1038/s41380-022-01921-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/29/2022]
Abstract
Williams syndrome (WS) is a neurodevelopmental disorder caused by a heterozygous micro-deletion in the WS critical region (WSCR) and is characterized by hyper-sociability and neurocognitive abnormalities. Nonetheless, whether and to what extent WSCR deletion leads to epigenetic modifications in the brain and induces pathological outcomes remains largely unknown. By examining DNA methylation in frontal cortex, we revealed genome-wide disruption in the methylome of individuals with WS, as compared to typically developed (TD) controls. Surprisingly, differentially methylated sites were predominantly annotated as introns and intergenic loci and were found to be highly enriched around binding sites for transcription factors that regulate neuronal development, plasticity and cognition. Moreover, by utilizing enhancer-promoter interactome data, we confirmed that most of these loci function as active enhancers in the human brain or as target genes of transcriptional networks associated with myelination, oligodendrocyte (OL) differentiation, cognition and social behavior. Cell type-specific methylation analysis revealed aberrant patterns in the methylation of active enhancers in neurons and OLs, and important neuron-glia interactions that might be impaired in individuals with WS. Finally, comparison of methylation profiles from blood samples of individuals with WS and healthy controls, along with other data collected in this study, identified putative targets of endophenotypes associated with WS, which can be used to define brain-risk loci for WS outside the WSCR locus, as well as for other associated pathologies. In conclusion, our study illuminates the brain methylome landscape of individuals with WS and sheds light on how these aberrations might be involved in social behavior and physiological abnormalities. By extension, these results may lead to better diagnostics and more refined therapeutic targets for WS.
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Affiliation(s)
- Sari Schokoroy Trangle
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tali Rosenberg
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Hadar Parnas
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Gilad Levy
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ela Bar
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.,The School of Neurobiology, Biochemistry & Biophysics, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Asaf Marco
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Boaz Barak
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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8
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Rosenberg T, Marco A, Kisliouk T, Haron A, Shinder D, Druyan S, Meiri N. Embryonic heat conditioning in chicks induces transgenerational heat/immunological resilience via methylation on regulatory elements. FASEB J 2022; 36:e22406. [PMID: 35713935 DOI: 10.1096/fj.202101948r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/18/2022] [Accepted: 05/28/2022] [Indexed: 11/11/2022]
Abstract
The question of whether behavioral traits are heritable is under debate. An obstacle in demonstrating transgenerational inheritance in mammals originates from the maternal environment's effect on offspring phenotype. Here, we used in ovo embryonic heat conditioning (EHC) of first-generation chicks, demonstrating heredity of both heat and immunological resilience, confirmed by a reduced fibril response in their untreated offspring to either heat or LPS challenge. Concordantly, transcriptome analysis confirmed that EHC induces changes in gene expression in the anterior preoptic hypothalamus (APH) that contribute to these phenotypes in the offspring. To study the association between epigenetic mechanisms and trait heritability, DNA-methylation patterns in the APH of offspring of control versus EHC fathers were evaluated. Genome-wide analysis revealed thousands of differentially methylated sites (DMSs), which were highly enriched in enhancers and CCCTC-binding factor (CTCF) sites. Overlap analysis revealed 110 differentially expressed genes that were associated with altered methylation, predominantly on enhancers. Gene-ontology analysis shows pathways associated with immune response, chaperone-mediated protein folding, and stress response. For the proof of concept, we focused on HSP25 and SOCS3, modulators of heat and immune responses, respectively. Chromosome conformational capture (3C) assay identified interactions between their promoters and methylated enhancers, with the strongest frequency on CTCF binding sites. Furthermore, gene expression corresponded with the differential methylation patterns, and presented increased CTCF binding in both hyper- and hypomethylated DMSs. Collectively, we demonstrate that EHC induces transgenerational thermal and immunological resilience traits. We propose that one of the mechanisms underlying inheritance depends on three-dimensional (3D) chromatin reorganization.
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Affiliation(s)
- Tali Rosenberg
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Asaf Marco
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tatiana Kisliouk
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Amit Haron
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dmitry Shinder
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Shelly Druyan
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Noam Meiri
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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9
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Bylino OV, Ibragimov AN, Pravednikova AE, Shidlovskii YV. Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure. Front Genet 2021; 12:733937. [PMID: 34616432 PMCID: PMC8488379 DOI: 10.3389/fgene.2021.733937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/16/2021] [Indexed: 12/05/2022] Open
Abstract
A constellation of chromosome conformation capture methods (С-methods) are an important tool for biochemical analysis of the spatial interactions between DNA regions that are separated in the primary sequence. All these methods are based on the long sequence of basic steps of treating cells, nuclei, chromatin, and finally DNA, thus representing a significant technical challenge. Here, we present an in-depth study of the basic steps in the chromatin conformation capture procedure (3С), which was performed using Drosophila Schneider 2 cells as a model. We investigated the steps of cell lysis, nuclei washing, nucleoplasm extraction, chromatin treatment with SDS/Triton X-100, restriction enzyme digestion, chromatin ligation, reversion of cross-links, DNA extraction, treatment of a 3C library with RNases, and purification of the 3C library. Several options were studied, and optimal conditions were found. Our work contributes to the understanding of the 3C basic steps and provides a useful guide to the 3C procedure.
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Affiliation(s)
- Oleg V. Bylino
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Airat N. Ibragimov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna E. Pravednikova
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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10
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Xiao K, Xiong D, Chen G, Yu J, Li Y, Chen K, Zhang L, Xu Y, Xu Q, Huang X, Gao A, Cao K, Yan K, Dai J, Hu X, Ruan Y, Fu Z, Li G, Cao G. RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription. SCIENCE ADVANCES 2021; 7:7/26/eabf8962. [PMID: 34162542 PMCID: PMC8221632 DOI: 10.1126/sciadv.abf8962] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/10/2021] [Indexed: 05/04/2023]
Abstract
Like most DNA viruses, herpesviruses precisely deliver their genomes into the sophisticatedly organized nuclei of the infected host cells to initiate subsequent transcription and replication. However, it remains elusive how the viral genome specifically interacts with the host genome and hijacks host transcription machinery. Using pseudorabies virus (PRV) as model virus, we performed chromosome conformation capture assays to demonstrate a genome-wide specific trans-species chromatin interaction between the virus and host. Our data show that the PRV genome is delivered by the host DNA binding protein RUNX1 into the open chromatin and active transcription zone. This facilitates virus hijacking host RNAPII to efficiently transcribe viral genes, which is significantly inhibited by either a RUNX1 inhibitor or RNA interference. Together, these findings provide insights into the chromatin interaction between viral and host genomes and identify new areas of research to advance the understanding of herpesvirus genome transcription.
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Affiliation(s)
- Ke Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Gong Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinsong Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Kening Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yangyang Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Anran Gao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Keji Yan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxia Dai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xueying Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yijun Ruan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Zhenfang Fu
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
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11
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Zha M, Wang N, Zhang C, Wang Z. Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential. Int J Mol Sci 2021; 22:ijms22115914. [PMID: 34072879 PMCID: PMC8199262 DOI: 10.3390/ijms22115914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/23/2021] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis-Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.
