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Manu DM, Mwinyi J, Schiöth HB. Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. Int J Mol Sci 2022; 23:ijms23105856. [PMID: 35628666 PMCID: PMC9147258 DOI: 10.3390/ijms23105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022] Open
Abstract
The formative period of adolescence plays a crucial role in the development of skills and abilities for adulthood. Adolescents who are affected by mental health conditions are at risk of suicide and social and academic impairments. Gene–environment complementary contributions to the molecular mechanisms involved in psychiatric disorders have emphasized the need to analyze epigenetic marks such as DNA methylation (DNAm) and non-coding RNAs. However, the large and diverse bioinformatic and statistical methods, referring to the confounders of the statistical models, application of multiple-testing adjustment methods, questions regarding the correlation of DNAm across tissues, and sex-dependent differences in results, have raised challenges regarding the interpretation of the results. Based on the example of generalized anxiety disorder (GAD) and depressive disorder (MDD), we shed light on the current knowledge and usage of methodological tools in analyzing epigenetics. Statistical robustness is an essential prerequisite for a better understanding and interpretation of epigenetic modifications and helps to find novel targets for personalized therapeutics in psychiatric diseases.
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2
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Wang H, Huang B, Wang J. Predict long-range enhancer regulation based on protein-protein interactions between transcription factors. Nucleic Acids Res 2021; 49:10347-10368. [PMID: 34570239 PMCID: PMC8501976 DOI: 10.1093/nar/gkab841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/10/2021] [Accepted: 09/10/2021] [Indexed: 12/18/2022] Open
Abstract
Long-range regulation by distal enhancers plays critical roles in cell-type specific transcriptional programs. Computational predictions of genome-wide enhancer-promoter interactions are still challenging due to limited accuracy and the lack of knowledge on the molecular mechanisms. Based on recent biological investigations, the protein-protein interactions (PPIs) between transcription factors (TFs) have been found to participate in the regulation of chromatin loops. Therefore, we developed a novel predictive model for cell-type specific enhancer-promoter interactions by leveraging the information of TF PPI signatures. Evaluated by a series of rigorous performance comparisons, the new model achieves superior performance over other methods. The model also identifies specific TF PPIs that may mediate long-range regulatory interactions, revealing new mechanistic understandings of enhancer regulation. The prioritized TF PPIs are associated with genes in distinct biological pathways, and the predicted enhancer-promoter interactions are strongly enriched with cis-eQTLs. Most interestingly, the model discovers enhancer-mediated trans-regulatory links between TFs and genes, which are significantly enriched with trans-eQTLs. The new predictive model, along with the genome-wide analyses, provides a platform to systematically delineate the complex interplay among TFs, enhancers and genes in long-range regulation. The novel predictions also lead to mechanistic interpretations of eQTLs to decode the genetic associations with gene expression.
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Affiliation(s)
- Hao Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, 428 S. Shaw Ln., East Lansing, MI 48824, USA
| | - Binbin Huang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, 428 S. Shaw Ln., East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, 428 S. Shaw Ln., East Lansing, MI 48824, USA
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3
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Zhou Y, Cheng X, Yang Y, Li T, Li J, Huang THM, Wang J, Lin S, Jin VX. Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. Genome Med 2020; 12:69. [PMID: 32787954 PMCID: PMC7425017 DOI: 10.1186/s13073-020-00769-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/28/2020] [Indexed: 01/04/2023] Open
Abstract
Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic relationship of chromatin structure and gene regulation. We developed a novel computational method HiSIF to identify genome-wide interacting loci. We illustrated HiSIF outperformed other tools for identifying chromatin loops. We applied it to Hi-C data in breast cancer cells and identified 21 genes with gained loops showing worse relapse-free survival in endocrine-treated patients, suggesting the genes with enhanced loops can be used for prognostic signatures for measuring the outcome of the endocrine treatment. HiSIF is available at https://github.com/yufanzhouonline/HiSIF .
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Affiliation(s)
- Yufan Zhou
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Xiaolong Cheng
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Yini Yang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Tian Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Jingwei Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0310, Oslo, Norway
| | - Shili Lin
- Department of Statistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
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4
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Golczyk H, Limanówka A, Uchman-Książek A. Pericentromere clustering in Tradescantia section Rhoeo involves self-associations of AT- and GC-rich heterochromatin fractions, is developmentally regulated, and increases during differentiation. Chromosoma 2020; 129:227-242. [PMID: 32681184 PMCID: PMC7666280 DOI: 10.1007/s00412-020-00740-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Abstract
A spectacular but poorly recognized nuclear repatterning is the association of heterochromatic domains during interphase. Using base-specific fluorescence and extended-depth-of-focus imaging, we show that the association of heterochromatic pericentromeres composed of AT- and GC-rich chromatin occurs on a large scale in cycling meiotic and somatic cells and during development in ring- and bivalent-forming Tradescantia spathacea (section Rhoeo) varieties. The mean number of pericentromere AT-rich domains per root meristem nucleus was ca. half the expected diploid number in both varieties, suggesting chromosome pairing via (peri)centromeric regions. Indeed, regular pairing of AT-rich domains was observed. The AT- and GC-rich associations in differentiated cells contributed to a significant reduction of the mean number of the corresponding foci per nucleus in relation to root meristem. Within the first 10 mm of the root, the pericentromere attraction was in progress, as if it was an active process and involved both AT- and GC-rich associations. Complying with Rabl arrangement, the pericentromeres preferentially located on one nuclear pole, clustered into diverse configurations. Among them, a strikingly regular one with 5-7 ring-arranged pericentromeric AT-rich domains may be potentially engaged in chromosome positioning during mitosis. The fluorescent pattern of pachytene meiocytes and somatic nuclei suggests the existence of a highly prescribed ring/chain type of chromocenter architecture with side-by-side arranged pericentromeric regions. The dynamics of pericentromere associations together with their non-random location within nuclei was compared with nuclear architecture in other organisms, including the widely explored Arabidopsis model.
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Affiliation(s)
- Hieronim Golczyk
- Department of Molecular Biology, Institute of Biological Sciences, John Paul II Catholic University of Lublin, Konstantynów 1i, 20-708, Lublin, Poland.
| | - Arleta Limanówka
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
| | - Anna Uchman-Książek
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
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5
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Abstract
Aneuploidy (i.e., abnormal chromosome number) is the leading cause of miscarriage and congenital defects in humans. Moreover, aneuploidy is ubiquitous in cancer. The deleterious phenotypes associated with aneuploidy are likely a result of the imbalance in the levels of gene products derived from the additional chromosome(s). Here, we summarize the current knowledge on how the presence of extra chromosomes impacts gene expression. We describe studies that have found a strict correlation between gene dosage and transcript levels as wells as studies that have found a less stringent correlation, hinting at the possible existence of dosage compensation mechanisms. We conclude by peering into the epigenetic changes found in aneuploid cells and outlining current knowledge gaps and potential areas of future investigation.
