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Hua P, Badat M, Hanssen LLP, Hentges LD, Crump N, Downes DJ, Jeziorska DM, Oudelaar AM, Schwessinger R, Taylor S, Milne TA, Hughes JR, Higgs DR, Davies JOJ. Defining genome architecture at base-pair resolution. Nature 2021; 595:125-129. [PMID: 34108683 DOI: 10.1038/s41586-021-03639-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/13/2021] [Indexed: 12/16/2022]
Abstract
In higher eukaryotes, many genes are regulated by enhancers that are 104-106 base pairs (bp) away from the promoter. Enhancers contain transcription-factor-binding sites (which are typically around 7-22 bp), and physical contact between the promoters and enhancers is thought to be required to modulate gene expression. Although chromatin architecture has been mapped extensively at resolutions of 1 kilobase and above; it has not been possible to define physical contacts at the scale of the proteins that determine gene expression. Here we define these interactions in detail using a chromosome conformation capture method (Micro-Capture-C) that enables the physical contacts between different classes of regulatory elements to be determined at base-pair resolution. We find that highly punctate contacts occur between enhancers, promoters and CCCTC-binding factor (CTCF) sites and we show that transcription factors have an important role in the maintenance of the contacts between enhancers and promoters. Our data show that interactions between CTCF sites are increased when active promoters and enhancers are located within the intervening chromatin. This supports a model in which chromatin loop extrusion1 is dependent on cohesin loading at active promoters and enhancers, which explains the formation of tissue-specific chromatin domains without changes in CTCF binding.
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Affiliation(s)
- Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mohsin Badat
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lars L P Hanssen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Danuta M Jeziorska
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Doug R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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2
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Tissue context determines the penetrance of regulatory DNA variation. Nat Commun 2021; 12:2850. [PMID: 33990600 PMCID: PMC8121920 DOI: 10.1038/s41467-021-23139-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
Functional assessment of disease-associated sequence variation at non-coding regulatory elements is complicated by their high degree of context sensitivity to both the local chromatin and nuclear environments. Allelic profiling of DNA accessibility across individuals has shown that only a select minority of sequence variation affects transcription factor (TF) occupancy, yet low sequence diversity in human populations means that no experimental assessment is available for the majority of disease-associated variants. Here we describe high-resolution in vivo maps of allelic DNA accessibility in liver, kidney, lung and B cells from 5 increasingly diverged strains of F1 hybrid mice. The high density of heterozygous sites in these hybrids enables precise quantification of effect size and cell-type specificity for hundreds of thousands of variants throughout the mouse genome. We show that chromatin-altering variants delineate characteristic sensitivity profiles for hundreds of TF motifs. We develop a compendium of TF-specific sensitivity profiles accounting for genomic context effects. Finally, we link maps of allelic accessibility to allelic transcript levels in the same samples. This work provides a foundation for quantitative prediction of cell-type specific effects of non-coding variation on TF activity, which will facilitate both fine-mapping and systems-level analyses of common disease-associated variation in human genomes.
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Mušo M, Dumbell R, Pulit S, Sinnott-Armstrong N, Laber S, Zolkiewski L, Bentley L, Claussnitzer M, Cox RD. A lead candidate functional single nucleotide polymorphism within the WARS2 gene associated with waist-hip-ratio does not alter RNA stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194640. [PMID: 33007465 PMCID: PMC7695619 DOI: 10.1016/j.bbagrm.2020.194640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 11/06/2022]
Abstract
We have prioritised a single nucleotide polymorphism (SNP) rs2645294 as one candidate functional SNP in the TBX15-WARS2 waist-hip-ratio locus using posterior probability analysis. This SNP is located in the 3' untranslated region of the WARS2 (tryptophanyl tRNA synthetase 2, mitochondrial) gene with which it has an expression quantitative trait in subcutaneous white adipose tissue. We show that transcripts of the WARS2 gene in a human white adipose cell line, heterozygous for the rs2645294 SNP, showed allelic imbalance. We tested whether the rs2645294 SNP altered WARS2 RNA stability using three different methods: actinomycin-D inhibition and RNA decay, mature and nascent RNA analysis and luciferase reporter assays. We found no evidence of a difference in RNA stability between the rs2645294 alleles indicating that the allelic expression imbalance was likely due to transcriptional regulation.