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Affiliation(s)
- Mengsheng Zha
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Dr, Hattiesburg, MS 39406, USA; (M.Z.); (C.Z.)
| | - Nan Wang
- Department of Computer Science, New Jersey City University, 2039 Kennedy Blvd, Jersey City, NJ 07305, USA;
| | - Chaoyang Zhang
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Dr, Hattiesburg, MS 39406, USA; (M.Z.); (C.Z.)
| | - Zheng Wang
- Department of Computer Science, University of Miami, 1364 Memorial Drive, Coral Gables, FL 33124, USA
- Correspondence:
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12
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Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis. Proc Natl Acad Sci U S A 2020; 117:13033-13043. [PMID: 32461362 DOI: 10.1073/pnas.1917286117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and ultrahigh-performance liquid chromatography (UHPLC), we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5-methylcytosine (5mC), is the main DNA methylation mark in T. vaginalis Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain superfamilies of DNA transposable elements. We show that 6mA in T. vaginalis is associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions, and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a role for 6mA in modulating three-dimensional (3D) chromatin structure and gene expression in this divergent member of the Excavata.
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13
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Chromosome conformation capture that detects novel cis- and trans-interactions in budding yeast. Methods 2019; 170:4-16. [PMID: 31252061 DOI: 10.1016/j.ymeth.2019.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/17/2019] [Accepted: 06/21/2019] [Indexed: 11/22/2022] Open
Abstract
Chromosome Conformation Capture (3C) has emerged as a powerful approach for revealing the conformation and features of three-dimensional (3D) genomic organization. Yet attainment of higher resolution in organisms with compact genomes presents a challenge. Here, we describe modifications in the 3C technique that substantially enhance its resolution and sensitivity when applied to the 3D genome of budding yeast. Keys to our approach include use of a 4 bp cutter, Taq I, for cleaving the genome and quantitative PCR for measuring the frequency of ligation. Most importantly, we normalize the percent digestion at each restriction site to account for variation in accessibility of local chromatin structure under a given physiological condition. This strategy has led to the detection of physical interactions between regulatory elements and gene coding regions as well as intricate, stimulus-specific interchromosomal interactions between activated genes. We provide an algorithm that incorporates these and other modifications and allows quantitative determination of chromatin interaction frequencies in yeast under any physiological condition.
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14
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Sun C, Lu C. Microfluidics-Based Chromosome Conformation Capture (3C) Technology for Examining Chromatin Organization with a Low Quantity of Cells. Anal Chem 2018; 90:3714-3719. [PMID: 29498513 PMCID: PMC5861017 DOI: 10.1021/acs.analchem.8b00310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Detecting three-dimensional (3D) genome organization in the form of physical interactions between various genomic loci is of great importance for understanding transcriptional regulations and cellular fate. Chromosome Conformation Capture (3C) method is the gold standard for examining chromatin organization, but usually requires a large number of cells (>107). This hinders studies of scarce tissue samples from animals and patients using the method. Here we developed a microfluidics-based approach for examining chromosome conformation by 3C technology. Critical 3C steps, such as digestion and religation of BAC DNA and cross-linked chromatin, were implemented on a microfluidic chip using a low quantity of cells (<104). Using this technology, we analyzed the chromatin looping interactions in the human β-globin. We envision that our method will provide a powerful tool for low-input analysis of chromosome conformation and epigenetic regulations.
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Affiliation(s)
- Chen Sun
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, 24061, USA
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15
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Jamge S, Stam M, Angenent GC, Immink RGH. A cautionary note on the use of chromosome conformation capture in plants. PLANT METHODS 2017; 13:101. [PMID: 29177001 PMCID: PMC5691870 DOI: 10.1186/s13007-017-0251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin interactions and their role in transcriptional gene regulation. As the plant scientific community continues to implement this technology, a discussion on critical controls, validations steps and interpretation of 3C data is essential to fully benefit from 3C in plants. RESULTS Here we assess the reliability and robustness of the 3C technique for the detection of chromatin interactions in Arabidopsis. As a case study, we applied this methodology to the genomic locus of a floral integrator gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and demonstrate the need of several controls and standard validation steps to allow a meaningful interpretation of 3C data. The intricacies of this promising but challenging technique are discussed in depth. CONCLUSIONS The 3C technique offers an interesting opportunity to study chromatin interactions at a resolution infeasible by microscopy. However, for interpretation of 3C interaction data and identification of true interactions, 3C technology demands a stringent experimental setup and extreme caution.
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Affiliation(s)
- Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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16
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Smirnov NA, Akopov SB, Didych DA, Nikolaev LG. In trans promoter activation by enhancers in transient transfection. Gene 2017; 603:15-20. [PMID: 27956170 DOI: 10.1016/j.gene.2016.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 11/15/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022]
Abstract
Earlier, it was reported that the strong cytomegalovirus enhancer can activate the cytomegalovirus promoter in trans, i.e. as a separate plasmid co-transfected with a promoter-reporter gene construct. Here we demonstrate that the ability of enhancers to activate promoters in trans in transient transfection experiments is a property of not only viral regulatory elements but also of various genomic enhancers and promoters. Enhancer-promoter activation in trans is promoter- and cell type-specific, and accompanied by physical interaction between promoter and enhancer as revealed by chromosome conformation capture assays. Thus, promoter activation in transient co-transfection of promoters and enhancers shares a number of important traits with long-distance promoter activation by enhancers in living cells and may therefore serve as a model of this fundamental cellular process.
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Affiliation(s)
- N A Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - S B Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - D A Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - L G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
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17
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Zhan J, Johnson IM, Wielgosz M, Nienhuis AW. The identification of hematopoietic-specific regulatory elements for WASp gene expression. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 3:16077. [PMID: 28035317 PMCID: PMC5155633 DOI: 10.1038/mtm.2016.77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 12/26/2022]
Abstract
Chromosome Conformation Capture (3C) technology was used to identify physical interactions between the proximal Wiskott-Aldrich Syndrome protein (WASp) promoter and its distant DNA segments in Jurkat-T cells. We found that two hematopoietic specific DNase I hypersensitive (DHS) sites (proximal DHS-A, and distal DHS-B) which had high interaction frequencies with the proximal WASp promoter indicating potential regulatory activity for these DHS sites. Subsequently, we cloned several DNA fragments around the proximal DHS-A site into a luciferase reporter vector. Interestingly, no fragments showed enhancer activity, but two fragments exhibited strong silencing activity in Jurkat-T cells. After aligning the chromatin state profiling for hematopoietic and nonhematopoietic cells using the human genome browser (UCSC), we found a 5 kb putative hematopoietic specific enhancer region located 250 kb downstream of the WAS gene. This putative enhancer region contains two hematopoietic cell specific DHS sites. Subsequently, the hematopoietic specific DHS sites enhanced luciferase expression from the proximal WASp promoter in all hematopoietic cells we tested. Finally, using a lentiviral vector stable expression system, the hematopoietic specific-enhancer(s) increased GFP reporter gene expression in hematopoietic cells, and increased WASp gene expression in WASp deficient cells. This enhancer may have the potential to be used in gene therapy for hematological diseases.