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Affiliation(s)
- Shihoko Kojima
- Department of Biological Sciences & Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Daniela Cimini
- Department of Biological Sciences & Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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6
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Male-Specific Long Noncoding RNA TTTY15 Inhibits Non-Small Cell Lung Cancer Proliferation and Metastasis via TBX4. Int J Mol Sci 2019; 20:ijms20143473. [PMID: 31311130 PMCID: PMC6678590 DOI: 10.3390/ijms20143473] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/11/2019] [Accepted: 07/13/2019] [Indexed: 12/20/2022] Open
Abstract
Gender affects cancer susceptibility. Currently, there are only a few studies on Y chromosome-linked long noncoding RNAs (lncRNAs), and the potential association between lncRNAs and cancers in males has not been fully elucidated. Here, we examined the expression of testis-specific transcript Y-linked 15 (TTTY15) in 37 males with non-small cell lung cancer (NSCLC), and performed circular chromosome conformation capture with next-generation sequencing to determine the genomic interaction regions of the TTTY15 gene. Our results showed that the expression levels of TTTY15 were lower in NSCLC tissues. Lower TTTY15 expression levels were associated with Tumor-Node-Metastasis (TNM) stage. A TTTY15 knockdown promoted malignant transformation of NSCLC cells. Based on the bioinformatics analysis of circular chromosome conformation capture data, we found that T-box transcription factor 4 (TBX4) may be a potential target gene of TTTY15. The RNA immunoprecipitation and chromatin immunoprecipitation results showed that TTTY15 may interact with DNA (cytosine-5)-methyltransferase 3A (DNMT3A), and the TTTY15 knockdown increased the binding of DNMT3A to the TBX4 promoter. We concluded that low TTTY15 expression correlates with worse prognosis among patients with NSCLC. TTTY15 promotes TBX4 expression via DNMT3A-mediated regulation. The identification of lncRNAs encoded by male-specific genes may help to identify potential targets for NSCLC therapy.
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7
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Krumm A, Duan Z. Understanding the 3D genome: Emerging impacts on human disease. Semin Cell Dev Biol 2019; 90:62-77. [PMID: 29990539 PMCID: PMC6329682 DOI: 10.1016/j.semcdb.2018.07.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022]
Abstract
Recent burst of new technologies that allow for quantitatively delineating chromatin structure has greatly expanded our understanding of how the genome is organized in the three-dimensional (3D) space of the nucleus. It is now clear that the hierarchical organization of the eukaryotic genome critically impacts nuclear activities such as transcription, replication, as well as cellular and developmental events such as cell cycle, cell fate decision and embryonic development. In this review, we discuss new insights into how the structural features of the 3D genome hierarchy are established and maintained, how this hierarchy undergoes dynamic rearrangement during normal development and how its perturbation will lead to human disease, highlighting the accumulating evidence that links the diverse 3D genome architecture components to a multitude of human diseases and the emerging mechanisms by which 3D genome derangement causes disease phenotypes.
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Affiliation(s)
- Anton Krumm
- Department of Microbiology, University of Washington, USA.
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA.
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8
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Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E. An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. Genome Res 2019; 29:223-235. [PMID: 30606742 PMCID: PMC6360806 DOI: 10.1101/gr.230243.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 12/13/2018] [Indexed: 01/10/2023]
Abstract
The aberrant activities of transcription factors such as the androgen receptor (AR) underpin prostate cancer development. While the AR cis-regulation has been extensively studied in prostate cancer, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited. In this paper, we propose a novel framework to profile long-range chromatin interactions associated with AR and its collaborative transcription factor, erythroblast transformation-specific related gene (ERG), using chromatin interaction analysis by paired-end tag (ChIA-PET). We identified ERG-associated long-range chromatin interactions as a cooperative component in the AR-associated chromatin interactome, acting in concert to achieve coordinated regulation of a subset of AR target genes. Through multifaceted functional data analysis, we found that AR-ERG interaction hub regions are characterized by distinct functional signatures, including bidirectional transcription and cotranscription factor binding. In addition, cancer-associated long noncoding RNAs were found to be connected near protein-coding genes through AR-ERG looping. Finally, we found strong enrichment of prostate cancer genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) at AR-ERG co-binding sites participating in chromatin interactions and gene regulation, suggesting GWAS target genes identified from chromatin looping data provide more biologically relevant findings than using the nearest gene approach. Taken together, our results revealed an AR-ERG-centric higher-order chromatin structure that drives coordinated gene expression in prostate cancer progression and the identification of potential target genes for therapeutic intervention.
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Affiliation(s)
- Zhizhuo Zhang
- School of Computing, National University of Singapore, Singapore 117417.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Shreyas Lingadahalli
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China.,Centre of Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
| | - Zikai Chen
- Genome Institute of Singapore, Singapore 138672.,Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China.,Centre of Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
| | - Mei Hui Liu
- Genome Institute of Singapore, Singapore 138672
| | | | | | - Nicola Rinaldi
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Guoliang Li
- Genome Institute of Singapore, Singapore 138672.,National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | | | | | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Si Kee Tan
- Genome Institute of Singapore, Singapore 138672
| | - Xiaoan Ruan
- Genome Institute of Singapore, Singapore 138672
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Yijun Ruan
- Genome Institute of Singapore, Singapore 138672
| | - Wing-Kin Sung
- School of Computing, National University of Singapore, Singapore 117417.,Genome Institute of Singapore, Singapore 138672
| | - Edwin Cheung
- Genome Institute of Singapore, Singapore 138672.,Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China.,Centre of Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
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9
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Gerrard DL, Wang Y, Gaddis M, Zhou Y, Wang J, Witt H, Lin S, Farnham PJ, Jin VX, Frietze SE. Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. J Cell Biochem 2018; 120:3056-3070. [PMID: 30548288 DOI: 10.1002/jcb.27449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/18/2018] [Indexed: 11/10/2022]
Abstract
Distal regulatory elements influence the activity of gene promoters through chromatin looping. Chromosome conformation capture (3C) methods permit identification of chromatin contacts across different regions of the genome. However, due to limitations in the resolution of these methods, the detection of functional chromatin interactions remains a challenge. In the current study, we employ an integrated approach to define and characterize the functional chromatin contacts of human pancreatic cancer cells. We applied tethered chromatin capture to define classes of chromatin domains on a genome-wide scale. We identified three types of structural domains (topologically associated, boundary, and gap) and investigated the functional relationships of these domains with respect to chromatin state and gene expression. We uncovered six distinct sub-domains associated with epigenetic states. Interestingly, specific epigenetically active domains are sensitive to treatment with histone acetyltransferase (HAT) inhibitors and decrease in H3K27 acetylation levels. To examine whether the subdomains that change upon drug treatment are functionally linked to transcription factor regulation, we compared TCF7L2 chromatin binding and gene regulation to HAT inhibition. We identified a subset of coding RNA genes that together can stratify pancreatic cancer patients into distinct survival groups. Overall, this study describes a process to evaluate the functional features of chromosome architecture and reveals the impact of epigenetic inhibitors on chromosome architecture and identifies genes that may provide insight into disease outcome.
