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Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D. Functionally conserved enhancers with divergent sequences in distant vertebrates. BMC Genomics 2015; 16:882. [PMID: 26519295 PMCID: PMC4628251 DOI: 10.1186/s12864-015-2070-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 10/13/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. Our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species. RESULTS We searched for sequences that were conserved within groups of closely related species but not between groups of more distant species, and were associated with an epigenetic mark of enhancer activity. To facilitate inferring orthology between non-conserved sequences, we limited our search to introns whose orthology could be unambiguously established by mapping the bracketing exons. We show that a subset of these non-conserved but syntenic sequences from the mouse and zebrafish genomes have homologous functions in a zebrafish transgenic enhancer assay. The conserved expression patterns driven by these enhancers are probably associated with short transcription factor-binding motifs present in the divergent sequences. CONCLUSIONS We have identified numerous potential enhancers with divergent sequences but a conserved function. These results indicate that selection on function, rather than sequence, may be a common mode of enhancer evolution; evidence for selection at the sequence level is not a necessary criterion to define a gene regulatory element.
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Affiliation(s)
- Song Yang
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Nir Oksenberg
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Sachiko Takayama
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Alexander Poliakov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Inna Dubchak
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
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52
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Douglas AT, Hill RD. Variation in vertebrate cis-regulatory elements in evolution and disease. Transcription 2015; 5:e28848. [PMID: 25764334 DOI: 10.4161/trns.28848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Much of the genetic information that drives animal diversity lies within the vast non-coding regions of the genome. Multi-species sequence conservation in non-coding regions of the genome flags important regulatory elements and more recently, techniques that look for functional signatures predicted for regulatory sequences have added to the identification of thousands more. For some time, biologists have argued that changes in cis-regulatory sequences creates the basic genetic framework for evolutionary change. Recent advances support this notion and show that there is extensive genomic variability in non-coding regulatory elements associated with trait variation, speciation and disease.
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Affiliation(s)
- Adam Thomas Douglas
- a MRC Human Genetics Unit; MRC Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh, UK
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53
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Mayes MB, Morgan T, Winston J, Buxton DS, Kamat MA, Smith D, Williams M, Martin RL, Kleinjan DA, Cooper DN, Upadhyaya M, Chuzhanova N. Remotely acting SMCHD1 gene regulatory elements: in silico prediction and identification of potential regulatory variants in patients with FSHD. Hum Genomics 2015; 9:25. [PMID: 26446085 PMCID: PMC4597391 DOI: 10.1186/s40246-015-0047-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/01/2015] [Indexed: 12/03/2022] Open
Abstract
Background Facioscapulohumeral dystrophy (FSHD) is commonly associated with contraction of the D4Z4 macro-satellite repeat on chromosome 4q35 (FSHD1) or mutations in the SMCHD1 gene (FSHD2). Recent studies have shown that the clinical manifestation of FSHD1 can be modified by mutations in the SMCHD1 gene within a given family. The absence of either D4Z4 contraction or SMCHD1 mutations in a small cohort of patients suggests that the disease could also be due to disruption of gene regulation. In this study, we postulated that mutations responsible for exerting a modifier effect on FSHD might reside within remotely acting regulatory elements that have the potential to interact at a distance with their cognate gene promoter via chromatin looping. To explore this postulate, genome-wide Hi-C data were used to identify genomic fragments displaying the strongest interaction with the SMCHD1 gene. These fragments were then narrowed down to shorter regions using ENCODE and FANTOM data on transcription factor binding sites and epigenetic marks characteristic of promoters, enhancers and silencers. Results We identified two regions, located respectively ~14 and ~85 kb upstream of the SMCHD1 gene, which were then sequenced in 229 FSHD/FSHD-like patients (200 with D4Z4 repeat units <11). Three heterozygous sequence variants were found ~14 kb upstream of the SMCHD1 gene. One of these variants was found to be of potential functional significance based on DNA methylation analysis. Further functional ascertainment will be required in order to establish the clinical/functional significance of the variants found. Conclusions In this study, we propose an improved approach to predict the possible locations of remotely acting regulatory elements that might influence the transcriptional regulation of their associated gene(s). It represents a new way to screen for disease-relevant mutations beyond the immediate vicinity of the specific disease gene. It promises to be useful for investigating disorders in which mutations could occur in remotely acting regulatory elements. Electronic supplementary material The online version of this article (doi:10.1186/s40246-015-0047-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mary B Mayes
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Taniesha Morgan
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Jincy Winston
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Daniel S Buxton
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Mihir Anant Kamat
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.,Present address: Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Debbie Smith
- Blood Sciences Department and Bristol Genetics Laboratory, Southmead Hospital, Westbury-on-Trym, Bristol, BS10 5NB, UK
| | - Maggie Williams
- Blood Sciences Department and Bristol Genetics Laboratory, Southmead Hospital, Westbury-on-Trym, Bristol, BS10 5NB, UK
| | - Rebecca L Martin
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Dirk A Kleinjan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Meena Upadhyaya
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Nadia Chuzhanova
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
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54
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Hsu PY, Hsu HK, Hsiao TH, Ye Z, Wang E, Profit AL, Jatoi I, Chen Y, Kirma NB, Jin VX, Sharp ZD, Huang THM. Spatiotemporal control of estrogen-responsive transcription in ERα-positive breast cancer cells. Oncogene 2015; 35:2379-89. [PMID: 26300005 PMCID: PMC4865474 DOI: 10.1038/onc.2015.298] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/20/2015] [Accepted: 07/05/2015] [Indexed: 12/29/2022]
Abstract
Recruitment of transcription machinery to target promoters for aberrant gene expression has been well studied, but underlying control directed by distant-acting enhancers remains unclear in cancer development. Our previous study demonstrated that distant estrogen response elements (DEREs) located on chromosome 20q13 are frequently amplified and translocated to other chromosomes in ERα-positive breast cancer cells. In this study, we used three-dimensional interphase fluorescence in situ hybridization to decipher spatiotemporal gathering of multiple DEREs in the nucleus. Upon estrogen stimulation, scattered 20q13 DEREs were mobilized to form regulatory depots for synchronized gene expression of target loci. A chromosome conformation capture assay coupled with chromatin immunoprecipitation further uncovered that ERα-bound regulatory depots are tethered to heterochromatin protein 1 (HP1) for coordinated chromatin movement and histone modifications of target loci, resulting in transcription repression. Neutralizing HP1 function dysregulated the formation of DERE-involved regulatory depots and transcription inactivation of candidate tumor-suppressor genes. Deletion of amplified DEREs using the CRISPR/Cas9 genomic-editing system profoundly altered transcriptional profiles of proliferation-associated signaling networks, resulting in reduction of cancer cell growth. These findings reveal a formerly uncharacterized feature wherein multiple copies of the amplicon congregate as transcriptional units in the nucleus for synchronous regulation of function-related loci in tumorigenesis. Disruption of their assembly can be a new strategy for treating breast cancers and other malignancies.