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Affiliation(s)
- Jun Zhan
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
| | - Irudayam Maria Johnson
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
| | - Matthew Wielgosz
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
| | - Arthur W Nienhuis
- Department of Hematology, Division of Experimental Hematology , St. Jude Children's Research Hospital , Memphis, Tennessee, USA
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18
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Doynova M, Berretta A, Jones M, Jasoni C, Vickers M, O'Sullivan J. Interactions between mitochondrial and nuclear DNA in mammalian cells are non-random. Mitochondrion 2016; 30:187-96. [DOI: 10.1016/j.mito.2016.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 12/18/2022]
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19
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Lin PC, Huang HD, Chang CC, Chang YS, Yen JC, Lee CC, Chang WH, Liu TC, Chang JG. Long noncoding RNA TUG1 is downregulated in non-small cell lung cancer and can regulate CELF1 on binding to PRC2. BMC Cancer 2016; 16:583. [PMID: 27485439 PMCID: PMC4971684 DOI: 10.1186/s12885-016-2569-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 07/15/2016] [Indexed: 12/16/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) play crucial roles in tumorigenesis, and lncRNA taurine-upregulated gene 1 (TUG1) has been proven to be associated with several human cancers. However, the mechanisms of TUG1-involved regulation remain largely unknown. Methods We examined the expressions of TUG1 in a cohort of 89 patients with non-small cell lung cancer (NSCLC) to determine the association between TUG1 expression and clinical parameters. We used circular chromosome conformation capture (4C) coupled with next-generation sequencing to explore the genome regions that interact with TUG1 and the TUG1-mediated regulation. Results TUG1 was significantly downregulated, and the TUG1 downregulation correlated with sex (p = 0.006), smoking status (p = 0.016), and tumor differentiation grade (p = 0.001). Knockdown of TUG1 significantly promoted the proliferation of NSCLC cells. According to the bioinformatic analysis result of TUG1 4C sequencing data, 83 candidate genes and their interaction regions were identified. Among these candidate genes, CUGBP and Elav-like family member 1 (CELF1) are potential targets of TUG1 in-trans regulation. To confirm the interaction between TUG1 and CELF1, relative expressions of CELF1 were examined in TUG1 knockdown H520 cells; results showed that CELF1 was significantly upregulated in TUG1 knockdown H520 cells. RNA immunoprecipitation was then performed to examine whether TUG1 RNA was bound to PRC2, a TUG1-involved regulation mechanism reported in previous studies. The results demonstrated that TUG1 RNA was bound to enhancer of zeste protein 2/embryonic ectoderm development (EZH2/EED), which is essential for PRC2. Finally, our designed ChIP assay revealed that the EZH2/EED was bound to the promotor region of CELF1 within 992 bp upstream of the transcript start site. Conclusion TUG1 is downregulated in NSCLC. Using TUG1 4C sequencing and bioinformatic analysis, we found CELF1 to be a potential target of TUG1 RNA in in-trans regulation. Moreover, subsequent experiments showed that TUG1 RNA could bind to PRC2 in the promotor region of CELF1 and negatively regulate CELF1 expressions in H520 cells. Our results may facilitate developing new treatment modalities targeting TUG1/PRC2/CELF1 interactions in patients with NSCLC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2569-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pei-Chin Lin
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, No. 100, Shih-Chuan 1st Road, Kaohsiung, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hsien-Da Huang
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chun-Chi Chang
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, No. 100, Shih-Chuan 1st Road, Kaohsiung, Taiwan.,Division of Chest Medicine, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, No. 2, Yuh-Der Road, Taichung, Taiwan
| | - Ju-Chen Yen
- Epigenome Research Center, China Medical University Hospital, No. 2, Yuh-Der Road, Taichung, Taiwan
| | - Chien-Chih Lee
- Epigenome Research Center, China Medical University Hospital, No. 2, Yuh-Der Road, Taichung, Taiwan
| | - Wen-Hsin Chang
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ta-Chih Liu
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, No. 100, Shih-Chuan 1st Road, Kaohsiung, Taiwan. .,Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, No. 2, Yuh-Der Road, Taichung, Taiwan. .,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan. .,School of Medicine, China Medical University, Taichung, Taiwan.
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20
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Abstract
3D organization of the genome, its structural and regulatory function of cell identity, is acquiring prominent features in epigenetics studies; more efforts have been done to develop techniques that allow studying nuclear structure. Chromosome conformation capture (3C) has been set up in 2002 from Dekker and from that moment great investments were made to develop genomics variants of 3C technology (4C, 5C, Hi-C) providing new tools to investigate the shape of the genome in a more systematic and unbiased manner. 3C method allows scientists to fix dynamic and variable 3D interactions in nuclear space, and consequently to study which sequences interact, how a gene is regulated by different and distant enhancer, or how a set of enhancer could regulate transcriptional units; to follow the conformation that mediates regulation change in development; and to evaluate if this fine epigenetic mechanism is impaired in disease condition.
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Affiliation(s)
- Alice Cortesi
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, 20122, Milano, Italy
| | - Beatrice Bodega
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, 20122, Milano, Italy.
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21
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Zhang Z, Zhang Y, Shi M, Ye B, Shen W, Li P, Xing L, Zhang X, Hou L, Xu J, Zhao Z, Chen W. Anthrax Susceptibility: Human Genetic Polymorphisms Modulating ANTXR2 Expression. Toxins (Basel) 2015; 8:toxins8010001. [PMID: 26703731 PMCID: PMC4728523 DOI: 10.3390/toxins8010001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/29/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023] Open
Abstract
Anthrax toxin causes anthrax pathogenesis and expression levels of ANTXR2 (anthrax toxin receptor 2) are strongly correlated with anthrax toxin susceptibility. Previous studies found that ANTXR2 transcript abundance varies considerably in individuals of different ethnic/geographical groups, but no eQTLs (expression quantitative trait loci) have been identified. By using 3C (chromatin conformation capture), CRISPR-mediated genomic deletion and dual-luciferase reporter assay, gene loci containing cis-regulatory elements of ANTXR2 were localized. Two SNPs (single nucleotide polymorphism) at the conserved CREB-binding motif, rs13140055 and rs80314910 in the promoter region of the gene, modulating ANTXR2 promoter activity were identified. Combining these two regulatory SNPs with a previously reported SNP, rs12647691, for the first time, a statistically significant correlation between human genetic variations and anthrax toxin sensitivity was observed. These findings further our understanding of human variability in ANTXR2 expression and anthrax toxin susceptibility.
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Affiliation(s)
- Zhang Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Yan Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Minglei Shi
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Bingyu Ye
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Wenlong Shen
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Ping Li
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Lingyue Xing
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Xiaopeng Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Lihua Hou
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Junjie Xu
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
| | - Wei Chen
- Beijing Institute of Biotechnology, No. 20, Dongdajie str., Fengtai District, Beijing 100071, China.
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Hoffman EA, Frey BL, Smith LM, Auble DT. Formaldehyde crosslinking: a tool for the study of chromatin complexes. J Biol Chem 2015; 290:26404-11. [PMID: 26354429 DOI: 10.1074/jbc.r115.651679] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function.
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Affiliation(s)
- Elizabeth A Hoffman
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
| | - Brian L Frey
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Lloyd M Smith
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - David T Auble
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
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23
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Choudhury M, Zaman S, Jiang JC, Jazwinski SM, Bastia D. Mechanism of regulation of 'chromosome kissing' induced by Fob1 and its physiological significance. Genes Dev 2015; 29:1188-201. [PMID: 26063576 PMCID: PMC4470286 DOI: 10.1101/gad.260844.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein-mediated "chromosome kissing" between two DNA sites in trans (or in cis) is known to facilitate three-dimensional control of gene expression and DNA replication. However, the mechanisms of regulation of the long-range interactions are unknown. Here, we show that the replication terminator protein Fob1 of Saccharomyces cerevisiae promoted chromosome kissing that initiated rDNA recombination and controlled the replicative life span (RLS). Oligomerization of Fob1 caused synaptic (kissing) interactions between pairs of terminator (Ter) sites that initiated recombination in rDNA. Fob1 oligomerization and Ter-Ter kissing were regulated by intramolecular inhibitory interactions between the C-terminal domain (C-Fob1) and the N-terminal domain (N-Fob1). Phosphomimetic substitutions of specific residues of C-Fob1 counteracted the inhibitory interaction. A mutation in either N-Fob1 that blocked Fob1 oligomerization or C-Fob1 that blocked its phosphorylation antagonized chromosome kissing and recombination and enhanced the RLS. The results provide novel insights into a mechanism of regulation of Fob1-mediated chromosome kissing.