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Affiliation(s)
- Diana L Gerrard
- Biomedical Health Sciences Department, University of Vermont, Burlington, VT, USA.,Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT, USA
| | - Yao Wang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Malaina Gaddis
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Yufan Zhou
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway
| | - Heather Witt
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Shili Lin
- Statistics Department, The Ohio State University, Columbus, OH, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Seth E Frietze
- Biomedical Health Sciences Department, University of Vermont, Burlington, VT, USA.,Cellular, Molecular, and Biomedical Sciences Program, University of Vermont, Burlington, VT, USA.,The University of Vermont Cancer Center, Burlington, VT, USA
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10
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Abstract
The spatiotemporal organization of chromatin plays central roles in cellular function. The ribosomal DNA (rDNA) chromatin undergoes dynamic structural changes during mitosis and stress. Here, we developed a CRISPR-based imaging system and tracked the condensation dynamics of rDNA chromatin in live yeast cells under glucose starvation. We found that acute glucose starvation triggers rapid condensation of rDNA. Time-lapse microscopy revealed two stages for rDNA condensation: a “primary stage,” when relaxed rDNA chromatin forms higher order loops or rings, and a “secondary stage,” when the rDNA rings further condense into compact clusters. Twisting of rDNA rings accompanies the secondary stage. The condensin complex, but not the cohesin complex, is required for efficient rDNA condensation in response to glucose starvation. Furthermore, we found that the DNA helicase Sgs1 is essential for the survival of cells expressing rDNA-bound dCas9, suggesting a role for helicases in facilitating DNA replication at dCas9-binding sites. A CRISPR-based imaging system allows tracking of rDNA condensation in single cells Glucose starvation triggers rDNA condensation in two prominent stages Condensin contributes to efficient rDNA condensation caused by glucose starvation Sgs1 helicase is required for normal rDNA replication at dCas9-binding sites
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Affiliation(s)
- Yuan Xue
- Department of Molecular Cellular and Developmental Biology, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA
- Corresponding author
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11
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Roy AR, Ahmed A, DiStefano PV, Chi L, Khyzha N, Galjart N, Wilson MD, Fish JE, Delgado-Olguín P. The transcriptional regulator CCCTC-binding factor limits oxidative stress in endothelial cells. J Biol Chem 2018; 293:8449-8461. [PMID: 29610276 PMCID: PMC5986204 DOI: 10.1074/jbc.m117.814699] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 03/28/2018] [Indexed: 12/22/2022] Open
Abstract
The CCCTC-binding factor (CTCF) is a versatile transcriptional regulator required for embryogenesis, but its function in vascular development or in diseases with a vascular component is poorly understood. Here, we found that endothelial Ctcf is essential for mouse vascular development and limits accumulation of reactive oxygen species (ROS). Conditional knockout of Ctcf in endothelial progenitors and their descendants affected embryonic growth, and caused lethality at embryonic day 10.5 because of defective yolk sac and placental vascular development. Analysis of global gene expression revealed Frataxin (Fxn), the gene mutated in Friedreich's ataxia (FRDA), as the most strongly down-regulated gene in Ctcf-deficient placental endothelial cells. Moreover, in vitro reporter assays showed that Ctcf activates the Fxn promoter in endothelial cells. ROS are known to accumulate in the endothelium of FRDA patients. Importantly, Ctcf deficiency induced ROS-mediated DNA damage in endothelial cells in vitro, and in placental endothelium in vivo Taken together, our findings indicate that Ctcf promotes vascular development and limits oxidative stress in endothelial cells. These results reveal a function for Ctcf in vascular development, and suggest a potential mechanism for endothelial dysfunction in FRDA.
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Affiliation(s)
- Anna R Roy
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Abdalla Ahmed
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter V DiStefano
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Lijun Chi
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Nadiya Khyzha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Genetics and Genome Biology Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Jason E Fish
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and
- Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Ontario M5S 3H2, Canada
| | - Paul Delgado-Olguín
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada,
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Ontario M5S 3H2, Canada
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12
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Abstract
Transcriptional enhancers constitute a subclass of regulatory elements that facilitate transcription. Such regions are generally organized by short stretches of DNA enriched in transcription factor-binding sites but also can include very large regions containing clusters of enhancers, termed super-enhancers. These regions increase the probability or the rate (or both) of transcription generally in
cis and sometimes over very long distances by altering chromatin states and the activity of Pol II machinery at promoters. Although enhancers were discovered almost four decades ago, their inner workings remain enigmatic. One important opening into the underlying principle has been provided by observations that enhancers make physical contacts with their target promoters to facilitate the loading of the RNA polymerase complex. However, very little is known about how such chromatin loops are regulated and how they govern transcription in the three-dimensional context of the nuclear architecture. Here, we present current themes of how enhancers may boost gene expression in three dimensions and we identify currently unresolved key questions.
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Affiliation(s)
- Anita Göndör
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Rolf Ohlsson
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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13
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Spatial organization of chromosome territories in the interphase nucleus of trisomy 21 cells. Chromosoma 2017; 127:247-259. [PMID: 29238858 DOI: 10.1007/s00412-017-0653-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 12/16/2022]
Abstract
In the interphase cell nucleus, chromosomes adopt a conserved and non-random arrangement in subnuclear domains called chromosome territories (CTs). Whereas chromosome translocation can affect CT organization in tumor cell nuclei, little is known about how aneuploidies can impact CT organization. Here, we performed 3D-FISH on control and trisomic 21 nuclei to track the patterning of chromosome territories, focusing on the radial distribution of trisomic HSA21 as well as 11 disomic chromosomes. We have established an experimental design based on cultured chorionic villus cells which keep their original mesenchymal features including a characteristic ellipsoid nuclear morphology and a radial CT distribution that correlates with chromosome size. Our study suggests that in trisomy 21 nuclei, the extra HSA21 induces a shift of HSA1 and HSA3 CTs out toward a more peripheral position in nuclear space and a higher compaction of HSA1 and HSA17 CTs. We posit that the presence of a supernumerary chromosome 21 alters chromosome compaction and results in displacement of other chromosome territories from their usual nuclear position.
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14
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Affiliation(s)
- Samuel Bell
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
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15
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Wang J, Zhou Y, Li X, Meng X, Fan M, Chen H, Xue J, Chen M. Genome-Wide Analysis of the Distinct Types of Chromatin Interactions in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:57-70. [PMID: 28064247 DOI: 10.1093/pcp/pcw194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors. We identified seven groups of interacting loci, which can be distinguished by their epigenetic profiles. Furthermore, the seven groups of interacting loci can be divided into three types of chromatin linkages based on expression status. We observed that two interacting loci sometimes share common epigenetic and transcription factor-binding profiles. Different groups of loci display very different relationships between epigenetic marks and the binding of transcription factors. Distinctive types of chromatin linkages exhibit different gene expression profiles. Our study unveils an entirely unexplored regulatory interaction, linking epigenetic profiles, transcription factor binding and the three-dimensional spatial organization of the Arabidopsis nuclear genome.
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Affiliation(s)
- Jingjing Wang
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Yincong Zhou
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Xue Li
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Miao Fan
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Hongjun Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Jitong Xue
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
| | - Ming Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
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16
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Djekidel MN, Wang M, Zhang MQ, Gao J. HiC-3DViewer: a new tool to visualize Hi-C data in 3D space. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-017-0091-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Computational inference of physical spatial organization of eukaryotic genomes. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0082-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Buffry AD, Mendes CC, McGregor AP. The Functionality and Evolution of Eukaryotic Transcriptional Enhancers. ADVANCES IN GENETICS 2016; 96:143-206. [PMID: 27968730 DOI: 10.1016/bs.adgen.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enhancers regulate precise spatial and temporal patterns of gene expression in eukaryotes and, moreover, evolutionary changes in these modular cis-regulatory elements may represent the predominant genetic basis for phenotypic evolution. Here, we review approaches to identify and functionally analyze enhancers and their transcription factor binding sites, including assay for transposable-accessible chromatin-sequencing (ATAC-Seq) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, respectively. We also explore enhancer functionality, including how transcription factor binding sites combine to regulate transcription, as well as research on shadow and super enhancers, and how enhancers can act over great distances and even in trans. Finally, we discuss recent theoretical and empirical data on how transcription factor binding sites and enhancers evolve. This includes how the function of enhancers is maintained despite the turnover of transcription factor binding sites as well as reviewing studies where mutations in enhancers have been shown to underlie morphological change.