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Affiliation(s)
- Milan Mušo
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rebecca Dumbell
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Sara Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Oxford University, Oxford, UK; Program in Medical Population Genetics, Broad Institute, Cambridge, MA, USA
| | | | - Samantha Laber
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Louisa Zolkiewski
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Liz Bentley
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Melina Claussnitzer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Gerontology Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Institute of Nutritional Science, University of Hohenheim, Stuttgart, Germany
| | - Roger D Cox
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK.
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4
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Vitobello A, Perner J, Beil J, Zhu J, Del Río-Espínola A, Morawiec L, Westphal M, Dubost V, Altorfer M, Naumann U, Mueller A, Kapur K, Borowsky M, Henderson C, Wolf CR, Schwarz M, Moggs J, Terranova R. Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion. Life Sci Alliance 2019; 2:e201900461. [PMID: 31615920 PMCID: PMC6795216 DOI: 10.26508/lsa.201900461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 12/27/2022] Open
Abstract
Liver cancer susceptibility varies amongst humans and between experimental animal models because of multiple genetic and epigenetic factors. The molecular characterization of such susceptibilities has the potential to enhance cancer risk assessment of xenobiotic exposures and disease prevention strategies. Here, using DNase I hypersensitivity mapping coupled with transcriptomic profiling, we investigate perturbations in cis-acting gene regulatory elements associated with the early stages of phenobarbital (PB)-mediated liver tumor promotion in susceptible versus resistant mouse strains (B6C3F1 versus C57BL/6J). Integrated computational analyses of strain-selective changes in liver chromatin accessibility underlying PB response reveal differential epigenetic regulation of molecular pathways associated with PB-mediated tumor promotion, including Wnt/β-catenin signaling. Complementary transcription factor motif analyses reveal mouse strain-selective gene regulatory networks and a novel role for Stat, Smad, and Fox transcription factors in the early stages of PB-mediated tumor promotion. Mapping perturbations in cis-acting gene regulatory elements provides novel insights into the molecular basis for susceptibility to xenobiotic-induced rodent liver tumor promotion and has the potential to enhance mechanism-based cancer risk assessments of xenobiotic exposures.
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Affiliation(s)
- Antonio Vitobello
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
- Inserm, Unité Mixte de Recherche (UMR) 1231, Université de Bourgogne-Franche Comté, Dijon, France
| | - Juliane Perner
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Johanna Beil
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | | | - Laurent Morawiec
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | - Valérie Dubost
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Marc Altorfer
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Ulrike Naumann
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Arne Mueller
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Karen Kapur
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | - Colin Henderson
- School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - C Roland Wolf
- School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - Michael Schwarz
- Department of Toxicology, University of Tübingen, Tübingen, Germany
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - Jonathan Moggs
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - Rémi Terranova
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
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Abstract
Heterogeneous Stock (HS) populations allow for fine-resolution genetic mapping of a variety of complex traits. HS mice and rats were created from breeding together eight inbred strains, followed by maintaining the colony in a manner that minimizes inbreeding. After 50 or more generations of breeding, the resulting animals' chromosomes represent a genetic mosaic of the founders' haplotypes, with the average distance between recombination events in the centiMorgan range. This allows for genetic mapping to only a few Mb, a much smaller region than what can be identified using traditional F2 intercross or backcross mapping strategies. HS animals have been used to fine-map a variety of complex traits including anxiety and fear behaviors, diabetes, asthma, and heart disease, among others. Once a quantitative trait locus (QTL) has been identified, founder sequence and expression analysis can be used to identify underlying causal genes. In the following review, we provide an overview of how HS rats and mice have been used to identify genetic loci, and in some cases the causal genes, underlying complex traits. We discuss the creation and breeding strategies for both HS rats and mice. We then discuss the statistical analyses used to identify genetic loci, as well as strategies to identify causal genes underlying these loci. We end the chapter by discussing limitations faced when using HS populations, including several statistical challenges that have not been fully resolved.