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Affiliation(s)
- Malay Choudhury
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Shamsu Zaman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - James C Jiang
- Tulane Center for Aging, Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - S Michal Jazwinski
- Tulane Center for Aging, Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Deepak Bastia
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA;
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24
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CTCF controls HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure in NT2/D1 cells. Mol Cell Biol 2014; 34:3867-79. [PMID: 25135475 DOI: 10.1128/mcb.00567-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HOX cluster genes are activated sequentially in their positional order along the chromosome during vertebrate development. This phenomenon, known as temporal colinearity, depends on transcriptional silencing of 5' HOX genes. Chromatin looping was recently identified as a conserved feature of silent HOX clusters, with CCCTC-binding factor (CTCF) binding sites located at the loop bases. However, the potential contribution of CTCF to HOX cluster silencing and the underlying mechanism have not been established. Here, we demonstrate that the HOXA locus is organized by CTCF into chromatin loops and that CTCF depletion causes significantly enhanced activation of HOXA3 to -A7, -A9 to -A11, and -A13 in response to retinoic acid, with the highest effect observed for HOXA9. Our subsequent analyses revealed that CTCF facilitates the stabilization of Polycomb repressive complex 2 (PRC2) and trimethylated lysine 27 of histone H3 (H3K27me3) at the human HOXA locus. Our results reveal that CTCF functions as a controller of HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure.
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25
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Sharaf N, Nicklin MJ, di Giovine FS. Long-range DNA interactions at the IL-1/IL-36/IL-37 gene cluster (2q13) are induced by activation of monocytes. Cytokine 2014; 68:16-22. [DOI: 10.1016/j.cyto.2014.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 03/02/2014] [Accepted: 03/14/2014] [Indexed: 10/25/2022]
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26
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Shi F, Ding S, Zhao S, Han M, Zhuang Y, Xu T, Wu X. A piggyBac insertion disrupts Foxl2 expression that mimics BPES syndrome in mice. Hum Mol Genet 2014; 23:3792-800. [PMID: 24565867 DOI: 10.1093/hmg/ddu092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Blepharophimosis, ptosis, epicanthus inversus syndrome (BPES) is an autosomal dominant genetic disorder characterized by small palpebral fissures and other craniofacial malformations, often with (type I) but could also without (type II) premature ovarian failure. While mutations of the forkhead transcription factor FOXL2 are associated with and likely be responsible for many BPES cases, how FOXL2 affects craniofacial development remain to be understood. Through a large-scale piggyBac (PB) insertion mutagenesis, we have identified a mouse mutant carrying a PB insertion ∼160 kb upstream of the transcription start site (TSS) of Foxl2. The insertion reduces, but not eliminates, the expression of Foxl2. This mutant, but not its revertant, displays BPES-like conditions such as midface hypoplasia, eyelid abnormalities and female subfertility. Further analysis indicates that the mutation does not affect mandible, but causes premature fusion of the premaxilla-maxilla suture, smaller premaxilla and malformed maxilla during midface development. We further identified an evolutionarily conserved fragment near the insertion site and observed enhancer activity of this element in tissue culture cells. Analyses using DNase I hypersensitivity assay and chromosome conformation capture assay in developing maxillary and periocular tissues suggest that the DNA region near the insertion site likely interacts with Foxl2 TSS. Therefore, this mutant presents an excellent animal model for mechanistic study of BPES and regulation of Foxl2.
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Affiliation(s)
- Fubiao Shi
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Sheng Ding
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Shimin Zhao
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Min Han
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China Howard Hughes Medical Institute, Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Yuan Zhuang
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
| | - Tian Xu
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Xiaohui Wu
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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27
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Williams RL, Starmer J, Mugford JW, Calabrese JM, Mieczkowski P, Yee D, Magnuson T. fourSig: a method for determining chromosomal interactions in 4C-Seq data. Nucleic Acids Res 2014; 42:e68. [PMID: 24561615 PMCID: PMC4005674 DOI: 10.1093/nar/gku156] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-Seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-Seq experiments generate large, complicated data sets and it is imperative that signal is properly distinguished from noise. Currently, there are a limited number of methods for analyzing 4C-Seq data. Here, we present a new method, fourSig, which in addition to being precise and simple to use also includes a new feature that prioritizes detected interactions. Our results demonstrate the efficacy of fourSig with previously published and novel 4C-Seq data sets and show that our significance prioritization correlates with the ability to reproducibly detect interactions among replicates.
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Affiliation(s)
- Rex L Williams
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA, Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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28
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LeBlanc SE, Wu Q, Barutcu AR, Xiao H, Ohkawa Y, Imbalzano AN. The PPARγ locus makes long-range chromatin interactions with selected tissue-specific gene loci during adipocyte differentiation in a protein kinase A dependent manner. PLoS One 2014; 9:e86140. [PMID: 24465921 PMCID: PMC3896465 DOI: 10.1371/journal.pone.0086140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 12/05/2013] [Indexed: 02/05/2023] Open
Abstract
Differentiation signaling results in reprogramming of cellular gene expression that leads to morphological changes and functional specialization of a precursor cell. This global change in gene expression involves temporal regulation of differentiation-specific genes that are located throughout the genome, raising the idea that genome structure may also be re-organized during cell differentiation to facilitate regulated gene expression. Using in vitro adipocyte differentiation as a model, we explored whether gene organization within the nucleus is altered upon exposure of precursor cells to signaling molecules that induce adipogenesis. The peroxisome proliferator-activated receptor gamma (PPARγ) nuclear hormone receptor is a master determinant of adipogenesis and is required for adipose differentiation. We utilized the chromosome conformation capture (3C) assay to determine whether the position of the PPARγ locus relative to other adipogenic genes is changed during differentiation. We report that the PPARγ2 promoter is transiently positioned in proximity to the promoters of genes encoding adipokines and lipid droplet associated proteins at 6 hours post-differentiation, a time that precedes expression of any of these genes. In contrast, the PPARγ2 promoter was not in proximity to the EF1α promoter, which drives expression of a constitutively active, housekeeping gene that encodes a translation elongation factor, nor was the PPARγ2 promoter in proximity to the promoter driving the expression of the C/EBPα regulatory protein. The formation of the long-range, intergenic interactions involving the PPARγ2 promoter required the regulatory factor C/EBPβ, elevated cyclic AMP (cAMP) levels, and protein kinase A (PKA) signaling. We conclude that genome organization is dynamically remodeled in response to adipogenic signaling, and we speculate that these transient inter-genic interactions may be formed for the purposes of selecting some of the transcriptionally silent tissue-specific loci for subsequent transcriptional activation.