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Affiliation(s)
- P-Y Hsu
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - H-K Hsu
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - T-H Hsiao
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Medical Research, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - Z Ye
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - E Wang
- Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - A L Profit
- Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Pathology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - I Jatoi
- Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Surgery, The University of Texas Health Science Center at San Antonio, San Antonio TX, USA
| | - Y Chen
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - N B Kirma
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - V X Jin
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Z D Sharp
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - T H-M Huang
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
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55
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Chandra S, Terragni J, Zhang G, Pradhan S, Haushka S, Johnston D, Baribault C, Lacey M, Ehrlich M. Tissue-specific epigenetics in gene neighborhoods: myogenic transcription factor genes. Hum Mol Genet 2015; 24:4660-73. [PMID: 26041816 PMCID: PMC4512632 DOI: 10.1093/hmg/ddv198] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022] Open
Abstract
Myogenic regulatory factor (MRF) genes, MYOD1, MYOG, MYF6 and MYF5, are critical for the skeletal muscle lineage. Here, we used various epigenome profiles from human myoblasts (Mb), myotubes (Mt), muscle and diverse non-muscle samples to elucidate the involvement of multigene neighborhoods in the regulation of MRF genes. We found more far-distal enhancer chromatin associated with MRF genes in Mb and Mt than previously reported from studies in mice. For the MYF5/MYF6 gene-pair, regions of Mb-associated enhancer chromatin were located throughout the adjacent 236-kb PTPRQ gene even though Mb expressed negligible amounts of PTPRQ mRNA. Some enhancer chromatin regions inside PTPRQ in Mb were also seen in PTPRQ mRNA-expressing non-myogenic cells. This suggests dual-purpose PTPRQ enhancers that upregulate expression of PTPRQ in non-myogenic cells and MYF5/MYF6 in myogenic cells. In contrast, the myogenic enhancer chromatin regions distal to MYOD1 were intergenic and up to 19 kb long. Two of them contain small, known MYOD1 enhancers, and one displayed an unusually high level of 5-hydroxymethylcytosine in a quantitative DNA hydroxymethylation assay. Unexpectedly, three regions of MYOD1-distal enhancer chromatin in Mb and Mt overlapped enhancer chromatin in umbilical vein endothelial cells, which might upregulate a distant gene (PIK3C2A). Lastly, genes surrounding MYOG were preferentially transcribed in Mt, like MYOG itself, and exhibited nearby myogenic enhancer chromatin. These neighboring chromatin regions may be enhancers acting in concert to regulate myogenic expression of multiple adjacent genes. Our findings reveal the very different and complex organization of gene neighborhoods containing closely related transcription factor genes.
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Affiliation(s)
- Sruti Chandra
- Program in Human Genetics, Tulane Cancer Center, and Center for Bioinformatics and Genomics, Tulane Health Sciences Center, New Orleans, LA 70122, USA
| | | | | | | | - Stephen Haushka
- Department of Biochemistry, University of Washington, Seattle, WA 98109, USA, and
| | - Douglas Johnston
- Department of Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, LA 70112, USA
| | - Carl Baribault
- Tulane Cancer Center and Department of Mathematics, Tulane Health Sciences Center and Tulane University, New Orleans, LA 70122, USA
| | - Michelle Lacey
- Tulane Cancer Center and Department of Mathematics, Tulane Health Sciences Center and Tulane University, New Orleans, LA 70122, USA
| | - Melanie Ehrlich
- Program in Human Genetics, Tulane Cancer Center, and Center for Bioinformatics and Genomics, Tulane Health Sciences Center, New Orleans, LA 70122, USA,
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56
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Almamun M, Levinson BT, Gater ST, Schnabel RD, Arthur GL, Davis JW, Taylor KH. Genome-wide DNA methylation analysis in precursor B-cells. Epigenetics 2015; 9:1588-95. [PMID: 25484143 PMCID: PMC4622941 DOI: 10.4161/15592294.2014.983379] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order to elucidate the influence of DNA methylation during B-cell development, genome-wide DNA methylation status of pro-B, pre-BI, pre-BII, and naïve-B-cells isolated from human umbilical cord blood was determined using the methylated CpG island recovery assay followed by next generation sequencing. On average, 182–200 million sequences were generated for each precursor B-cell subset in 10 biological replicates. An overall decrease in methylation was observed during the transition from pro-B to pre-BI, whereas no differential methylation was observed in the pre-BI to pre-BII transition or in the pre-BII to naïve B-cell transition. Most of the methylated regions were located within intergenic and intronic regions not present in a CpG island context. Putative novel enhancers were identified in these regions that were differentially methylated between pro-B and pre-BI cells. The genome-wide methylation profiles are publically available and may be used to gain a better understanding of the involvement of atypical DNA methylation in the pathogenesis of malignancies associated with precursor B-cells.
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Key Words
- CG dinucleotide
- CLP, common lymphoid progenitor cells
- CpGI, CpG island
- DMRs, differentially methylated regions
- DNA methylation
- FDR, false discovery rate.
- H3K27ac, histone H3 lysine 27 acetylation
- H3K4me1, histone H3 lysine 4 monomethylation
- HCB, human umbilical cord blood
- HSCs, haematopoietic stem cells
- MBDs, methyl CpG binding domains
- MIRA-seq, methylated CpG island recovery assay (MIRA) followed by next generation sequencing
- MeCP2, methyl CpG binding protein 2
- Pre-B, precursor B-cell; CD
- Pro-B, progenitor B-cell
- ROIs, regions of interest
- TFs, transcription factors
- acute lymphoblastic leukemia; CpG
- cluster of differentiation; ALL
- enhancer
- next-generation sequencing
- precursor B-cell
- umbilical cord blood
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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57
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Le Dily F, Beato M. TADs as modular and dynamic units for gene regulation by hormones. FEBS Lett 2015; 589:2885-92. [DOI: 10.1016/j.febslet.2015.05.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 12/28/2022]
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Poletti V, Delli Carri A, Malagoli Tagliazucchi G, Faedo A, Petiti L, Mazza EMC, Peano C, De Bellis G, Bicciato S, Miccio A, Cattaneo E, Mavilio F. Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells. PLoS One 2015; 10:e0126590. [PMID: 25978676 PMCID: PMC4433211 DOI: 10.1371/journal.pone.0126590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/06/2015] [Indexed: 11/21/2022] Open
Abstract
Genome-wide mapping of transcriptional regulatory elements is an essential tool for understanding the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of transcription start sites with genome-wide profiling of histones modifications to map active promoters and enhancers in embryonic stem cells (ESCs) induced to neuroepithelial-like stem cells (NESCs). Our analysis showed that most promoters are active in both cell types while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provides a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and of gene expression programs characterizing the transition from a pluripotent to a neural-restricted cell fate.