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Affiliation(s)
- Leah C Solberg Woods
- Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53130, USA.
| | - Richard Mott
- UCL Genetics Institute, University College London, Gower St., London, WC1E 6BT, UK
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Schwessinger R, Suciu MC, McGowan SJ, Telenius J, Taylor S, Higgs DR, Hughes JR. Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints. Genome Res 2017; 27:1730-1742. [PMID: 28904015 PMCID: PMC5630036 DOI: 10.1101/gr.220202.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/07/2017] [Indexed: 12/22/2022]
Abstract
In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mer's potential for protein binding in a specific cell type and how this may be changed by sequence variants. Therefore, Sasquatch uses an unbiased approach, independent of known transcription factor binding sites and motifs. Sasquatch only requires a single DNase-seq data set per cell type, from any genotype, and produces consistent predictions from data generated by different experimental procedures and at different sequence depths. Here we demonstrate the effectiveness of Sasquatch using previously validated functional SNPs and benchmark its performance against existing approaches. Sasquatch is available as a versatile webtool incorporating publicly available data, including the human ENCODE collection. Thus, Sasquatch provides a powerful tool and repository for prioritizing likely regulatory SNPs in the noncoding genome.
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Affiliation(s)
- Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Maria C Suciu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Stephen Taylor
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Doug R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
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7
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Hanssen LLP, Kassouf MT, Oudelaar AM, Biggs D, Preece C, Downes DJ, Gosden M, Sharpe JA, Sloane-Stanley JA, Hughes JR, Davies B, Higgs DR. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nat Cell Biol 2017; 19:952-961. [PMID: 28737770 PMCID: PMC5540176 DOI: 10.1038/ncb3573] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/15/2017] [Indexed: 12/16/2022]
Abstract
The genome is organized via CTCF-cohesin-binding sites, which partition chromosomes into 1-5 megabase (Mb) topologically associated domains (TADs), and further into smaller sub-domains (sub-TADs). Here we examined in vivo an ∼80 kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ∼1 Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF-cohesin sites that are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. Whereas the α-globin regulatory elements normally act solely on promoters downstream of the enhancers, removal of a conserved upstream CTCF-cohesin boundary extends the sub-TAD to adjacent upstream CTCF-cohesin-binding sites. The α-globin enhancers now interact with the flanking chromatin, upregulating expression of genes within this extended sub-TAD. Rather than acting solely as a barrier to chromatin modification, CTCF-cohesin boundaries in this sub-TAD delimit the region of chromatin to which enhancers have access and within which they interact with receptive promoters.
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Affiliation(s)
- Lars L P Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Mira T Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Daniel Biggs
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Preece
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Matthew Gosden
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Benjamin Davies
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
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Wang X, Ma Z, Kong X, Lv Z. Effects of RNAs on chromatin accessibility and gene expression suggest RNA-mediated activation. Int J Biochem Cell Biol 2016; 79:24-32. [PMID: 27497987 DOI: 10.1016/j.biocel.2016.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 01/20/2023]
Abstract
The study of the interaction between RNA and DNA sequences in activating genes has important significance for understanding the mechanisms of RNA-mediated activation. Here, we used in vitro chromatin reconstitution approach to observe whether RNAs increase DNase I digestion, plasmid transfection to observe whether RNAs promote gene expression, and bioinformatics analysis to predict the binding ability of RNAs to centromere DNA (constitutive heterochromatin). Synthetic RNAs (23nt) that were complementary to mouse albumin gene and total liver RNA increased DNase I digestion sensitivity of mouse albumin gene, suggesting that RNAs can increase chromatin accessibility. Transcribed sense-antisense tandem Alu elements activated an enhanced green fluorescent protein reporter gene after stable transfection. Bioinformatics analysis showed that the binding strength of RNA population to centromere DNAs is significantly lower than that of their flanking sequences, which suggests that the centromere is not easily affected by RNAs produced from other transcribed regions and may be the reason why centromeres consist of constitutive heterochromatin. The results in this paper illustrate that RNAs complementary to DNA sequences play roles in activating genes. Since RNA is mainly produced from the cell's own DNA, the work presented in this paper suggests that RNAs transcribed from DNA create feedback that activates DNA transcription.