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Affiliation(s)
- Scott E. LeBlanc
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Qiong Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - A. Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Hengyi Xiao
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Laboratory of Aging Research, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yasuyuki Ohkawa
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Advanced Medical Initiatives, JST-CREST, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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29
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Gavrilov AA, Chetverina HV, Chermnykh ES, Razin SV, Chetverin AB. Quantitative analysis of genomic element interactions by molecular colony technique. Nucleic Acids Res 2013; 42:e36. [PMID: 24369423 PMCID: PMC3950710 DOI: 10.1093/nar/gkt1322] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde-cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA-protein complex cannot be stabilized by formaldehyde cross-linking.
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Affiliation(s)
- Alexey A Gavrilov
- Group of Genome Spatial Organization, Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia, Laboratory of Viral RNA Biochemistry, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia, Laboratory of Cell Proliferation Problems, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow 119334, Russia, Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia and Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
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30
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Dalvai M, Fleury L, Bellucci L, Kocanova S, Bystricky K. TIP48/Reptin and H2A.Z requirement for initiating chromatin remodeling in estrogen-activated transcription. PLoS Genet 2013; 9:e1003387. [PMID: 23637611 PMCID: PMC3630088 DOI: 10.1371/journal.pgen.1003387] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 01/31/2013] [Indexed: 01/06/2023] Open
Abstract
Histone variants, including histone H2A.Z, are incorporated into specific genomic sites and participate in transcription regulation. The role of H2A.Z at these sites remains poorly characterized. Our study investigates changes in the chromatin environment at the Cyclin D1 gene (CCND1) during transcriptional initiation in response to estradiol in estrogen receptor positive mammary tumour cells. We show that H2A.Z is present at the transcription start-site and downstream enhancer sequences of CCND1 when the gene is poorly transcribed. Stimulation of CCND1 expression required release of H2A.Z concomitantly from both these DNA elements. The AAA+ family members TIP48/reptin and the histone variant H2A.Z are required to remodel the chromatin environment at CCND1 as a prerequisite for binding of the estrogen receptor (ERα) in the presence of hormone. TIP48 promotes acetylation and exchange of H2A.Z, which triggers a dissociation of the CCND1 3′ enhancer from the promoter, thereby releasing a repressive intragenic loop. This release then enables the estrogen receptor to bind to the CCND1 promoter. Our findings provide new insight into the priming of chromatin required for transcription factor access to their target sequence. Dynamic release of gene loops could be a rapid means to remodel chromatin and to stimulate transcription in response to hormones. Our study investigates changes in the chromatin environment at the Cyclin D1 gene that are a prerequisite for transcriptional initiation in response to estradiol. Gene expression is under control of chromatin structure. Histone variants, including histone H2A.Z, are incorporated into specific genomic sites and participate in transcription regulation. We show that H2A.Z is present at the transcription start-site and downstream enhancer sequences of CCND1 when the gene is poorly transcribed. Stimulation of CCND1 expression required release of H2A.Z concomitantly from both these DNA elements. The TIP48/reptin protein, which is part of several chromatin remodeling complexes, also associated with the CCND1 regulatory elements. Here, TIP48 promotes exchange of H2A.Z, which triggers a dissociation of the CCND1 enhancer from the promoter, thereby releasing a repressive intragenic loop. This release then enables estrogen receptor binding to the CCND1 promoter. Acetylation of H2A.Z is required for these processes. Our findings provide new insight into the priming of chromatin required for transcription factor access to their target sequence. Hence, we propose a new model for early events in transcription activation that were not shown before. Specifically, release of looping could be a rapid means to activate transcription efficiently in response to stimuli, in particular estrogen.
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Affiliation(s)
- Mathieu Dalvai
- Université de Toulouse, UPS, Laboratoire de Biologie Moléculaire Eucaryote (LBME), Toulouse, France
- CNRS, UMR5099, Toulouse, France
| | - Laurence Fleury
- Université de Toulouse, UPS, Laboratoire de Biologie Moléculaire Eucaryote (LBME), Toulouse, France
- CNRS, UMR5099, Toulouse, France
| | - Luca Bellucci
- Université de Toulouse, UPS, Laboratoire de Biologie Moléculaire Eucaryote (LBME), Toulouse, France
- CNRS, UMR5099, Toulouse, France
| | - Silvia Kocanova
- Université de Toulouse, UPS, Laboratoire de Biologie Moléculaire Eucaryote (LBME), Toulouse, France
- CNRS, UMR5099, Toulouse, France
| | - Kerstin Bystricky
- Université de Toulouse, UPS, Laboratoire de Biologie Moléculaire Eucaryote (LBME), Toulouse, France
- CNRS, UMR5099, Toulouse, France
- * E-mail:
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31
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Gavrilov AA, Golov AK, Razin SV. Actual ligation frequencies in the chromosome conformation capture procedure. PLoS One 2013; 8:e60403. [PMID: 23555968 PMCID: PMC3608588 DOI: 10.1371/journal.pone.0060403] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/25/2013] [Indexed: 11/19/2022] Open
Abstract
Chromosome conformation capture (3C) and derivative experimental procedures are used to estimate the spatial proximity between different genomic elements, thus providing information about the 3D organization of genomic domains and whole genomes within the nucleus. All C-methods are based on the proximity ligation-the preferential ligation of joined DNA fragments obtained upon restriction enzyme digestion of in vivo cross-linked chromatin. Here, using the mouse beta-globin genes in erythroid cells as a model, we estimated the actual frequencies of ligation between the fragments bearing the promoter of the major beta-globin gene and its distant enhancers and showed that the number of ligation products produced does not exceed 1% of all fragments subjected to the ligation. Although this low yield of 3C ligation products may be explained entirely by technical issues, it may as well reflect a low frequency of interaction between DNA regulatory elements in vivo.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.
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32
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Gavrilov AA, Gushchanskaya ES, Strelkova O, Zhironkina O, Kireev II, Iarovaia OV, Razin SV. Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub. Nucleic Acids Res 2013; 41:3563-75. [PMID: 23396278 PMCID: PMC3616722 DOI: 10.1093/nar/gkt067] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The current progress in the study of the spatial organization of interphase chromosomes became possible owing to the development of the chromosome conformation capture (3C) protocol. The crucial step of this protocol is the proximity ligation—preferential ligation of DNA fragments assumed to be joined within nuclei by protein bridges and solubilized as a common complex after formaldehyde cross-linking and DNA cleavage. Here, we show that a substantial, and in some cases the major, part of DNA is not solubilized from cross-linked nuclei treated with restriction endonuclease(s) and sodium dodecyl sulphate and that this treatment neither causes lysis of the nucleus nor drastically affects its internal organization. Analysis of the ligation frequencies of the mouse β-globin gene domain DNA fragments demonstrated that the previously reported 3C signals were generated predominantly, if not exclusively, in the insoluble portion of the 3C material. The proximity ligation thus occurs within the cross-linked chromatin cage in non-lysed nuclei. The finding does not compromise the 3C protocol but allows the consideration of an active chromatin hub as a folded chromatin domain or a nuclear compartment rather than a rigid complex of regulatory elements.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia, University of Oslo, Center for Medical Studies in Russia, 119334 Moscow, Russia
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33
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Dalvai M, Bellucci L, Fleury L, Lavigne AC, Moutahir F, Bystricky K. H2A.Z-dependent crosstalk between enhancer and promoter regulates cyclin D1 expression. Oncogene 2012; 32:4243-51. [PMID: 23108396 DOI: 10.1038/onc.2012.442] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 08/09/2012] [Accepted: 08/10/2012] [Indexed: 02/08/2023]
Abstract
H2A.Z association with specific genomic loci is thought to contribute to a chromatin structure that promotes transcription activation. Acetylation of H2A.Z at promoters of oncogenes has been linked to tumorigenesis. The mechanism is unknown. Here, we show that in triple negative breast cancer cells, H2A.Z bound to the promoter of the constitutively, weakly expressed cyclin D1 oncogene (CCND1), a key regulator of cellular proliferation. Depleting the pool of H2A.Z stimulated transcription of CCND1 in the absence of its cognate transcription factor, the estrogen receptor (ER). During activation of CCND1, H2A.Z was released from the transcription start site (TSS) and downstream enhancer (enh2) sequences. Concurrently, acetylation of H2A.Z, H3 and H4 at the TSS was increased but only H2A.Z was acetylated at enh2. Acetylation of H2A.Z required the Tip60 acetyltransferase to be associated with the activated CCND1 on both TSS and enh2 sites. Depletion of Tip60 prevented CCND1 activation. Chromosome conformation capture experiments (3C) revealed specific contacts between the TSS and enh2 chromatin regions. These results suggest that release of a histone H2A.Z-mediated repression loop activates CCND1 for transcription. Our findings open new avenues for controlling and understanding aberrant gene expression associated with tumorigenesis.