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Affiliation(s)
- Valentina Poletti
- Division of Genetics and Cell Biology, Scientific Institute H. San Raffaele, Milan, Italy
- Genethon, Evry, France
| | | | | | - Andrea Faedo
- Department of Biosciences, University of Milano, Milan, Italy
| | - Luca Petiti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Imagine Institute, Paris, France
| | - Elena Cattaneo
- Department of Biosciences, University of Milano, Milan, Italy
| | - Fulvio Mavilio
- Genethon, Evry, France
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- * E-mail:
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59
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Kaufmann S, Fuchs C, Gonik M, Khrameeva EE, Mironov AA, Frishman D. Inter-chromosomal contact networks provide insights into Mammalian chromatin organization. PLoS One 2015; 10:e0126125. [PMID: 25961318 PMCID: PMC4427453 DOI: 10.1371/journal.pone.0126125] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/30/2015] [Indexed: 11/18/2022] Open
Abstract
The recent advent of conformation capture techniques has provided unprecedented insights into the spatial organization of chromatin. We present a large-scale investigation of the inter-chromosomal segment and gene contact networks in embryonic stem cells of two mammalian organisms: humans and mice. Both interaction networks are characterized by a high degree of clustering of genome regions and the existence of hubs. Both genomes exhibit similar structural characteristics such as increased flexibility of certain Y chromosome regions and co-localization of centromere-proximal regions. Spatial proximity is correlated with the functional similarity of genes in both species. We also found a significant association between spatial proximity and the co-expression of genes in the human genome. The structural properties of chromatin are also species specific, including the presence of two highly interactive regions in mouse chromatin and an increased contact density on short, gene-rich human chromosomes, thereby indicating their central nuclear position. Trans-interacting segments are enriched in active marks in human and had no distinct feature profile in mouse. Thus, in contrast to interactions within individual chromosomes, the inter-chromosomal interactions in human and mouse embryonic stem cells do not appear to be conserved.
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Affiliation(s)
- Stefanie Kaufmann
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Christiane Fuchs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technical University Munich, Institute for Mathematical Sciences, Garching, Germany
| | - Mariya Gonik
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Munich, Germany
| | - Ekaterina E. Khrameeva
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Andrey A. Mironov
- Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrij Frishman
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
- Institute for Bioinformatics and Systems Biology, HMGU German Research Center for Environmental Health, Neuherberg, Germany
- Department of Bioinformatics, St Petersburg State Polytechnical University, St Petersburg, Russia
- * E-mail:
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60
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Antony J, Dasgupta T, Rhodes JM, McEwan MV, Print CG, O'Sullivan JM, Horsfield JA. Cohesin modulates transcription of estrogen-responsive genes. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1849:257-69. [PMID: 25542856 DOI: 10.1016/j.bbagrm.2014.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/24/2014] [Accepted: 12/19/2014] [Indexed: 12/19/2022]
Abstract
The cohesin complex has essential roles in cell division, DNA damage repair and gene transcription. The transcriptional function of cohesin is thought to derive from its ability to connect distant regulatory elements with gene promoters. Genome-wide binding of cohesin in breast cancer cells frequently coincides with estrogen receptor alpha (ER), leading to the hypothesis that cohesin facilitates estrogen-dependent gene transcription. We found that cohesin modulates the expression of only a subset of genes in the ER transcription program, either activating or repressing transcription depending on the gene target. Estrogen-responsive genes most significantly influenced by cohesin were enriched in pathways associated with breast cancer progression such as PI3K and ErbB1. In MCF7 breast cancer cells, cohesin depletion enhanced transcription of TFF1 and TFF2, and was associated with increased ER binding and increased interaction between TFF1 and its distal enhancer situated within TMPRSS3. In contrast, cohesin depletion reduced c-MYC mRNA and was accompanied by reduced interaction between a distal enhancer of c-MYC and its promoters. Our data indicates that cohesin is not a universal facilitator of ER-induced transcription and can even restrict enhancer-promoter communication. We propose that cohesin modulates transcription of estrogen-dependent genes to achieve appropriate directionality and amplitude of expression.
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Affiliation(s)
- Jisha Antony
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin, 9016, New Zealand
| | - Tanushree Dasgupta
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin, 9016, New Zealand
| | - Jenny M Rhodes
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin, 9016, New Zealand
| | - Miranda V McEwan
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin, 9016, New Zealand
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, School of Medical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, The University of Otago, Dunedin, 9016, New Zealand.
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61
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Meluzzi D, Arya G. Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064120. [PMID: 25563926 DOI: 10.1088/0953-8984/27/6/064120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The estimation of contact probabilities (CP) from conformations of simulated bead-chain polymer models is a key step in methods that aim to elucidate the spatial organization of chromatin from analysis of experimentally determined contacts between different genomic loci. Although CPs can be estimated simply by counting contacts between beads in a sample of simulated chain conformations, reliable estimation of small CPs through this approach requires a large number of conformations, which can be computationally expensive to obtain. Here we describe an alternative computational method for estimating relatively small CPs without requiring large samples of chain conformations. In particular, we estimate the CPs from functional approximations to the cumulative distribution function (cdf) of the inter-bead distance for each pair of beads. These cdf approximations are obtained by fitting the extended generalized lambda distribution (EGLD) to inter-bead distances determined from a sample of chain conformations, which are in turn generated by Monte Carlo simulations. We find that CPs estimated from fitted EGLD cdfs are significantly more accurate than CPs estimated using contact counts from samples of limited size, and are more precise with all sample sizes, permitting as much as a tenfold reduction in conformation sample size for chains of 200 beads and samples smaller than 10(5) conformations. This method of CP estimation thus has potential to accelerate computational efforts to elucidate the spatial organization of chromatin.
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Affiliation(s)
- Dario Meluzzi
- Department of NanoEngineering, University of California San Diego, 9500 Gilman La Jolla, CA 92093, USA
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Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
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Abstract
DNA methylation and histone modification are epigenetic mechanisms that result in altered gene expression and cellular phenotype. The exact role of methylation in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) remains unclear. However, aberrations (e.g. loss-/gain-of-function or up-/down-regulation) in components of epigenetic transcriptional regulation in general, and of the methylation machinery in particular, have been implicated in the pathogenesis of these diseases. In addition, many of these components have been identified as therapeutic targets for patients with MDS/AML, and are also being assessed as potential biomarkers of response or resistance to hypomethylating agents (HMAs). The HMAs 5-azacitidine (AZA) and 2'-deoxy-5-azacitidine (decitabine, DAC) inhibit DNA methylation and have shown significant clinical benefits in patients with myeloid malignancies. Despite being viewed as mechanistically similar drugs, AZA and DAC have differing mechanisms of action. DAC is incorporated 100% into DNA, whereas AZA is incorporated into RNA (80-90%) as well as DNA (10-20%). As such, both drugs inhibit DNA methyltransferases (DNMTs; dependently or independently of DNA replication) resulting in the re-expression of tumor-suppressor genes; however, AZA also has an impact on mRNA and protein metabolism via its inhibition of ribonucleotide reductase, resulting in apoptosis. Herein, we first give an overview of transcriptional regulation, including DNA methylation, post-translational histone-tail modifications, the role of micro-RNA and long-range epigenetic gene silencing. We place special emphasis on epigenetic transcriptional regulation and discuss the implication of various components in the pathogenesis of MDS/AML, their potential as therapeutic targets, and their therapeutic modulation by HMAs and other substances (if known). The main focus of this review is laid on dissecting the rapidly evolving knowledge of AZA and DAC with a special focus on their differing mechanisms of action, and the effect of HMAs on transcriptional regulation.