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Affiliation(s)
- A D Buffry
- Oxford Brookes University, Oxford, United Kingdom
| | - C C Mendes
- Oxford Brookes University, Oxford, United Kingdom
| | - A P McGregor
- Oxford Brookes University, Oxford, United Kingdom
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19
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Relationship between spatial organization and biological function, analyzed using gene ontology and chromosome conformation capture of human and fission yeast genomes. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Vernimmen D, Bickmore WA. The Hierarchy of Transcriptional Activation: From Enhancer to Promoter. Trends Genet 2016; 31:696-708. [PMID: 26599498 DOI: 10.1016/j.tig.2015.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Regulatory elements (enhancers) that are remote from promoters play a critical role in the spatial, temporal, and physiological control of gene expression. Studies on specific loci, together with genome-wide approaches, suggest that there may be many common mechanisms involved in enhancer-promoter communication. Here, we discuss the multiprotein complexes that are recruited to enhancers and the hierarchy of events taking place between regulatory elements and promoters.
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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21
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Taqi MM, Waseem D, Ismatullah H, Haider SA, Faisal M. In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes. Funct Integr Genomics 2016; 16:335-45. [PMID: 27038471 PMCID: PMC4850189 DOI: 10.1007/s10142-016-0489-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 12/24/2022]
Abstract
Single nucleotide polymorphisms (SNPs) in PLCE1 and MICB genes increase risk for the development of dengue shock syndrome (DSS). We used Bioinformatics tools to predict alterations at the transcriptional and posttranslational levels driven by PLCE1 and MICB SNPs associated with DSS. Functional and phenotypic analysis conducted to determine deleterious SNPs and impact of amino acid substitution on the structure and function of proteins identified rs2274223 (H1619R) as deleterious to protein coding as it induces structural change in the C2 domain of PLCε, with the mutant residue more positively charged than the wild-type residue (RMSD score, 1.75 Å). Moreover, rs2274223 condenses the chromatin-repressing PLCε expression in DSS. Briefly, this study presents the impact of a single nucleotide transition at SNPs associated with DSS on differential protein binding patterns with PLCE1 and MICB genes and on protein structure modification and their possible role in the pathogenesis of DSS.
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Affiliation(s)
- Malik Mumtaz Taqi
- Division of Mental Health and Addiction, NORMENT, University of Oslo, Oslo, Norway
| | - Durdana Waseem
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Humaira Ismatullah
- Research Center for Modelling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan
| | - Syed Aleem Haider
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Faisal
- Faculty of Health Studies, University of Bradford, BD7 1DP, Bradford, UK.
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK.
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22
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Liu T, Zhang J, Zhou T. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression. PLoS Comput Biol 2016; 12:e1004917. [PMID: 27153118 PMCID: PMC4859557 DOI: 10.1371/journal.pcbi.1004917] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023] Open
Abstract
According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
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Affiliation(s)
- Tuoqi Liu
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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23
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Loucas BD, Shuryak I, Cornforth MN. Three-Color Chromosome Painting as Seen through the Eyes of mFISH: Another Look at Radiation-Induced Exchanges and Their Conversion to Whole-Genome Equivalency. Front Oncol 2016; 6:52. [PMID: 27014627 PMCID: PMC4791380 DOI: 10.3389/fonc.2016.00052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/22/2016] [Indexed: 01/25/2023] Open
Abstract
Whole-chromosome painting (WCP) typically involves the fluorescent staining of a small number of chromosomes. Consequently, it is capable of detecting only a fraction of exchanges that occur among the full complement of chromosomes in a genome. Mathematical corrections are commonly applied to WCP data in order to extrapolate the frequency of exchanges occurring in the entire genome [whole-genome equivalency (WGE)]. However, the reliability of WCP to WGE extrapolations depends on underlying assumptions whose conditions are seldom met in actual experimental situations, in particular the presumed absence of complex exchanges. Using multi-fluor fluorescence in situ hybridization (mFISH), we analyzed the induction of simple exchanges produced by graded doses of 137Cs gamma rays (0–4 Gy), and also 1.1 GeV 56Fe ions (0–1.5 Gy). In order to represent cytogenetic damage as it would have appeared to the observer following standard three-color WCP, all mFISH information pertaining to exchanges that did not specifically involve chromosomes 1, 2, or 4 was ignored. This allowed us to reconstruct dose–responses for three-color apparently simple (AS) exchanges. Using extrapolation methods similar to those derived elsewhere, these were expressed in terms of WGE for comparison to mFISH data. Based on AS events, the extrapolated frequencies systematically overestimated those actually observed by mFISH. For gamma rays, these errors were practically independent of dose. When constrained to a relatively narrow range of doses, the WGE corrections applied to both 56Fe and gamma rays predicted genome-equivalent damage with a level of accuracy likely sufficient for most applications. However, the apparent accuracy associated with WCP to WGE corrections is both fortuitous and misleading. This is because (in normal practice) such corrections can only be applied to AS exchanges, which are known to include complex aberrations in the form of pseudosimple exchanges. When WCP to WGE corrections are applied to true simple exchanges, the results are less than satisfactory, leading to extrapolated values that underestimate the true WGE response by unacceptably large margins. Likely explanations for these results are discussed, as well as their implications for radiation protection. Thus, in seeming contradiction to notion that complex aberrations be avoided altogether in WGE corrections – and in violation of assumptions upon which these corrections are based – their inadvertent inclusion in three-color WCP data is actually required in order for them to yield even marginally acceptable results.
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Affiliation(s)
- Bradford D Loucas
- Department of Radiation Oncology, University of Texas Medical Branch , Galveston, TX , USA
| | - Igor Shuryak
- Center for Radiological Research, Columbia University , New York, NY , USA
| | - Michael N Cornforth
- Department of Radiation Oncology, University of Texas Medical Branch , Galveston, TX , USA
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24
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Djekidel MN, Liang Z, Wang Q, Hu Z, Li G, Chen Y, Zhang MQ. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome Biol 2015; 16:288. [PMID: 26694485 PMCID: PMC4716632 DOI: 10.1186/s13059-015-0851-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/02/2015] [Indexed: 12/11/2022] Open
Abstract
Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control, making it a valuable downstream analysis tool in chromatin conformation studies. 3CPET does so by combining data from ChIA-PET, transcription factor binding sites, and protein interactions. 3CPET results show biologically significant and accurate predictions when validated against experimental and simulation data.
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Affiliation(s)
- Mohamed Nadhir Djekidel
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Zhengyu Liang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Qi Wang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Zhirui Hu
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Guipeng Li
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. .,Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas, Dallas, 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA.