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Affiliation(s)
- M Dalvai
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), University of Toulouse, Toulouse, France
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34
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Markova EN, Kantidze OL, Razin SV. Transcription of the AML1/ETO chimera is guided by the P2 promoter of the AML1 gene in the Kasumi-1 cell line. Gene 2012; 510:142-6. [PMID: 22995345 DOI: 10.1016/j.gene.2012.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/31/2012] [Accepted: 09/07/2012] [Indexed: 02/06/2023]
Abstract
Chromosomal translocation t (8;21)(q22;22) is one of the most frequent cytogenetic abnormalities found in acute myeloid leukaemia (AML). It generates the AML1/ETO fusion gene, which itself supports human haematopoietic stem cell self-renewal. However, the mechanism guiding transcription of this chimeric gene remains unclear. In our work, we attempted to shed light on this essential issue. We investigated the promoter from which transcription of the AML1/ETO gene is initiated and defined the three-dimensional structure of the whole rearranged locus.
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Affiliation(s)
- Elena N Markova
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia
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35
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Hövel I, Louwers M, Stam M. 3C Technologies in plants. Methods 2012; 58:204-11. [PMID: 22728034 DOI: 10.1016/j.ymeth.2012.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/11/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022] Open
Abstract
Chromosome conformation capture (3C) and 3C-based technology have revolutionized studies on chromosomal interactions and their role in gene regulation and chromosome organization. 3C allows the in vivo identification of physical interactions between chromosomal regions. Such interactions are shown to play a role in various aspects of gene regulation, for example transcriptional activation of genes by remote enhancer sequences, or the silencing by Polycomb-group complexes. The last few years the number of publications involving chromosomal interactions increased significantly. Until now, however, the vast majority of the studies reported are performed in yeast or animal systems. So far, studies on plant systems are extremely limited, possibly due to the plant-specific characteristics that hamper the implementation of the 3C technique. In this paper we provide a plant-specific 3C protocol, optimized for maize tissue, and an extensive discussion on (i) plant-specific adjustments to the protocol, and (ii) solutions to problems that may arise when optimizing the protocol for the tissue or plant of interest. Together, this paper should facilitate the application of 3C technology to plant tissue and stimulate studies on the 3D conformation of chromosomal regions and chromosomes in plants.
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Affiliation(s)
- Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
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36
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Higher-order chromatin regulation and differential gene expression in the human tumor necrosis factor/lymphotoxin locus in hepatocellular carcinoma cells. Mol Cell Biol 2012; 32:1529-41. [PMID: 22354988 DOI: 10.1128/mcb.06478-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The three-dimensional context of endogenous chromosomal regions may contribute to the regulation of gene clusters by influencing interactions between transcriptional regulatory elements. In this study, we investigated the effects of tumor necrosis factor (TNF) signaling on spatiotemporal enhancer-promoter interactions in the human tumor necrosis factor (TNF)/lymphotoxin (LT) gene locus, mediated by CCCTC-binding factor (CTCF)-dependent chromatin insulators. The cytokine genes LTα, TNF, and LTβ are differentially regulated by NF-κB signaling in inflammatory and oncogenic responses. We identified at least four CTCF-enriched sites with enhancer-blocking activities and a TNF-responsive TE2 enhancer in the TNF/LT locus. One of the CTCF-enriched sites is located between the early-inducible LTα/TNF promoters and the late-inducible LTβ promoter. Depletion of CTCF reduced TNF expression and accelerated LTβ induction. After TNF stimulation, via intrachromosomal dynamics, these insulators mediated interactions between the enhancer and the LTα/TNF promoters, followed by interaction with the LTβ promoter. These results suggest that insulators mediate the spatiotemporal control of enhancer-promoter associations in the TNF/LT gene cluster.
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37
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Ren L, Wang Y, Shi M, Wang X, Yang Z, Zhao Z. CTCF mediates the cell-type specific spatial organization of the Kcnq5 locus and the local gene regulation. PLoS One 2012; 7:e31416. [PMID: 22347474 PMCID: PMC3275579 DOI: 10.1371/journal.pone.0031416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 01/07/2012] [Indexed: 11/30/2022] Open
Abstract
Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial organization, and mediates the ubiquitous chromatin loops within the genome. Using circular chromosome conformation capture (4C) methodology, we discovered that CTCF may be a master organizer in mediating the spatial organization of the kcnq5 gene locus. We characterized the cell-type specific spatial organization of the kcnq5 gene locus mediated by CTCF in detail using chromosome conformation capture (3C) and 3C-derived techniques. Cohesion also participated in mediating the organization of this locus. RNAi-mediated knockdown of CTCF sharply diminished the interaction frequencies between the chromatin loops of the kcnq5 gene locus and down-regulated local gene expression. Functional analysis showed that the interacting chromatin loops of the kcnq5 gene locus can repress the gene expression in a luciferase reporter assay. These interacting chromatin fragments were a series of repressing elements whose contacts were mediated by CTCF. Therefore, these findings suggested that the dynamical spatial organization of the kcnq5 locus regulates local gene expression.
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Affiliation(s)
- Licheng Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yang Wang
- Beijing Institute of Biotechnology, Fengtai District, Beijing, China
| | - Minglei Shi
- Beijing Institute of Biotechnology, Fengtai District, Beijing, China
| | - Xiaoning Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Genetic Engineering and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (ZZ); (ZY); (XW)
| | - Zhong Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Genetic Engineering and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (ZZ); (ZY); (XW)
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Fengtai District, Beijing, China
- * E-mail: (ZZ); (ZY); (XW)
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38
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Nativio R, Ito Y, Murrell A. Quantitative chromosome conformation capture. Methods Mol Biol 2012; 925:173-185. [PMID: 22907497 DOI: 10.1007/978-1-62703-011-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
It is becoming increasingly apparent that chromatin is not randomly folded into the nucleus, but instead is highly organized into specific conformations within the nucleus. One consequence of such higher order structure is that chromatin looping can bring together genomic elements which are separated by several hundreds of kilobases, such as enhancers and promoters, and functionally facilitate their interaction. The Chromosome Conformation Capture (3C) assay is a powerful technique to detect looping structures and assess the probability of interaction between distant genomic elements (1-3). Here we describe the 3C methodology, its power, and limitations, together with the controls and normalization steps required for an accurate analysis.