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Affiliation(s)
- Lisa Pleyer
- 3rd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Laboratory for Immunological and Molecular Cancer Research, Oncologic Center, Paracelsus Medical University Hospital Salzburg, Center for Clinical Cancer and Immunology Trials at Salzburg Cancer Research Institute , Salzburg , Austria
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64
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Antonini D, Sirico A, Aberdam E, Ambrosio R, Campanile C, Fagoonee S, Altruda F, Aberdam D, Brissette JL, Missero C. A composite enhancer regulates p63 gene expression in epidermal morphogenesis and in keratinocyte differentiation by multiple mechanisms. Nucleic Acids Res 2015; 43:862-74. [PMID: 25567987 PMCID: PMC4333422 DOI: 10.1093/nar/gku1396] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
p63 is a crucial regulator of epidermal development, but its transcriptional control has remained elusive. Here, we report the identification of a long-range enhancer (p63LRE) that is composed of two evolutionary conserved modules (C38 and C40), acting in concert to control tissue- and layer-specific expression of the p63 gene. Both modules are in an open and active chromatin state in human and mouse keratinocytes and in embryonic epidermis, and are strongly bound by p63. p63LRE activity is dependent on p63 expression in embryonic skin, and also in the commitment of human induced pluripotent stem cells toward an epithelial cell fate. A search for other transcription factors involved in p63LRE regulation revealed that the CAAT enhancer binding proteins Cebpa and Cebpb and the POU domain-containing protein Pou3f1 repress p63 expression during keratinocyte differentiation by binding the p63LRE enhancer. Collectively, our data indicate that p63LRE is composed of additive and partly redundant enhancer modules that act to direct robust p63 expression selectively in the basal layer of the epidermis.
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Affiliation(s)
| | - Anna Sirico
- CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Edith Aberdam
- INSERM UMR-S 976, Paris, France Université Paris-Diderot, Hopital St-Louis, Paris, France
| | | | | | - Sharmila Fagoonee
- Institute for Biostructures and Bioimages (CNR), c/o Molecular Biotechnology Center, University of Turin, Torino, Italy
| | - Fiorella Altruda
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy
| | - Daniel Aberdam
- INSERM UMR-S 976, Paris, France Université Paris-Diderot, Hopital St-Louis, Paris, France
| | - Janice L Brissette
- Department of Cell Biology, State University of New York Downstate Medical Center, NY, USA
| | - Caterina Missero
- CEINGE Biotecnologie Avanzate, Napoli, Italy Department of Biology, University of Naples Federico II, Napoli, Italy
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65
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Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Kerényi MA, Sasidharan R, Rubbi L, Fujiwara Y, Pellegrini M, Orkin SH, Kurdistani SK, Mikkola HK. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. EMBO J 2015; 34:759-77. [PMID: 25564442 PMCID: PMC4369313 DOI: 10.15252/embj.201490542] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Scl/Tal1 confers hemogenic competence and prevents ectopic cardiomyogenesis in embryonic endothelium by unknown mechanisms. We discovered that Scl binds to hematopoietic and cardiac enhancers that become epigenetically primed in multipotent cardiovascular mesoderm, to regulate the divergence of hematopoietic and cardiac lineages. Scl does not act as a pioneer factor but rather exploits a pre-established epigenetic landscape. As the blood lineage emerges, Scl binding and active epigenetic modifications are sustained in hematopoietic enhancers, whereas cardiac enhancers are decommissioned by removal of active epigenetic marks. Our data suggest that, rather than recruiting corepressors to enhancers, Scl prevents ectopic cardiogenesis by occupying enhancers that cardiac factors, such as Gata4 and Hand1, use for gene activation. Although hematopoietic Gata factors bind with Scl to both activated and repressed genes, they are dispensable for cardiac repression, but necessary for activating genes that enable hematopoietic stem/progenitor cell development. These results suggest that a unique subset of enhancers in lineage-specific genes that are accessible for regulators of opposing fates during the time of the fate decision provide a platform where the divergence of mutually exclusive fates is orchestrated.
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Affiliation(s)
- Tõnis Org
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Dan Duan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Roberto Ferrari
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Amelie Montel-Hagen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Ben Van Handel
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Marc A Kerényi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Rajkumar Sasidharan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Yuko Fujiwara
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Children's Hospital Boston, Howard Hughes Medical Institute Harvard Stem Cell Institute Harvard Medical School, Boston, MA, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| | - Hanna Ka Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
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66
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Fessing MY. Gene regulation at a distance: higher-order chromatin folding and the coordinated control of gene transcription at the epidermal differentiation complex locus. J Invest Dermatol 2014; 134:2307-2310. [PMID: 25120147 DOI: 10.1038/jid.2014.247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatin structure and spatial interactions between proximal and distal gene regulatory elements, including gene core promoters and enhancers, are important in the control of gene transcription. In this issue, Oh et al. characterized an AP-1-dependent enhancer at the epidermal differentiation complex locus that establishes spatial interactions with numerous gene promoter regions at that locus.
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Affiliation(s)
- Michael Y Fessing
- Centre for Skin Sciences and School of Medical Sciences, School of Life Sciences, University of Bradford, Bradford, UK.
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67
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Bharadwaj R, Peter CJ, Jiang Y, Roussos P, Vogel-Ciernia A, Shen EY, Mitchell AC, Mao W, Whittle C, Dincer A, Jakovcevski M, Pothula V, Rasmussen TP, Giakoumaki SG, Bitsios P, Sherif A, Gardner PD, Ernst P, Ghose S, Sklar P, Haroutunian V, Tamminga C, Myers RH, Futai K, Wood MA, Akbarian S. Conserved higher-order chromatin regulates NMDA receptor gene expression and cognition. Neuron 2014; 84:997-1008. [PMID: 25467983 PMCID: PMC4258154 DOI: 10.1016/j.neuron.2014.10.032] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2014] [Indexed: 12/17/2022]
Abstract
Three-dimensional chromosomal conformations regulate transcription by moving enhancers and regulatory elements into spatial proximity with target genes. Here we describe activity-regulated long-range loopings bypassing up to 0.5 Mb of linear genome to modulate NMDA glutamate receptor GRIN2B expression in human and mouse prefrontal cortex. Distal intronic and 3' intergenic loop formations competed with repressor elements to access promoter-proximal sequences, and facilitated expression via a "cargo" of AP-1 and NRF-1 transcription factors and TALE-based transcriptional activators. Neuronal deletion or overexpression of Kmt2a/Mll1 H3K4- and Kmt1e/Setdb1 H3K9-methyltransferase was associated with higher-order chromatin changes at distal regulatory Grin2b sequences and impairments in working memory. Genetic polymorphisms and isogenic deletions of loop-bound sequences conferred liability for cognitive performance and decreased GRIN2B expression. Dynamic regulation of chromosomal conformations emerges as a novel layer for transcriptional mechanisms impacting neuronal signaling and cognition.