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25
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Popken J, Koehler D, Brero A, Wuensch A, Guengoer T, Thormeyer T, Wolf E, Cremer T, Zakhartchenko V. Positional changes of a pluripotency marker gene during structural reorganization of fibroblast nuclei in cloned early bovine embryos. Nucleus 2015; 5:542-54. [PMID: 25495180 PMCID: PMC4615807 DOI: 10.4161/19491034.2014.970107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cloned bovine preimplantation embryos were generated by somatic cell nuclear transfer (SCNT) of bovine fetal fibroblasts with a silent copy of the pluripotency reporter gene GOF, integrated at a single site of a chromosome 13. GOF combines the regulatory Oct4/Pou5f1 sequence with the coding sequence for EGFP. EGFP expression served as a marker for pluripotency gene activation and was consistently detected in preimplantation embryos with 9 and more cells. Three-dimensional radial nuclear positions of GOF, its carrier chromosome territory and non-carrier homolog were measured in nuclei of fibroblasts, and of day 2 and day 4 embryos, carrying 2 to 9 and 15 to 22 cells, respectively. We tested, whether transcriptional activation was correlated with repositioning of GOF toward the nuclear interior either with a corresponding movement of its carrier chromosome territory 13 or via the formation of a giant chromatin loop. A significant shift of GOF away from the nuclear periphery was observed in day 2 embryos together with both carrier and non-carrier chromosome territories. At day 4, GOF, its carrier chromosome territory 13 and the non-carrier homolog had moved back toward the nuclear periphery. Similar movements of both chromosome territories ruled out a specific GOF effect. Pluripotency gene activation was preceded by a transient, radial shift of GOF toward the nuclear interior. The persistent co-localization of GOF with its carrier chromosome territory rules out the formation of a giant chromatin loop during GOF activation.
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Key Words
- (bovine) preimplantation embryos, chromosome territories, nuclear architecture, nuclear reprogramming, pluripotency gene activation, somatic cell nuclear transfer
- BFF, bovine fetal fibroblasts; BTA, Bos taurus; CLSM, confocal laser scanning microscopy; CT, chromosome territory; eADS, enhanced absolute 3D distances to surfaces; IVF, in vitro fertilization; MGA, major embryonic genome activation; GOF, Oct4/Pou5f1-EGF
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Affiliation(s)
- Jens Popken
- a Division of Anthropology and Human Genetics Biocenter ; LMU Munich ; Martinsried , Germany
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26
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Zhao H, Sifakis E, Sumida N, Millán-Ariño L, Scholz B, Svensson J, Chen X, Ronnegren A, Mallet de Lima C, Varnoosfaderani F, Shi C, Loseva O, Yammine S, Israelsson M, Rathje LS, Németi B, Fredlund E, Helleday T, Imreh M, Göndör A. PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription. Mol Cell 2015; 59:984-97. [DOI: 10.1016/j.molcel.2015.07.019] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 05/20/2015] [Accepted: 07/21/2015] [Indexed: 11/28/2022]
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27
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Metastasis-related genes in hepatocellular carcinoma cell-lines are clustered on chromosome territories predicted by transcriptome and proteome. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5478-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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28
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Dobigny G, Britton-Davidian J, Robinson TJ. Chromosomal polymorphism in mammals: an evolutionary perspective. Biol Rev Camb Philos Soc 2015; 92:1-21. [PMID: 26234165 DOI: 10.1111/brv.12213] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 06/23/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022]
Abstract
Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.
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Affiliation(s)
- Gauthier Dobigny
- Institut de Recherche pour le Développement, Centre de Biologie pour la Gestion des Populations (UMR IRD-INRA-Cirad-Montpellier SupAgro), Campus International de Baillarguet, CS30016, 34988, Montferrier-sur-Lez, France
| | - Janice Britton-Davidian
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Cc065, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7062, South Africa
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29
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Chen X, Yammine S, Shi C, Tark-Dame M, Göndör A, Ohlsson R. The visualization of large organized chromatin domains enriched in the H3K9me2 mark within a single chromosome in a single cell. Epigenetics 2015; 9:1439-45. [PMID: 25482057 DOI: 10.4161/15592294.2014.971633] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Despite considerable efforts, our understanding of the organization of higher order chromatin conformations in single cells and how these relate to chromatin marks remains poor. We have earlier invented the Chromatin In Situ Proximity (ChrISP) technique to determine proximities between chromatin fibers within a single chromosome. Here we used ChrISP to identify chromosome 11-specific hubs that are enriched in the H3K9me2 mark and that project toward the nuclear membrane in finger-like structures. Conversely, chromosome 11-specfic chromatin hubs, visualized by the presence of either H3K9me1 or H3K9me3 marks, are chromosome-wide and largely absent at the nuclear periphery. As the nuclear periphery-specific chromatin hubs were lost in the induced reduction of H3K9me2 levels, they likely represent Large Organization Chromatin in Lysine Methylation (LOCK) domains, previously identified by ChIP-seq analysis. Strikingly, the downregulation of the H3K9me2/3 marks also led to the chromosome-wide compaction of chromosome 11, suggesting a pleiotropic function of these features not recognized before. The ChrISP-mediated visualization of dynamic chromatin states in single cells thus provides an analysis of chromatin structures with a resolution far exceeding that of any other light microscopic technique.
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Affiliation(s)
- Xingqi Chen
- a Department of Microbiology; Tumor and Cell Biology ; Stockholm , Sweden
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30
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Phanstiel DH, Boyle AP, Heidari N, Snyder MP. Mango: a bias-correcting ChIA-PET analysis pipeline. Bioinformatics 2015; 31:3092-8. [PMID: 26034063 DOI: 10.1093/bioinformatics/btv336] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/26/2015] [Indexed: 01/04/2023] Open
Abstract
MOTIVATION Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity. RESULTS Comparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs. AVAILABILITY AND IMPLEMENTATION Mango is open source and distributed through github at https://github.com/dphansti/mango. CONTACT mpsnyder@standford.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Douglas H Phanstiel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 and
| | - Alan P Boyle
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nastaran Heidari
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 and
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 and
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31
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Shen W, Wang D, Ye B, Shi M, Zhang Y, Zhao Z. A possible role of Drosophila CTCF in mitotic bookmarking and maintaining chromatin domains during the cell cycle. Biol Res 2015; 48:27. [PMID: 26013116 PMCID: PMC4485355 DOI: 10.1186/s40659-015-0019-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/20/2015] [Indexed: 11/10/2022] Open
Abstract
Background The CCCTC-binding factor (CTCF) is a highly conserved insulator protein that plays various roles in many cellular processes. CTCF is one of the main architecture proteins in higher eukaryotes, and in combination with other architecture proteins and regulators, also shapes the three-dimensional organization of a genome. Experiments show CTCF partially remains associated with chromatin during mitosis. However, the role of CTCF in the maintenance and propagation of genome architectures throughout the cell cycle remains elusive. Results We performed a comprehensive bioinformatics analysis on public datasets of Drosophila CTCF (dCTCF). We characterized dCTCF-binding sites according to their occupancy status during the cell cycle, and identified three classes: interphase-mitosis-common (IM), interphase-only (IO) and mitosis-only (MO) sites. Integrated function analysis showed dCTCF-binding sites of different classes might be involved in different biological processes, and IM sites were more conserved and more intensely bound. dCTCF-binding sites of the same class preferentially localized closer to each other, and were highly enriched at chromatin syntenic and topologically associating domains boundaries. Conclusions Our results revealed different functions of dCTCF during the cell cycle and suggested that dCTCF might contribute to the establishment of the three-dimensional architecture of the Drosophila genome by maintaining local chromatin compartments throughout the whole cell cycle. Electronic supplementary material The online version of this article (doi:10.1186/s40659-015-0019-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenlong Shen
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China.
| | - Dong Wang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China.
| | - Bingyu Ye
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China. .,College of Life Science, Capital Normal University, 105 Xisihuanbei Road, Beijing, Haidian District, 100048, China.
| | - Minglei Shi
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China.
| | - Yan Zhang
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China.