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Affiliation(s)
- Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
| | - Zhihong Ma
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, The Second Hospital of Tangshan, 21 North Jianshe Road, Tangshan, Hebei Province, China.
| | - Xianglong Kong
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China; Clinical Laboratory, Hebei Chest Hospital, 372 Shengli North Street, Shijiazhuang, Hebei Province, China.
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China.
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Hay D, Hughes JR, Babbs C, Davies JO, Graham BJ, Hanssen L, Kassouf MT, Marieke Oudelaar AM, Sharpe JA, Suciu MC, Telenius J, Williams R, Rode C, Li PS, Pennacchio LA, Sloane-Stanley JA, Ayyub H, Butler S, Sauka-Spengler T, Gibbons RJ, Smith AJ, Wood WG, Higgs DR. Genetic dissection of the α-globin super-enhancer in vivo. Nat Genet 2016; 48:895-903. [PMID: 27376235 PMCID: PMC5058437 DOI: 10.1038/ng.3605] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/01/2016] [Indexed: 12/18/2022]
Abstract
Many genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. These super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer individually and in informative combinations, we demonstrate that each constituent enhancer seems to act independently and in an additive fashion with respect to hematological phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.
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Affiliation(s)
- Deborah Hay
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - James O.J. Davies
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Bryony J. Graham
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Lars Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Mira T. Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | | | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Maria C. Suciu
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Ruth Williams
- Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Pik-Shan Li
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Len A. Pennacchio
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California
| | | | - Helena Ayyub
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Sue Butler
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | | | - Richard J. Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Andrew J.H. Smith
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - William G. Wood
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Douglas R. Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
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10
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Du J, Leung A, Trac C, Lee M, Parks BW, Lusis AJ, Natarajan R, Schones DE. Chromatin variation associated with liver metabolism is mediated by transposable elements. Epigenetics Chromatin 2016; 9:28. [PMID: 27398095 PMCID: PMC4939004 DOI: 10.1186/s13072-016-0078-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/29/2016] [Indexed: 01/23/2023] Open
Abstract
Background Functional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of transcriptional regulation, and variation in chromatin accessibility across individuals has been linked to complex traits and disease susceptibility. While mechanisms responsible for chromatin variation across individuals have been investigated, the overwhelming majority of chromatin variation remains unexplained. Furthermore, the processes through which the variation of chromatin accessibility contributes to phenotypic diversity remain poorly understood. Results We profiled chromatin accessibility in liver from seven strains of mice with phenotypic diversity in response to a high-fat/high-sucrose (HF/HS) diet and identified reproducible chromatin variation across the individuals. We found that sites of variable chromatin accessibility were more likely to coincide with particular classes of transposable elements (TEs) than sites with common chromatin signatures. Evolutionarily younger long interspersed nuclear elements (LINEs) are particularly likely to harbor variable chromatin sites. These younger LINEs are enriched for binding sites of immune-associated transcription factors, whereas older LINEs are enriched for liver-specific transcription factors. Genomic region enrichment analysis indicates that variable chromatin sites at TEs may function to regulate liver metabolic pathways. CRISPR-Cas9 deletion of a number of variable chromatin sites at TEs altered expression of nearby metabolic genes. Finally, we show that polymorphism of TEs and differential DNA methylation at TEs can both influence chromatin variation. Conclusions Our results demonstrate that specific classes of TEs show variable chromatin accessibility across strains of mice that display phenotypic diversity in response to a HF/HS diet. These results indicate that chromatin variation at TEs is an important contributor to phenotypic variation among populations. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0078-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Du
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA USA ; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA USA
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA USA
| | - Candi Trac
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA USA
| | - Michael Lee
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA USA ; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA USA
| | - Brian W Parks
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Aldons J Lusis
- Department of Medicine, University of California, Los Angeles, CA USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA USA ; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA USA
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA USA ; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA USA
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11
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Bai L, Yang HH, Hu Y, Shukla A, Ha NH, Doran A, Faraji F, Goldberger N, Lee MP, Keane T, Hunter KW. An Integrated Genome-Wide Systems Genetics Screen for Breast Cancer Metastasis Susceptibility Genes. PLoS Genet 2016; 12:e1005989. [PMID: 27074153 PMCID: PMC4830524 DOI: 10.1371/journal.pgen.1005989] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