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Affiliation(s)
- Rahul Bharadwaj
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cyril J Peter
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Jiang
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; James J. Peters Veterans Affairs Medical Center, Bronx, New York, NY 10468, USA
| | - Annie Vogel-Ciernia
- Department of Neurobiology and Behavior, University of California at Irvine, Irvine, CA 92697, USA
| | - Erica Y Shen
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amanda C Mitchell
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wenjie Mao
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Catheryne Whittle
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Aslihan Dincer
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Venu Pothula
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences and U.Conn Stem Cell Institute, University of Connecticut, Storrs, CT 06269, USA
| | - Stella G Giakoumaki
- Department of Psychiatry, University of Crete, 71003 Iraklion, Greece; Department of Psychology, University of Crete, 71003 Iraklion, Greece
| | - Panos Bitsios
- Computational Medicine Laboratory, Institute of Computer Science, Foundation for Research and Technology Hellas, 71003 Iraklion, Greece; Department of Psychiatry, University of Crete, 71003 Iraklion, Greece
| | - Ajfar Sherif
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paul D Gardner
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Patricia Ernst
- Department of Genetics and Department of Microbiology and Immunology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Subroto Ghose
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pamela Sklar
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vahram Haroutunian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; James J. Peters Veterans Affairs Medical Center, Bronx, New York, NY 10468, USA
| | - Carol Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Richard H Myers
- Department of Neurology, Boston University, Boston, MA 02118, USA
| | - Kensuke Futai
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California at Irvine, Irvine, CA 92697, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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68
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Doyle B, Fudenberg G, Imakaev M, Mirny LA. Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput Biol 2014; 10:e1003867. [PMID: 25340767 PMCID: PMC4207457 DOI: 10.1371/journal.pcbi.1003867] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/20/2014] [Indexed: 11/29/2022] Open
Abstract
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site. In eukaryotes, enhancers directly contact promoters over large genomic distances to regulate gene expression. Characterizing the principles underlying these long-range enhancer-promoter contacts is crucial for a full understanding of gene expression. Recent experimental mapping of chromosomal interactions by the Hi-C method shows an intricate network of local looping interactions surrounding enhancers and promoters. We model a region of chromatin fiber as a long polymer and study how the formation of loops between certain regulatory elements can insulate or facilitate enhancer-promoter interactions. We find 2–5 fold insulation or facilitation, depending on the location of looping elements relative to an enhancer-promoter pair. These effects originate from the polymer nature of chromatin, without requiring additional mechanisms beyond the formation of a chromatin loop. Our findings suggest that loop-mediated gene regulation by elements in the vicinity of an enhancer-promoter pair can be understood as an allosteric effect. This highlights the complex effects that local chromatin organization can have on gene regulation.
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Affiliation(s)
- Boryana Doyle
- Program for Research in Mathematics, Engineering and Science for High School Students, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Undergraduate Research Opportunities Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Maxim Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Leonid A. Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, United States of America
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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69
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Langevin SM, Butler RA, Eliot M, Pawlita M, Maccani JZJ, McClean MD, Kelsey KT. Novel DNA methylation targets in oral rinse samples predict survival of patients with oral squamous cell carcinoma. Oral Oncol 2014; 50:1072-80. [PMID: 25242135 DOI: 10.1016/j.oraloncology.2014.08.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/01/2014] [Accepted: 08/26/2014] [Indexed: 02/03/2023]
Abstract
OBJECTIVES The objective of this study was to identify novel survival-associated biomarkers in oral rinse samples collected from patients with oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS We screened for putative survival-associated markers using publicly available methylation array data from 88 OSCC tumors. Cox models were then fit to methylation array data restricted to these putative loci in oral rinse samples of 82 OSCC patients from greater Boston. Pyrosequencing assays were designed for each locus that replicated in the oral rinse samples and applied to a validation set of oral rinse samples from another 61 OSCC patients. RESULTS We identified 7 survival-associated methylation markers in oral rinse samples from OSCC patients, and have validated one, located in the body of GABBR1, by pyrosequencing. CONCLUSION The 7 CpG loci identified through this study represent novel prognostic biomarkers for patients with OSCC that can be detected using a non-invasive oral rinse collection technique.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Michael Pawlita
- Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Z J Maccani
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA; Centers for Behavioral and Preventive Medicine, The Miriam Hospital, Providence, RI, USA
| | - Michael D McClean
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Karl T Kelsey
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
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70
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Bipartite recognition of DNA by TCF/Pangolin is remarkably flexible and contributes to transcriptional responsiveness and tissue specificity of wingless signaling. PLoS Genet 2014; 10:e1004591. [PMID: 25188465 PMCID: PMC4154663 DOI: 10.1371/journal.pgen.1004591] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 07/08/2014] [Indexed: 11/19/2022] Open
Abstract
The T-cell factor (TCF) family of transcription factors are major mediators of Wnt/β-catenin signaling in metazoans. All TCFs contain a High Mobility Group (HMG) domain that possesses specific DNA binding activity. In addition, many TCFs contain a second DNA binding domain, the C-clamp, which binds to DNA motifs referred to as Helper sites. While HMG and Helper sites are both important for the activation of several Wnt dependent cis-regulatory modules (W-CRMs), the rules of what constitutes a functional HMG-Helper site pair are unknown. In this report, we employed a combination of in vitro binding, reporter gene analysis and bioinformatics to address this question, using the Drosophila family member TCF/Pangolin (TCF/Pan) as a model. We found that while there were constraints for the orientation and spacing of HMG-Helper pairs, the presence of a Helper site near a HMG site in any orientation increased binding and transcriptional response, with some orientations displaying tissue-specific patterns. We found that altering an HMG-Helper site pair from a sub-optimal to optimal orientation/spacing dramatically increased the responsiveness of a W-CRM in several fly tissues. In addition, we used the knowledge gained to bioinformatically identify two novel W-CRMs, one that was activated by Wnt/β-catenin signaling in the prothoracic gland, a tissue not previously connected to this pathway. In sum, this work extends the importance of Helper sites in fly W-CRMs and suggests that the type of HMG-Helper pair is a major factor in setting the threshold for Wnt activation and tissue-responsiveness. Regulation of gene expression is controlled in large part by proteins known as transcription factors, which bind to specific DNA sequences in the genome. The DNA binding domains of transcription factors recognize short stretches (5–11 base pairs) of DNA with considerable sequence degeneracy. This means that a single DNA binding domain, on its own, cannot find its targets in the vast excess of genomic sequence. We are studying this question using TCF/Pangolin, a Drosophila transcription factor that mediates Wnt/β-catenin signaling, an important developmental cell-cell communication pathway. TCF/Pangolin contains two DNA binding domains that bind to a pair of DNA motifs known as HMG and Helper sites. We used a combination of biochemistry, genetics and bioinformatics to elucidate the spacing and orientation constraints of HMG-Helper site pairs. We found that HMG-Helper site spacing/orientation influenced the sensitivity of a target to Wnt signaling, as well as its tissue-responsiveness. We used this information to improve our ability to search the Drosophila genome for Wnt targets, one of which was activated by the pathway in the fly ring gland, the major endocrine organ in insects. Our work is relevant to related mammalian TCF family members, which are implicated in development, stem cell biology and the progression of cancer.