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Affiliation(s)
- Raffaella Nativio
- Department of Oncology, CRUK Cambridge Research Institute, University of Cambridge, Cambridge, UK
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39
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Markova EN, Kantidze OL, Razin SV. Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene. J Cell Biochem 2011; 112:1997-2005. [PMID: 21445863 DOI: 10.1002/jcb.23117] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The transcription factor RUNX1 is a key regulator of haematopoiesis in vertebrates. In humans, the 260-kb long gene coding for this transcription factor is located on chromosome 21. This gene is transcribed from two alternative promoters that are commonly referred to as the distal and the proximal promoters. In model experiments, these two promoters were found to be active in cells of different lineages, although RUNX1 is preferentially expressed in haematopoietic cells. In the present study, we attempted to identify the regulatory elements that could guide tissue-specific expression of the RUNX1 gene. Two such regulatory elements were found within the RUNX1 gene. One of these elements, located within intron 1, is a haematopoietic-specific enhancer. The second regulatory element, located within intron 5.2, contributes to the formation of an active chromatin hub, which integrates the above-mentioned enhancer and the P1 and P2 promoters.
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Affiliation(s)
- Elena N Markova
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, Moscow, Russia
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40
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Minbuta T, Ono M. Scattered regulatory regions of the chicken immunoglobulin-β gene and two adjacent promoters of ubiquitously expressed genes interact with the immunoglobulin-β promoter in DT40 cells. Biol Pharm Bull 2011; 34:1710-6. [PMID: 22040884 DOI: 10.1248/bpb.34.1710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent studies indicate that several transcription units assemble to form a 'transcription factory' where active transcription occurs in the nuclei. Previously, we generated chicken B-lymphocyte-derived DT40 cells lacking six transcriptional regulatory regions scattered in and around the immunoglobulin (Ig)-β gene. The deletions caused a complete shut down of transcription and epigenetic regulation of the Ig-β gene, demonstrating that the scattered regulatory regions cooperated in the transcriptional and epigenetic regulation of the gene. However, the in vivo 3-dimensional spatial relationships between the Ig-β promoter and these six regulatory regions were not investigated. In this study, we used chromosome conformation capture (3C) technology and demonstrated that the Ig-β promoter physically interacted with the scattered regulatory regions. We found that the Ig-β promoter also interacted with two downstream promoters of ubiquitously expressed genes, rad motif 1 (RDM1) and Plekhm1, to form a transcription factory, but not with three ubiquitously expressed genes, BAF60b, p45/SUG, and RRMJ3, located upstream of the Ig-β gene. In this factory, the chromatin from the three promoters and the scattered regulatory regions of the Ig-β gene formed a complex structure with many chromatin loops.
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Affiliation(s)
- Tomohiro Minbuta
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
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41
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A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. Genetics 2011; 189:441-54. [PMID: 21840866 DOI: 10.1534/genetics.111.132662] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In mammals, X-chromosome inactivation (XCI) equalizes X-linked gene expression between XY males and XX females and is controlled by a specialized region known as the X-inactivation center (Xic). The Xic harbors two chromatin interaction domains, one centered around the noncoding Xist gene and the other around the antisense Tsix counterpart. Previous work demonstrated the existence of a chromatin transitional zone between the two domains. Here, we investigate the region and discover a conserved element, RS14, that presents a strong binding site for Ctcf protein. RS14 possesses an insulatory function suggestive of a boundary element and is crucial for cell differentiation and growth. Knocking out RS14 results in compromised Xist induction and aberrant XCI in female cells. These data demonstrate that a junction element between Tsix and Xist contributes to the initiation of XCI.
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Razin SV, Gavrilov AA, Yarovaya OV. Transcription factories and spatial organization of eukaryotic genomes. BIOCHEMISTRY (MOSCOW) 2011; 75:1307-15. [PMID: 21314597 DOI: 10.1134/s0006297910110015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The phenomenon of association of transcribed genes into so-called transcription factories and also the role of these associations in spatial organization of the eukaryotic genome are actively discussed in the modern literature. Some authors think that the association of transcribed genes into transcription factories constitutes a major factor supporting the function-dependent three-dimensional organization of the interphase genome. In spite of the obvious interest in the problem of spatial organization of transcription in the eukaryotic cell nucleus, the number of experimental studies of transcriptional factories remains rather limited and the results of these studies are often contradictory. In the current review we have tried to critically re-evaluate the published experimental results that constitute the basis for current models and also the models themselves. We have especially analyzed the existing contradictions and attempted to explain them whenever possible. We also discuss new models that can explain the biological significance of clustering of transcribed genes and show possible mechanisms of the origin of transcription factories in the course of evolution.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.
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43
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Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE. Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One 2011; 6:e17634. [PMID: 21408183 PMCID: PMC3049788 DOI: 10.1371/journal.pone.0017634] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 02/04/2011] [Indexed: 02/02/2023] Open
Abstract
Comparative analyses of various mammalian genomes have identified numerous conserved non-coding (CNC) DNA elements that display striking conservation among species, suggesting that they have maintained specific functions throughout evolution. CNC function remains poorly understood, although recent studies have identified a role in gene regulation. We hypothesized that the identification of genomic loci that interact physically with CNCs would provide information on their functions. We have used circular chromosome conformation capture (4C) to characterize interactions of 10 CNCs from human chromosome 21 in K562 cells. The data provide evidence that CNCs are capable of interacting with loci that are enriched for CNCs. The number of trans interactions varies among CNCs; some show interactions with many loci, while others interact with few. Some of the tested CNCs are capable of driving the expression of a reporter gene in the mouse embryo, and associate with the oligodendrocyte genes OLIG1 and OLIG2. Our results underscore the power of chromosome conformation capture for the identification of targets of functional DNA elements and raise the possibility that CNCs exert their functions by physical association with defined genomic regions enriched in CNCs. These CNC-CNC interactions may in part explain their stringent conservation as a group of regulatory sequences.
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Affiliation(s)
- Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
- * E-mail: (SEA); (DR)
| | - Marc Friedli
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Mélanie Arcangeli
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Marilyn Marin
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
| | | | - Isabelle Barde
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sonia Verp
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Geneva, Switzerland
- * E-mail: (SEA); (DR)
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44
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Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription. Nat Struct Mol Biol 2011; 18:372-8. [PMID: 21336277 PMCID: PMC6402586 DOI: 10.1038/nsmb.1993] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 11/30/2010] [Indexed: 02/07/2023]
Abstract
Insulin (INS) synthesis and secretion from pancreatic β cells are tightly regulated; their deregulation causes diabetes. Here we map INS-associated loci in human pancreatic islets by 4C and 3C techniques and show that the INS gene physically interacts with the SYT8 gene, located over 300 kb away. This interaction is elevated by glucose and accompanied by increases in SYT8 expression. Inactivation of the INS promoter by promoter-targeting siRNA reduces SYT8 gene expression. SYT8-INS interaction and SYT8 transcription are attenuated by CTCF depletion. Furthermore, SYT8 knockdown decreases insulin secretion in islets. These results reveal a non-redundant role for SYT8 in insulin secretion and indicate that the INS promoter acts from a distance to stimulate SYT8 transcription. This suggests a function for the INS promoter in coordinating insulin transcription and secretion through long-range regulation of SYT8 expression in human islets.