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, Fengtai District, 100071, China.
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Bashir S, Tariq M, Aslam HM, Hashmi ASM, Malik B, Amin A, Mumtaz S. Orbital dermatofibrosarcoma protuberans with intracranial extension preceded by recurrent leiomyoma of the orbit: a case report. J Med Case Rep 2015; 9:96. [PMID: 25924890 PMCID: PMC4423146 DOI: 10.1186/s13256-015-0561-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/03/2015] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Dermatofibrosarcoma protuberans is a rare, locally aggressive cutaneous tumor of intermediate to low-grade malignancy. COL1A1-PDGFβ translocation is specific to dermatofibrosarcoma protuberans, where the abnormally fused COL1A1-PDGFβ gene directs formation of an abnormal combined (fusion) protein that researchers believe to ultimately function like the platelet-derived growth factor-beta protein. CASE PRESENTATION In this report, we present a case of a 63-year-old Asian man with dermatofibrosarcoma protuberans of the right orbit with intracranial extension. He had a prior history of recurrent leiomyomas at the identical site. He underwent near-total en bloc resection of the tumor through a wide craniectomy with a 6 cm rim of the frontal scalp, allowing the tumor to be resected en bloc, leaving negative margins. Microscopically, the tumor comprised spindle cells with mild nuclear atypia and a low mitotic index embedded in a spiraling pattern of decussating fascicles consistent with dermatofibrosarcoma protuberans. The lesion was positive for CD34 and BCL2. Following resection, the patient was started on imatinib mesylate therapy (800 mg/day). CONCLUSIONS We propose that platelet-derived growth factor, which has been implicated in the progression of leiomyomas by augmenting mitogenesis, may have acted in an autocrine manner to cause cell division, which may have led to the development of dermatofibrosarcoma protuberans in our patient. Further research is imperative to find certain molecular associations between the discussed soft tissue tumors. Also important is the effective utilization of platelet-derived growth factor receptor kinase inhibitors to prevent transformation to any platelet-derived growth factor-driven tumor, which in our patient was a dermatofibrosarcoma protuberans.
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Affiliation(s)
- Sanaullah Bashir
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan.
| | - Maryam Tariq
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan.
| | | | | | - Baber Malik
- Department of Molecular Diagnostic and Immunology Laboratory, Sindh Institute of Urology and Transplantation, Aga Khan University, Karachi, Pakistan.
| | - Akhtar Amin
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan.
| | - Sidra Mumtaz
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan.
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Cao J, Luo Z, Cheng Q, Xu Q, Zhang Y, Wang F, Wu Y, Song X. Three-dimensional regulation of transcription. Protein Cell 2015; 6:241-53. [PMID: 25670626 PMCID: PMC4383755 DOI: 10.1007/s13238-015-0135-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 01/09/2015] [Indexed: 12/20/2022] Open
Abstract
Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underlying DNA sequences. These alterations, namely epigenetic changes, occur during cell division, differentiation and cell death. Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, histone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non-coding RNAs (ncRNAs). Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.
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Affiliation(s)
- Jun Cao
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Zhengyu Luo
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Qingyu Cheng
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Qianlan Xu
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Yan Zhang
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Fei Wang
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Yan Wu
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Xiaoyuan Song
- CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
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Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. Genome-wide map of regulatory interactions in the human genome. Genome Res 2014; 24:1905-17. [PMID: 25228660 PMCID: PMC4248309 DOI: 10.1101/gr.176586.114] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/11/2014] [Indexed: 01/09/2023]
Abstract
Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.
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Affiliation(s)
- Nastaran Heidari
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Douglas H Phanstiel
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Chao He
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fereshteh Jahanbani
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China; Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080-3021, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
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Mapping of long-range INS promoter interactions reveals a role for calcium-activated chloride channel ANO1 in insulin secretion. Proc Natl Acad Sci U S A 2014; 111:16760-5. [PMID: 25385647 DOI: 10.1073/pnas.1419240111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We used circular chromatin conformation capture (4C) to identify a physical contact in human pancreatic islets between the region near the insulin (INS) promoter and the ANO1 gene, lying 68 Mb away on human chromosome 11, which encodes a Ca(2+)-dependent chloride ion channel. In response to glucose, this contact was strengthened and ANO1 expression increased, whereas inhibition of INS gene transcription by INS promoter targeting siRNA decreased ANO1 expression, revealing a regulatory effect of INS promoter on ANO1 expression. Knockdown of ANO1 expression caused decreased insulin secretion in human islets, establishing a physical proximity-dependent feedback loop involving INS transcription, ANO1 expression, and insulin secretion. To explore a possible role of ANO1 in insulin metabolism, we carried out experiments in Ano1(+/-) mice. We observed reduced serum insulin levels and insulin-to-glucose ratios in high-fat diet-fed Ano1(+/-) mice relative to Ano1(+/+) mice fed the same diet. Our results show that determination of long-range contacts within the nucleus can be used to detect novel and physiologically relevant mechanisms. They also show that networks of long-range physical contacts are important to the regulation of insulin metabolism.
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36
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Davidsson J. The epigenetic landscape of aneuploidy: constitutional mosaicism leading the way? Epigenomics 2014; 6:45-58. [PMID: 24579946 DOI: 10.2217/epi.13.78] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The role of structural genetic changes in human disease has received substantial attention in recent decades, but surprisingly little is known about numerical chromosomal abnormalities, even though they have been recognized since the days of Boveri as partaking in different cellular pathophysiological processes such as cancer and genomic disorders. The current knowledge of the genetic and epigenetic consequences of aneuploidy is reviewed herein, with a special focus on using mosaic genetic syndromes to study the DNA methylation footprints and expressional effects associated with whole-chromosomal gains. Recent progress in understanding the debated role of aneuploidy as a driver or passenger in malignant transformation, as well as how the cell responds to and regulates excess genetic material in experimental settings, is also discussed in detail.
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Affiliation(s)
- Josef Davidsson
- Division of Molecular Medicine & Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 84 Lund, Sweden
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37
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Strickfaden H, Zunhammer A, van Koningsbruggen S, Köhler D, Cremer T. 4D Chromatin dynamics in cycling cells. Nucleus 2014. [DOI: 10.4161/nucl.11969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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38
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Faisal M, Waseem D, Ismatullah H, Taqi MM. A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. Comput Biol Med 2014; 53:250-7. [PMID: 25177835 DOI: 10.1016/j.compbiomed.2014.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 07/24/2014] [Accepted: 07/26/2014] [Indexed: 12/15/2022]
Abstract
Single nucleotide polymorphisms (SNPs) both in coding and non-coding regions govern gene functions prompting differential vulnerability to diseases, heterogeneous response to pharmaceutical regimes and environmental anomalies. These genetic variations, SNPs, may alter an individual׳s susceptibility for alcohol dependence by remodeling DNA-protein interaction patterns in prodynorphin (PDYN) and the κ-opioid receptor (OPRK1) genes. In order to elaborate the underlying molecular mechanism behind these susceptibility differences we used bioinformatics tools to retrieve differential DNA-protein interactions at PDYN and OPRK1 SNPs significantly associated with alcohol dependence. Our results show allele-specific DNA-protein interactions depicting allele-specific mechanisms implicated in differential regulation of gene expression. Several transcription factors, for instance, VDR, RXR-alpha, NFYA, CTF family, USF-1, USF2, ER, AR and predominantly SP family show an allele-specific binding affinity with PDYN gene; likewise, GATA, TBP, AP-1, USF-2, C/EBPbeta, Cart-1 and ER interact with OPRK1 SNPs on intron 2 in an allele-specific manner. In a nutshell, transition of a single nucleotide may modify differential DNA-protein interactions at OPRK1 and PDYN׳s SNPs, significantly associated with pathology that may lead to altered individual vulnerability for alcohol dependence.