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71
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Benedetti F, Dorier J, Stasiak A. Effects of supercoiling on enhancer-promoter contacts. Nucleic Acids Res 2014; 42:10425-32. [PMID: 25123662 PMCID: PMC4176356 DOI: 10.1093/nar/gku759] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using Brownian dynamics simulations, we investigate here one of possible roles of supercoiling within topological domains constituting interphase chromosomes of higher eukaryotes. We analysed how supercoiling affects the interaction between enhancers and promoters that are located in the same or in neighbouring topological domains. We show here that enhancer–promoter affinity and supercoiling act synergistically in increasing the fraction of time during which enhancer and promoter stay in contact. This stabilizing effect of supercoiling only acts on enhancers and promoters located in the same topological domain. We propose that the primary role of recently observed supercoiling of topological domains in interphase chromosomes of higher eukaryotes is to assure that enhancers contact almost exclusively their cognate promoters located in the same topological domain and avoid contacts with very similar promoters but located in neighbouring topological domains.
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Affiliation(s)
- Fabrizio Benedetti
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015-Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015-Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015-Lausanne, Switzerland
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72
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Quintin J, Le Péron C, Palierne G, Bizot M, Cunha S, Sérandour AA, Avner S, Henry C, Percevault F, Belaud-Rotureau MA, Huet S, Watrin E, Eeckhoute J, Legagneux V, Salbert G, Métivier R. Dynamic estrogen receptor interactomes control estrogen-responsive trefoil Factor (TFF) locus cell-specific activities. Mol Cell Biol 2014; 34:2418-36. [PMID: 24752895 PMCID: PMC4054307 DOI: 10.1128/mcb.00918-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/03/2013] [Accepted: 04/09/2014] [Indexed: 12/28/2022] Open
Abstract
Estradiol signaling is ideally suited for analyzing the molecular and functional linkages between the different layers of information directing transcriptional regulations: the DNA sequence, chromatin modifications, and the spatial organization of the genome. Hence, the estrogen receptor (ER) can bind at a distance from its target genes and engages timely and spatially coordinated processes to regulate their expression. In the context of the coordinated regulation of colinear genes, identifying which ER binding sites (ERBSs) regulate a given gene still remains a challenge. Here, we investigated the coordination of such regulatory events at a 2-Mb genomic locus containing the estrogen-sensitive trefoil factor (TFF) cluster of genes in breast cancer cells. We demonstrate that this locus exhibits a hormone- and cohesin-dependent reduction in the plasticity of its three-dimensional organization that allows multiple ERBSs to be dynamically brought to the vicinity of estrogen-sensitive genes. Additionally, by using triplex-forming oligonucleotides, we could precisely document the functional links between ER engagement at given ERBSs and the regulation of particular genes. Hence, our data provide evidence of a formerly suggested cooperation of enhancers toward gene regulation and also show that redundancy between ERBSs can occur.
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Affiliation(s)
- Justine Quintin
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Christine Le Péron
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Gaëlle Palierne
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Maud Bizot
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Stéphanie Cunha
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Aurélien A Sérandour
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Stéphane Avner
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Catherine Henry
- Cytogenetics and Cellular Biology Department, CHU, Rennes, France
| | - Frédéric Percevault
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Cytogenetics and Cellular Biology Department, CHU, Rennes, France BIOSIT, UMR CNRS 6290, Université de Rennes I, Faculté de Médecine, Rennes, France
| | - Sébastien Huet
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Erwan Watrin
- Equipe CC, UMR CNRS 6290, Université de Rennes I, Faculté de Médecine, Rennes, France
| | - Jérôme Eeckhoute
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France INSERM U1011, Université Lille-Nord de France, Faculté de Médecine de Lille-Pôle Recherche, Lille, France
| | - Vincent Legagneux
- Equipe EGD, UMR CNRS 6290, Université de Rennes I, Faculté de Médecine, Rennes, France
| | - Gilles Salbert
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
| | - Raphaël Métivier
- Equipe SP@RTE, UMR CNRS 6290, Equipe Labellisée Ligue contre le Cancer, Université de Rennes I, Rennes, France
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73
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Bastonini E, Jeznach M, Field M, Juszczyk K, Corfield E, Dezfouli M, Ahmat N, Smith A, Womersley H, Jordan P, Ramadass A, Akoulitchev A, Goding CR. Chromatin barcodes as biomarkers for melanoma. Pigment Cell Melanoma Res 2014; 27:788-800. [PMID: 24807349 DOI: 10.1111/pcmr.12258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/29/2014] [Indexed: 01/27/2023]
Abstract
The major barrier to effective cancer therapy is the presence of genetic and phenotypic heterogeneity within cancer cell populations that provides a reservoir of therapeutically resistant cells. As the degree of heterogeneity present within tumours will be proportional to tumour burden, the development of rapid, robust, accurate and sensitive biomarkers for cancer progression that could detect clinically occult disease before substantial heterogeneity develops would provide a major therapeutic benefit. Here, we explore the application of chromatin conformation capture technology to generate a diagnostic epigenetic barcode for melanoma. The results indicate that binary states from chromatin conformations at 15 loci within five genes can be used to provide rapid, non-invasive multivariate test for the presence of melanoma using as little as 200 μl of patient blood.