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45
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Nagy PL, Price DH. Formaldehyde-assisted isolation of regulatory elements. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 1:400-406. [PMID: 20046543 DOI: 10.1002/wsbm.36] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) is based on locus-specific variations in the ability of protein components of chromatin to trap genomic DNA following formaldehyde treatment. This variation is mostly due to uneven nucleosome distribution since histones are the most abundant and highly crosslinkable components of chromatin. The method can identify and enrich for physically accessible DNA segments of the eukaryotic genome corresponding to known regulatory regions and regions that might have thus far unidentified structural role in the nuclear organization of chromatin. The enrichment patterns are cell type specific and thus might provide information about how transcriptional systems are organized and regulated in various tissues and how they might be disrupted in disease states. Analysis of a 268 kb region of chromosome 19 in human fibroblasts shown here demonstrates that while most DNA fragments detected by FAIRE correspond to sites of DNaseI hypersensitivity in active regions of chromatin, some are found in otherwise repressed chromatin domains and at other sites that are not found with other methods used to probe chromatin structure. Further exploration of FAIRE is warrented due to the simplicity of the protocol and recent advancements in massively parallel sequencing.
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Affiliation(s)
- Peter L Nagy
- Departments of Pathology, Biochemistry and Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Departments of Pathology, Biochemistry and Pediatrics, University of Iowa, Iowa City, IA 52242, USA
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46
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A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One 2010; 5:e15741. [PMID: 21206754 PMCID: PMC3012086 DOI: 10.1371/journal.pone.0015741] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/23/2010] [Indexed: 01/22/2023] Open
Abstract
Finding sequences that control expression of genes is central to understanding genome function. Previous studies have used evolutionary conservation as an indicator of regulatory potential. Here, we present a method for the unbiased in vivo screen of putative enhancers in large DNA regions, using the mouse as a model. We cloned a library of 142 overlapping fragments from a 200 kb-long murine BAC in a lentiviral vector expressing LacZ from a minimal promoter, and used the resulting vectors to infect fertilized murine oocytes. LacZ staining of E11 embryos obtained by first using the vectors in pools and then testing individual candidates led to the identification of 3 enhancers, only one of which shows significant evolutionary conservation. In situ hybridization and 3C/4C experiments suggest that this enhancer, which is active in the neural tube and posterior diencephalon, influences the expression of the Olig1 and/or Olig2 genes. This work provides a new approach for the large-scale in vivo screening of transcriptional regulatory sequences, and further demonstrates that evolutionary conservation alone seems too limiting a criterion for the identification of enhancers.
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47
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Gavrilov AA, Zukher IS, Philonenko ES, Razin SV, Iarovaia OV. Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure. Nucleic Acids Res 2010; 38:8051-60. [PMID: 20705651 PMCID: PMC3001081 DOI: 10.1093/nar/gkq712] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed an experimental procedure to analyze the spatial proximity of nuclear matrix-bound DNA fragments. This protocol, referred to as Matrix 3C (M3C), includes a high salt extraction of nuclei, the removal of distal parts of unfolded DNA loops using restriction enzyme treatment, ligation of the nuclear matrix-bound DNA fragments and a subsequent analysis of ligation frequencies. Using the M3C procedure, we have demonstrated that CpG islands of at least three housekeeping genes that surround the chicken α-globin gene domain are assembled into a complex (presumably, a transcription factory) that is stabilized by the nuclear matrix in both erythroid and non-erythroid cells. In erythroid cells, the regulatory elements of the α-globin genes are attracted to this complex to form a new assembly: an active chromatin hub that is linked to the pre-existing transcription factory. The erythroid-specific part of the assembly is removed by high salt extraction. Based on these observations, we propose that mixed transcription factories that mediate the transcription of both housekeeping and tissue-specific genes are composed of a permanent compartment containing integrated into the nuclear matrix promoters of housekeeping genes and a ‘guest’ compartment where promoters and regulatory elements of tissue-specific genes can be temporarily recruited.
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Affiliation(s)
- Alexey A Gavrilov
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
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48
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Haffner MC, Aryee MJ, Toubaji A, Esopi DM, Albadine R, Gurel B, Isaacs WB, Bova GS, Liu W, Xu J, Meeker AK, Netto G, De Marzo AM, Nelson WG, Yegnasubramanian S. Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nat Genet 2010; 42:668-75. [PMID: 20601956 PMCID: PMC3157086 DOI: 10.1038/ng.613] [Citation(s) in RCA: 466] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 06/02/2010] [Indexed: 12/21/2022]
Abstract
DNA double strand breaks (DSB) can lead to development of genomic rearrangements, which are hallmarks of cancer. TMPRSS2-ERG gene fusions in prostate cancer (PCa) are among the most common genomic rearrangements observed in human cancer. We show that androgen signaling promotes co-recruitment of androgen receptor (AR) and topoisomerase II beta (TOP2B) to sites of TMPRSS2-ERG genomic breakpoints, triggering recombinogenic TOP2B-mediated DSB. Furthermore, androgen stimulation resulted in de novo production of TMPRSS2-ERG fusion transcripts in a process requiring TOP2B and components of DSB repair machinery. Finally, unlike normal prostate epithelium, prostatic intraepithelial neoplasia (PIN) cells showed strong co-expression of AR and TOP2B. These findings implicate androgen-induced TOP2B-mediated DSB in generating TMPRSS2-ERG rearrangements.
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Affiliation(s)
- Michael C Haffner
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
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49
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Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res 2010; 38:4325-36. [PMID: 20360044 PMCID: PMC2910055 DOI: 10.1093/nar/gkq175] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Revised: 03/01/2010] [Accepted: 03/03/2010] [Indexed: 12/20/2022] Open
Abstract
Identification of regulatory elements and their target genes is complicated by the fact that regulatory elements can act over large genomic distances. Identification of long-range acting elements is particularly important in the case of disease genes as mutations in these elements can result in human disease. It is becoming increasingly clear that long-range control of gene expression is facilitated by chromatin looping interactions. These interactions can be detected by chromosome conformation capture (3C). Here, we employed 3C as a discovery tool for identification of long-range regulatory elements that control the cystic fibrosis transmembrane conductance regulator gene, CFTR. We identified four elements in a 460-kb region around the locus that loop specifically to the CFTR promoter exclusively in CFTR expressing cells. The elements are located 20 and 80 kb upstream; and 109 and 203 kb downstream of the CFTR promoter. These elements contain DNase I hypersensitive sites and histone modification patterns characteristic of enhancers. The elements also interact with each other and the latter two activate the CFTR promoter synergistically in reporter assays. Our results reveal novel long-range acting elements that control expression of CFTR and suggest that 3C-based approaches can be used for discovery of novel regulatory elements.
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Affiliation(s)
- Nele Gheldof
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA, European Bioinformatics Institute (EBI), The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Emily M. Smith
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA, European Bioinformatics Institute (EBI), The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Tomoko M. Tabuchi
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA, European Bioinformatics Institute (EBI), The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christoph M. Koch
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA, European Bioinformatics Institute (EBI), The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ian Dunham
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA, European Bioinformatics Institute (EBI), The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - John A. Stamatoyannopoulos
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA, European Bioinformatics Institute (EBI), The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Job Dekker
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA, European Bioinformatics Institute (EBI), The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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50
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Tiwari VK, Baylin SB. Combined 3C-ChIP-cloning (6C) assay: a tool to unravel protein-mediated genome architecture. Cold Spring Harb Protoc 2010; 2009:pdb.prot5168. [PMID: 20147103 DOI: 10.1101/pdb.prot5168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Vijay K Tiwari
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.
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