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Affiliation(s)
- Muhammad Faisal
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Durdana Waseem
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Humaira Ismatullah
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Malik Mumtaz Taqi
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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39
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Bracha D, Karzbrun E, Daube SS, Bar-Ziv RH. Emergent properties of dense DNA phases toward artificial biosystems on a surface. Acc Chem Res 2014; 47:1912-21. [PMID: 24856257 DOI: 10.1021/ar5001428] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CONSPECTUS: The expression of genes in a cell in response to external signals or internal programs occurs within an environment that is compartmentalized and dense. Reconstituting gene expression in man-made systems is relevant for the basic understanding of gene regulation, as well as for the development of applications in bio- and nanotechnology. DNA polymer brushes assembled on a surface emulate a dense cellular environment. In a regime of significant chain overlap, the highly charged nature of DNA, its entropic degrees of freedom, and its interaction with transcription/translation machinery lead to emergent collective biophysical and biochemical properties, which are summarized in this Account. First, we describe a single-step photolithographic biochip on which biomolecules can be immobilized. Then, we present the assembly of localized DNA brushes, a few kilo-base pairs long, with spatially varying density, reaching a DNA concentration of ∼10(7) base pairs/μm(3), which is comparable to the value in E. coli. We then summarize the response of brush height to changes in density and mono- and divalent ionic strength. The balance between entropic elasticity and swelling forces leads to a rich phase behavior. At no added salt, polymers are completely stretched due to the osmotic pressure of ions, and at high salt they assume a relaxed coil conformation. Midrange, the brush height scales with ratio of density and ionic strength to the third power, in agreement with the general theory of polyelectrolyte brushes. In response to trivalent cations, DNA brushes collapse into macroscopic dendritic condensates with hysteresis, coexistence, and a hierarchy of condensation with brush density. We next present an investigation of RNA transcription in the DNA brush. In general, the brush density entropically excludes macromolecules, depleting RNA polymerase concentration in the brush compared to the bulk, therefore reducing transcription rate. The orientation of transcription promoters with respect to the surface also affects the rate with a lower value for outward compared to inward transcription, likely due to local changes of RNA polymerase concentrations. We hypothesize that equalizing the macromolecular osmotic pressure between bulk and brush with the addition of inert macromolecules would overcome the entropic exclusion of DNA associated proteins, and lead to enhanced biochemical activity. Finally, we present protein synthesis cascades in DNA brushes patterned at close proximity, as a step toward biochemical signaling between brushes. Examining the synthesis of proteins polymerizing into crystalline tubes suggests that on-chip molecular traps serve as nucleation sites for protein assembly, thereby opening possibilities for reconstituting nanoscale protein assembly pathways.
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Affiliation(s)
- Dan Bracha
- Department of Materials and
Interfaces Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal Karzbrun
- Department of Materials and
Interfaces Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shirley S. Daube
- Department of Materials and
Interfaces Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roy H. Bar-Ziv
- Department of Materials and
Interfaces Weizmann Institute of Science, Rehovot 76100, Israel
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40
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Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, Dostie J. Classifying leukemia types with chromatin conformation data. Genome Biol 2014; 15:R60. [PMID: 24995990 PMCID: PMC4038739 DOI: 10.1186/gb-2014-15-4-r60] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/30/2014] [Indexed: 11/10/2022] Open
Abstract
Background Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.
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41
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Su M, Han D, Boyd-Kirkup J, Yu X, Han JDJ. Evolution of Alu elements toward enhancers. Cell Rep 2014; 7:376-385. [PMID: 24703844 DOI: 10.1016/j.celrep.2014.03.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 01/29/2014] [Accepted: 03/05/2014] [Indexed: 01/24/2023] Open
Abstract
The human genome contains approximately one million Alu repetitive elements comprising 10% of the genome, yet their functions are not well understood. Here, we show that Alu elements resemble enhancers. Alu elements are bound by two well-phased nucleosomes that contain histones bearing marks of active chromatin, and they show tissue-specific enrichment for the enhancer mark H3K4me1. A proportion of Alu elements were experimentally validated as bona fide active enhancers with an in vitro reporter assay. In addition, Hi-C data indicate that Alus show long-range interactions with gene promoters. We also find that Alus are generally more conserved when located in the proximal upstream region of genes. Their similarity to enhancers becomes more prominent with their age in the human genome, following a clear evolutionary continuum reminiscent of the evolutionary pattern of proto-genes. Therefore, we conclude that some Alu elements can function as enhancers and propose that many more may be proto-enhancers that serve as a repertoire for the de novo birth of enhancers.
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Affiliation(s)
- Ming Su
- Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; Center of Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Lincui East Road, Beijing 100101, China
| | - Dali Han
- Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; Center of Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Lincui East Road, Beijing 100101, China
| | - Jerome Boyd-Kirkup
- Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Xiaoming Yu
- Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; Center of Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Lincui East Road, Beijing 100101, China
| | - Jing-Dong J Han
- Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.
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42
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Chen X, Shi C, Yammine S, Göndör A, Rönnlund D, Fernandez-Woodbridge A, Sumida N, Widengren J, Ohlsson R. Chromatin in situ proximity (ChrISP): single-cell analysis of chromatin proximities at a high resolution. Biotechniques 2014; 56:117-8, 120-4. [PMID: 24641475 DOI: 10.2144/000114145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/16/2014] [Indexed: 11/23/2022] Open
Abstract
Current techniques for analyzing chromatin structures are hampered by either poor resolution at the individual cell level or the need for a large number of cells to obtain higher resolution. This is a major problem as it hampers our understanding of chromatin conformation in single cells and how these respond to environmental cues. Here we describe a new method, chromatin in situ proximity (ChrISP), which reproducibly scores for proximities between two different chromatin fibers in 3-D with a resolution of ~170Å in single cells. The technique is based on the in situ proximity ligation assay (ISPLA), but ChrISP omits the rolling circle amplification step (RCA). Instead, the proximities between chromatin fibers are visualized by a fluorescent connector oligonucleotide DNA, here termed splinter, forming a circular DNA with another circle-forming oligonucleotide, here termed backbone, upon ligation. In contrast to the regular ISPLA technique, our modification enables detection of chromatin fiber proximities independent of steric hindrances from nuclear structures. We use this method to identify higher order structures of individual chromosomes in relation to structural hallmarks of interphase nuclei and beyond the resolution of the light microscope.