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Affiliation(s)
- Emanuela Bastonini
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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An J, Zhang X, Qin J, Wan Y, Hu Y, Liu T, Li J, Dong W, Du E, Pan C, Zeng W. The histone methyltransferase ESET is required for the survival of spermatogonial stem/progenitor cells in mice. Cell Death Dis 2014; 5:e1196. [PMID: 24763053 PMCID: PMC4001319 DOI: 10.1038/cddis.2014.171] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/22/2022]
Abstract
Self-renewal and differentiation of spermatogonial stem cells (SSCs) are the foundation of spermatogenesis throughout a male's life. SSC transplantation will be a valuable solution for young male patients to preserve their fertility. As SSCs in the collected testis tissue from the patients are very limited, it is necessary to expansion the SSCs in vitro. Previous studies suggested that histone methyltransferase ERG-associated protein with SET domain (ESET) represses gene expression and is essential for the maintenance of the pool of embryonic stem cells and neurons. The objective of this study was to determine the role of ESET in SSCs using in vitrocell culture and germ cell transplantation. Cell transplantation assay showed that knockdown of ESET reduced the number of seminiferous tubules with spermatogenesis when compared with that of the control. Knockdown of ESET also upregulated the expression of apoptosis-associated genes (such as P53, Caspase9, Apaf1), whereas inhibited the expression of apoptosis-suppressing genes (such as Bcl2l1, X-linked inhibitor of apoptosis protein). In addition, suppression of ESET led to increase in expression of Caspase9 and activation of Caspase3 (P17) as well as cleavage of poly (ADP-ribose) polymerase. Among the five ESET-targeting genes (Cox4i2, spermatogenesis and oogenesis Specific Basic Helix-Loop-Helix 2, Nobox, Foxn1 and Dazl) examined by ChIP assay, Cox4i2 was found to regulate SSC apoptosis by the rescue experiment. BSP analyses further showed that DNA methylation in the promoter loci of Cox4i2was influenced by ESET, indicating that ESET also regulated gene expression through DNA methylation in addition to histone methylation. In conclusion, we found that ESET regulated SSC apoptosis by suppressing of Cox4i2 expression through histone H3 lysine 9 tri-methylation and DNA methylation. The results obtained will provide unique insights that would broaden the research on SSC biology and contribute to the treatment of male infertility.
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Affiliation(s)
- J An
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - X Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - J Qin
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Y Wan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Y Hu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - T Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - J Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - W Dong
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - E Du
- College of Veterinary Medicine, Northwest A&F University, Shaanxi, China
| | - C Pan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - W Zeng
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
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75
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Alyea RA, Gollapudi BB, Rasoulpour RJ. Are we ready to consider transgenerational epigenetic effects in human health risk assessment? ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:292-298. [PMID: 24259352 DOI: 10.1002/em.21831] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/25/2013] [Accepted: 10/25/2013] [Indexed: 06/02/2023]
Abstract
Recently, there has been a growing concern that chemically or nutritionally mediated epigenetic changes might lead to adverse health outcomes. The natural question is whether the existing chemical safety assessment paradigm is or is not protective of epigenetic-mediated effects, and if there is a need to incorporate new endpoints to specifically address epigenetics. Of particular interest are transgenerational epigenetic effects, which can be passed on through multiple generations. To investigate these questions, a comparison was performed between OECD guideline rat toxicology studies versus several rat transgenerational epigenetic studies. This analysis focused on vinclozolin owing to the availability of a comprehensive suite of dose-response data (NOAEL, reference dose, and human exposure estimates) for both conventional and epigenetic endpoints. This analysis revealed that vinclozolin transgenerational effects were demonstrated at a dose level (100 mg/kg/day) that was: (1) ∼40-fold higher than the overall lowest-observed-adverse-effect level (LOAEL) from rat guideline studies, (2) ∼80-fold higher than the lowest NOAEL from rat guideline studies, (3) ∼80,000-fold higher than the reference dose for the molecule, and (4) ∼1.2-million fold above human exposure estimates. Through this analysis, we conclude that additional research across a spectrum of doses is necessary to elucidate the interplay between epigenetics and apical endpoints before considering epigenetics in human health risk assessment. Therefore, we recommend focusing future research toward (1) examining for potential causal relationships between epigenetic alterations and adverse apical endpoints, and (2) understanding the dose-response relationship of these causal epigenetic alterations when compared with those of the apical endpoints.
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Affiliation(s)
- Rebecca A Alyea
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, Michigan
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76
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Sarda S, Hannenhalli S. Next-generation sequencing and epigenomics research: a hammer in search of nails. Genomics Inform 2014; 12:2-11. [PMID: 24748856 PMCID: PMC3990762 DOI: 10.5808/gi.2014.12.1.2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 12/26/2022] Open
Abstract
After the initial enthusiasm of the human genome project, it became clear that without additional data pertaining to the epigenome, i.e., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. This realization prompted several large-scale efforts to map the epigenome, most notably the Encyclopedia of DNA Elements (ENCODE) project. While there is essentially a single genome in an individual, there are hundreds of epigenomes, corresponding to various types of epigenomic marks at different developmental times and in multiple tissue types. Unprecedented advances in next-generation sequencing (NGS) technologies, by virtue of low cost and high speeds that continue to improve at a rate beyond what is anticipated by Moore's law for computer hardware technologies, have revolutionized molecular biology and genetics research, and have in turn prompted innovative ways to reduce the problem of measuring cellular events involving DNA or RNA into a sequencing problem. In this article, we provide a brief overview of the epigenome, the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects. We also provide ample references for the reader to get in-depth information on these topics.
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Affiliation(s)
- Shrutii Sarda
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740, USA
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740, USA
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77
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Schwartz M, Hakim O. 3D view of chromosomes, DNA damage, and translocations. Curr Opin Genet Dev 2014; 25:118-25. [PMID: 24632298 DOI: 10.1016/j.gde.2013.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/26/2013] [Indexed: 02/02/2023]
Abstract
The cell nucleus is a busy and organized organelle. In this megalopolis made of billions of nucleotides, protein factors find their target loci to exert nuclear functions such as transcription and replication. Remarkably, despite the lack of internal membrane barrier, the interlinked and tightly regulated nuclear processes occur in spatially organized fashion. These processes can lead to double-strand breaks (DSBs) that compromise the integrity of the genome. Moreover, in some cells like lymphocytes, DNA damage is also targeted within the context of immunoglobulin gene recombination. If not repaired correctly, DSBs can cause chromosomal rearrangements, including translocations which are etiological in numerous tumors. Therefore, the chromosomal locations of DSBs, as well as their spatial positioning, are important contributors to formation of chromosomal translocations at specific genomic loci. To obtain a mechanistic understanding of chromosomal translocations these parameters should be accounted for in a global and integrative fashion. In this review we will discuss recent findings addressing how genome architecture, DNA damage, and repair contribute to the genesis of chromosomal translocations.
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Affiliation(s)
- Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel.
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Abstract
The unremitting demand to replenish differentiated cells in tissues requires efficient mechanisms to generate and regulate stem and progenitor cells. Although master regulatory transcription factors, including GATA binding protein-2 (GATA-2), have crucial roles in these mechanisms, how such factors are controlled in developmentally dynamic systems is poorly understood. Previously, we described five dispersed Gata2 locus sequences, termed the -77, -3.9, -2.8, -1.8, and +9.5 GATA switch sites, which contain evolutionarily conserved GATA motifs occupied by GATA-2 and GATA-1 in hematopoietic precursors and erythroid cells, respectively. Despite common attributes of transcriptional enhancers, targeted deletions of the -2.8, -1.8, and +9.5 sites revealed distinct and unpredictable contributions to Gata2 expression and hematopoiesis. Herein, we describe the targeted deletion of the -3.9 site and mechanistically compare the -3.9 site with other GATA switch sites. The -3.9(-/-) mice were viable and exhibited normal Gata2 expression and steady-state hematopoiesis in the embryo and adult. We established a Gata2 repression/reactivation assay, which revealed unique +9.5 site activity to mediate GATA factor-dependent chromatin structural transitions. Loss-of-function analyses provided evidence for a mechanism in which a mediator of long-range transcriptional control [LIM domain binding 1 (LDB1)] and a chromatin remodeler [Brahma related gene 1 (BRG1)] synergize through the +9.5 site, conferring expression of GATA-2, which is known to promote the genesis and survival of hematopoietic stem cells.