Metastasis remains the primary cause of patient morbidity and mortality in solid tumors and is due to the action of a large number of tumor-autonomous and non-autonomous factors. Here we report the results of a genome-wide integrated strategy to identify novel metastasis susceptibility candidate genes and molecular pathways in breast cancer metastasis. This analysis implicates a number of transcriptional regulators and suggests cell-mediated immunity is an important determinant. Moreover, the analysis identified novel or FDA-approved drugs as potentially useful for anti-metastatic therapy. Further explorations implementing this strategy may therefore provide a variety of information for clinical applications in the control and treatment of advanced neoplastic disease. Metastasis, the spread and growth of tumor cells from the original tumor to secondary sites throughout the body, is the primary cause of cancer-related death for most solid tumor types. The process of metastasis is very complex, requiring multiple individual steps and the cooperation of different cell types during the dissemination and proliferation steps. Many genes are involved in this process, but at present few have been identified and characterized. In this study, we have integrated multiple genome-wide analysis methods to try to identify large numbers of candidate metastasis-associated genes and pathways based on a highly metastatic mouse model. Using this strategy, we have identified a number of genes that predict outcome of human breast cancer. These genes implicate specific molecular and cellular pathways in the metastatic process that might be used to intervene in the process. Furthermore, this integrated analysis implicates pre-existing drugs that might be re-purposed to help prevent or reduce metastatic burden in patients. The combined results obtained from this analytical strategy therefore provide an important platform for further genome-wide analysis into the etiology of metastatic disease.
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Affiliation(s)
- Ling Bai
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Howard H. Yang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ying Hu
- Center for Bioinformatics and Information Technology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anjali Shukla
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ngoc-Han Ha
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anthony Doran
- Computational Genomics Program, Welcome Trust Sanger Centre, Hinxton, Cambridge, United Kingdom
| | - Farhoud Faraji
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Natalie Goldberger
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maxwell P. Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas Keane
- Computational Genomics Program, Welcome Trust Sanger Centre, Hinxton, Cambridge, United Kingdom
| | - Kent W. Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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12
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Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C. Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. THE JOURNAL OF IMMUNOLOGY 2014; 193:4485-96. [PMID: 25267973 DOI: 10.4049/jimmunol.1401280] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database. Considering both cell types, a large number of transcripts showed significant variation across the inbred strains, with 22% of the transcriptome varying by 2-fold or more. These included 119 loci with apparent complete loss of function, where the corresponding transcript was not expressed in some of the strains, representing a useful resource of "natural knockouts." We identified 1222 cis-expression quantitative trait loci (cis-eQTL) that control some of this variation. Most (60%) cis-eQTLs were shared between T cells and neutrophils, but a significant portion uniquely impacted one of the cell types, suggesting cell type-specific regulatory mechanisms. Using a conditional regression algorithm, we predicted regulatory interactions between transcription factors and potential targets, and we demonstrated that these predictions overlap with regulatory interactions inferred from transcriptional changes during immunocyte differentiation. Finally, comparison of these and parallel data from CD4(+) T cells of healthy humans demonstrated intriguing similarities in variability of a gene's expression: the most variable genes tended to be the same in both species, and there was an overlap in genes subject to strong cis-acting genetic variants. We speculate that this "conservation of variation" reflects a differential constraint on intraspecies variation in expression levels of different genes, either through lower pressure for some genes, or by favoring variability for others.
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Affiliation(s)
- Sara Mostafavi
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Adriana Ortiz-Lopez
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
| | | | - Kimie Hattori
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
| | - Cristina Pop
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Daphne Koller
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
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13
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Leung A, Parks BW, Du J, Trac C, Setten R, Chen Y, Brown K, Lusis AJ, Natarajan R, Schones DE. Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. J Biol Chem 2014; 289:23557-67. [PMID: 25006255 DOI: 10.1074/jbc.m114.581439] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Metabolic diseases result from multiple genetic and environmental factors. We report here that one manner in which environmental factors can contribute to metabolic disease progression is through modification to chromatin. We demonstrate that high fat diet leads to chromatin remodeling in the livers of C57BL/6J mice, as compared with mice fed a control diet, and that these chromatin changes are associated with changes in gene expression. We further show that the regions of greatest variation in chromatin accessibility are targeted by liver transcription factors, including HNF4α, CCAAT/enhancer-binding protein α (CEBP/α), and FOXA1. Repeating the chromatin and gene expression profiling in another mouse strain, DBA/2J, revealed that the regions of greatest chromatin change are largely strain-specific and that integration of chromatin, gene expression, and genetic data can be used to characterize regulatory regions. Our data indicate dramatic changes in the epigenome due to diet and demonstrate strain-specific dynamics in chromatin remodeling.