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Affiliation(s)
- Xingqi Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Chengxi Shi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Samer Yammine
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anita Göndör
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Rönnlund
- Applied Physics, AlbaNova University Center, Royal Institute of Technology, Sweden
| | | | - Noriyuki Sumida
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jerker Widengren
- Applied Physics, AlbaNova University Center, Royal Institute of Technology, Sweden
| | - Rolf Ohlsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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43
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Rousseau M, Crutchley JL, Miura H, Suderman M, Blanchette M, Dostie J. Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res 2014; 42:1524-40. [PMID: 24174538 PMCID: PMC3919592 DOI: 10.1093/nar/gkt998] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 08/28/2013] [Accepted: 10/02/2013] [Indexed: 12/26/2022] Open
Abstract
Three-dimensional genome organization is an important higher order transcription regulation mechanism that can be studied with the chromosome conformation capture techniques. Here, we combined chromatin organization analysis by chromosome conformation capture-carbon copy, computational modeling and epigenomics to achieve the first integrated view, through time, of a connection between chromatin state and its architecture. We used this approach to examine the chromatin dynamics of the HoxA cluster in a human myeloid leukemia cell line at various stages of differentiation. We found that cellular differentiation involves a transient activation of the 5'-end HoxA genes coinciding with a loss of contacts throughout the cluster, and by specific silencing at the 3'-end with H3K27 methylation. The 3D modeling of the data revealed an extensive reorganization of the cluster between the two previously reported topologically associated domains in differentiated cells. Our results support a model whereby silencing by polycomb group proteins and reconfiguration of CTCF interactions at a topologically associated domain boundary participate in changing the HoxA cluster topology, which compartmentalizes the genes following differentiation.
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Affiliation(s)
- Mathieu Rousseau
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Jennifer L. Crutchley
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Hisashi Miura
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Matthew Suderman
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Mathieu Blanchette
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
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44
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Relevance and limitations of crowding, fractal, and polymer models to describe nuclear architecture. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:443-79. [PMID: 24380602 DOI: 10.1016/b978-0-12-800046-5.00013-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chromosome architecture plays an essential role for all nuclear functions, and its physical description has attracted considerable interest over the last few years among the biophysics community. These researches at the frontiers of physics and biology have been stimulated by the demand for quantitative analysis of molecular biology experiments, which provide comprehensive data on chromosome folding, or of live cell imaging experiments that enable researchers to visualize selected chromosome loci in living or fixed cells. In this review our goal is to survey several nonmutually exclusive models that have emerged to describe the folding of DNA in the nucleus, the dynamics of proteins in the nucleoplasm, or the movements of chromosome loci. We focus on three classes of models, namely molecular crowding, fractal, and polymer models, draw comparisons, and discuss their merits and limitations in the context of chromosome structure and dynamics, or nuclear protein navigation in the nucleoplasm. Finally, we identify future challenges in the roadmap to a unified model of the nuclear environment.
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45
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Hajjoul H, Mathon J, Ranchon H, Goiffon I, Mozziconacci J, Albert B, Carrivain P, Victor JM, Gadal O, Bystricky K, Bancaud A. High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome. Genome Res 2013; 23:1829-38. [PMID: 24077391 PMCID: PMC3814883 DOI: 10.1101/gr.157008.113] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chromosome dynamics are recognized to be intimately linked to genomic transactions, yet the physical principles governing spatial fluctuations of chromatin are still a matter of debate. Using high-throughput single-particle tracking, we recorded the movements of nine fluorescently labeled chromosome loci located on chromosomes III, IV, XII, and XIV of Saccharomyces cerevisiae over an extended temporal range spanning more than four orders of magnitude (10(-2)-10(3) sec). Spatial fluctuations appear to be characterized by an anomalous diffusive behavior, which is homogeneous in the time domain, for all sites analyzed. We show that this response is consistent with the Rouse polymer model, and we confirm the relevance of the model with Brownian dynamics simulations and the analysis of the statistical properties of the trajectories. Moreover, the analysis of the amplitude of fluctuations by the Rouse model shows that yeast chromatin is highly flexible, its persistence length being qualitatively estimated to <30 nm. Finally, we show that the Rouse model is also relevant to analyze chromosome motion in mutant cells depleted of proteins that bind to or assemble chromatin, and suggest that it provides a consistent framework to study chromatin dynamics. We discuss the implications of our findings for yeast genome architecture and for target search mechanisms in the nucleus.
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Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells. Mol Cell Biol 2013; 33:4504-16. [PMID: 24043305 DOI: 10.1128/mcb.00545-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells.
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Epigenetic control of cytokine gene expression: regulation of the TNF/LT locus and T helper cell differentiation. Adv Immunol 2013; 118:37-128. [PMID: 23683942 DOI: 10.1016/b978-0-12-407708-9.00002-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Epigenetics encompasses transient and heritable modifications to DNA and nucleosomes in the native chromatin context. For example, enzymatic addition of chemical moieties to the N-terminal "tails" of histones, particularly acetylation and methylation of lysine residues in the histone tails of H3 and H4, plays a key role in regulation of gene transcription. The modified histones, which are physically associated with gene regulatory regions that typically occur within conserved noncoding sequences, play a functional role in active, poised, or repressed gene transcription. The "histone code" defined by these modifications, along with the chromatin-binding acetylases, deacetylases, methylases, demethylases, and other enzymes that direct modifications resulting in specific patterns of histone modification, shows considerable evolutionary conservation from yeast to humans. Direct modifications at the DNA level, such as cytosine methylation at CpG motifs that represses promoter activity, are another highly conserved epigenetic mechanism of gene regulation. Furthermore, epigenetic modifications at the nucleosome or DNA level can also be coupled with higher-order intra- or interchromosomal interactions that influence the location of regulatory elements and that can place them in an environment of specific nucleoprotein complexes associated with transcription. In the mammalian immune system, epigenetic gene regulation is a crucial mechanism for a range of physiological processes, including the innate host immune response to pathogens and T cell differentiation driven by specific patterns of cytokine gene expression. Here, we will review current findings regarding epigenetic regulation of cytokine genes important in innate and/or adaptive immune responses, with a special focus upon the tumor necrosis factor/lymphotoxin locus and cytokine-driven CD4+ T cell differentiation into the Th1, Th2, and Th17 lineages.
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Lovén J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 2013; 153:320-34. [PMID: 23582323 DOI: 10.1016/j.cell.2013.03.036] [Citation(s) in RCA: 2085] [Impact Index Per Article: 189.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/25/2013] [Accepted: 03/25/2013] [Indexed: 12/17/2022]
Abstract
Chromatin regulators have become attractive targets for cancer therapy, but it is unclear why inhibition of these ubiquitous regulators should have gene-specific effects in tumor cells. Here, we investigate how inhibition of the widely expressed transcriptional coactivator BRD4 leads to selective inhibition of the MYC oncogene in multiple myeloma (MM). BRD4 and Mediator were found to co-occupy thousands of enhancers associated with active genes. They also co-occupied a small set of exceptionally large super-enhancers associated with genes that feature prominently in MM biology, including the MYC oncogene. Treatment of MM tumor cells with the BET-bromodomain inhibitor JQ1 led to preferential loss of BRD4 at super-enhancers and consequent transcription elongation defects that preferentially impacted genes with super-enhancers, including MYC. Super-enhancers were found at key oncogenic drivers in many other tumor cells. These observations have implications for the discovery of cancer therapeutics directed at components of super-enhancers in diverse tumor types.
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Affiliation(s)
- Jakob Lovén
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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