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79
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Cao S, Kumimoto RW, Gnesutta N, Calogero AM, Mantovani R, Holt BF. A distal CCAAT/NUCLEAR FACTOR Y complex promotes chromatin looping at the FLOWERING LOCUS T promoter and regulates the timing of flowering in Arabidopsis. THE PLANT CELL 2014; 26:1009-17. [PMID: 24610724 PMCID: PMC4001365 DOI: 10.1105/tpc.113.120352] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
For many plant species, reproductive success relies on the proper timing of flowering, and photoperiod provides a key environmental input. Photoperiod-dependent flowering depends on timely expression of FLOWERING LOCUS T (FT); however, the coordination of various cis-regulatory elements in the FT promoter is not well understood. Here, we provide evidence that long-distance chromatin loops bring distal enhancer elements into close association with the proximal promoter elements bound by CONSTANS (CO). Additionally, we show that NUCLEAR FACTOR Y (NF-Y) binds a CCAAT box in the distal enhancer element and that CCAAT disruption dramatically reduces FT promoter activity. Thus, we propose the recruitment model of photoperiod-dependent flowering where NF-Y complexes, bound at the FT distal enhancer element, help recruit CO to proximal cis-regulatory elements and initiate the transition to reproductive growth.
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Affiliation(s)
- Shuanghe Cao
- Department of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019
| | - Roderick W. Kumimoto
- Department of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019
| | - Nerina Gnesutta
- Dipartimento di BioScienze, Università degli Studi
di Milano, 20133 Milan, Italy
| | | | - Roberto Mantovani
- Dipartimento di BioScienze, Università degli Studi
di Milano, 20133 Milan, Italy
| | - Ben F. Holt
- Department of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019
- Address correspondence to
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80
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Burgess D, Freeling M. The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. THE PLANT CELL 2014; 26:946-61. [PMID: 24681619 PMCID: PMC4001403 DOI: 10.1105/tpc.113.121905] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In vertebrates, conserved noncoding elements (CNEs) are functionally constrained sequences that can show striking conservation over >400 million years of evolutionary distance and frequently are located megabases away from target developmental genes. Conserved noncoding sequences (CNSs) in plants are much shorter, and it has been difficult to detect conservation among distantly related genomes. In this article, we show not only that CNS sequences can be detected throughout the eudicot clade of flowering plants, but also that a subset of 37 CNSs can be found in all flowering plants (diverging ∼170 million years ago). These CNSs are functionally similar to vertebrate CNEs, being highly associated with transcription factor and development genes and enriched in transcription factor binding sites. Some of the most highly conserved sequences occur in genes encoding RNA binding proteins, particularly the RNA splicing-associated SR genes. Differences in sequence conservation between plants and animals are likely to reflect differences in the biology of the organisms, with plants being much more able to tolerate genomic deletions and whole-genome duplication events due, in part, to their far greater fecundity compared with vertebrates.
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81
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Abstract
Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy-referring to the multiple pathways that a system recruits to achieve functional plasticity-is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability.
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82
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Rubinstein M, de Souza FSJ. Evolution of transcriptional enhancers and animal diversity. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130017. [PMID: 24218630 DOI: 10.1098/rstb.2013.0017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Deciphering the genetic bases that drive animal diversity is one of the major challenges of modern biology. Although four decades ago it was proposed that animal evolution was mainly driven by changes in cis-regulatory DNA elements controlling gene expression rather than in protein-coding sequences, only now are powerful bioinformatics and experimental approaches available to accelerate studies into how the evolution of transcriptional enhancers contributes to novel forms and functions. In the introduction to this Theme Issue, we start by defining the general properties of transcriptional enhancers, such as modularity and the coexistence of tight sequence conservation with transcription factor-binding site shuffling as different mechanisms that maintain the enhancer grammar over evolutionary time. We discuss past and current methods used to identify cell-type-specific enhancers and provide examples of how enhancers originate de novo, change and are lost in particular lineages. We then focus in the central part of this Theme Issue on analysing examples of how the molecular evolution of enhancers may change form and function. Throughout this introduction, we present the main findings of the articles, reviews and perspectives contributed to this Theme Issue that together illustrate some of the great advances and current frontiers in the field.
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Affiliation(s)
- Marcelo Rubinstein
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, , C1428ADN Buenos Aires, Argentina
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83
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Merelli I, Liò P, Milanesi L. NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations. PLoS One 2013; 8:e75146. [PMID: 24069388 PMCID: PMC3777921 DOI: 10.1371/journal.pone.0075146] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/11/2013] [Indexed: 11/23/2022] Open
Abstract
Long-range chromosomal associations between genomic regions, and their repositioning in the 3D space of the nucleus, are now considered to be key contributors to the regulation of gene expression and important links have been highlighted with other genomic features involved in DNA rearrangements. Recent Chromosome Conformation Capture (3C) measurements performed with high throughput sequencing (Hi-C) and molecular dynamics studies show that there is a large correlation between colocalization and coregulation of genes, but these important researches are hampered by the lack of biologists-friendly analysis and visualisation software. Here, we describe NuChart, an R package that allows the user to annotate and statistically analyse a list of input genes with information relying on Hi-C data, integrating knowledge about genomic features that are involved in the chromosome spatial organization. NuChart works directly with sequenced reads to identify the related Hi-C fragments, with the aim of creating gene-centric neighbourhood graphs on which multi-omics features can be mapped. Predictions about CTCF binding sites, isochores and cryptic Recombination Signal Sequences are provided directly with the package for mapping, although other annotation data in bed format can be used (such as methylation profiles and histone patterns). Gene expression data can be automatically retrieved and processed from the Gene Expression Omnibus and ArrayExpress repositories to highlight the expression profile of genes in the identified neighbourhood. Moreover, statistical inferences about the graph structure and correlations between its topology and multi-omics features can be performed using Exponential-family Random Graph Models. The Hi-C fragment visualisation provided by NuChart allows the comparisons of cells in different conditions, thus providing the possibility of novel biomarkers identification. NuChart is compliant with the Bioconductor standard and it is freely available at ftp://fileserver.itb.cnr.it/nuchart.
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Affiliation(s)
- Ivan Merelli
- Institute for Biomedical Technologies, National Research Council, Segrate (Milan), Italy
- * E-mail:
| | - Pietro Liò
- Computer Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Luciano Milanesi
- Institute for Biomedical Technologies, National Research Council, Segrate (Milan), Italy
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