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Affiliation(s)
- Amy Leung
- From the Departments of Diabetes and
| | - Brian W Parks
- the Department of Medicine, UCLA, Los Angeles, California 90095
| | - Juan Du
- Cancer Biology, Beckman Research Institute and the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Candi Trac
- Cancer Biology, Beckman Research Institute and
| | - Ryan Setten
- the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Yin Chen
- the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Kevin Brown
- Cancer Biology, Beckman Research Institute and
| | - Aldons J Lusis
- the Department of Medicine, UCLA, Los Angeles, California 90095
| | - Rama Natarajan
- From the Departments of Diabetes and the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Dustin E Schones
- Cancer Biology, Beckman Research Institute and the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
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14
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Abstract
Mammals express thousands of long noncoding (lnc) RNAs, a few of which are known to function in tissue development. However, the entire repertoire of lncRNAs in most tissues and species is not defined. Indeed, most lncRNAs are not conserved, raising questions about function. We used RNA sequencing to identify 1109 polyadenylated lncRNAs expressed in erythroblasts, megakaryocytes, and megakaryocyte-erythroid precursors of mice, and 594 in erythroblasts of humans. More than half of these lncRNAs were unannotated, emphasizing the opportunity for new discovery through studies of specialized cell types. Analysis of the mouse erythro-megakaryocytic polyadenylated lncRNA transcriptome indicates that ~75% arise from promoters and 25% from enhancers, many of which are regulated by key transcription factors including GATA1 and TAL1. Erythroid lncRNA expression is largely conserved among 8 different mouse strains, yet only 15% of mouse lncRNAs are expressed in humans and vice versa, reflecting dramatic species-specificity. RNA interference assays of 21 abundant erythroid-specific murine lncRNAs in primary mouse erythroid precursors identified 7 whose knockdown inhibited terminal erythroid maturation. At least 6 of these 7 functional lncRNAs have no detectable expression in human erythroblasts, suggesting that lack of conservation between mammalian species does not predict lack of function.
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15
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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 2014; 46:205-12. [PMID: 24413732 DOI: 10.1038/ng.2871] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/12/2013] [Indexed: 12/19/2022]
Abstract
Gene expression during development and differentiation is regulated in a cell- and stage-specific manner by complex networks of intergenic and intragenic cis-regulatory elements whose numbers and representation in the genome far exceed those of structural genes. Using chromosome conformation capture, it is now possible to analyze in detail the interaction between enhancers, silencers, boundary elements and promoters at individual loci, but these techniques are not readily scalable. Here we present a high-throughput approach (Capture-C) to analyze cis interactions, interrogating hundreds of specific interactions at high resolution in a single experiment. We show how this approach will facilitate detailed, genome-wide analysis to elucidate the general principles by which cis-acting sequences control gene expression. In addition, we show how Capture-C will expedite identification of the target genes and functional effects of SNPs that are associated with complex diseases, which most frequently lie in intergenic cis-acting regulatory elements.
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Abstract
Progress in complex trait mapping in mice has been accelerated by the development of new populations suited to high-resolution mapping and by statistical methodologies that control for population structure. When combined with newly acquired catalogs of sequence variation in inbred strains, the genetic architecture of these new populations makes it possible to dissect complex traits down to the level of single variants. These analyses have shown not only that complex traits are caused by multiple contributing loci but also that each locus is likely due to the combined effects of multiple causal DNA variants. In combination with new rapid methods for producing transgenic mice that make it efficient to test candidate genes and variants, these advances significantly enhance the mouse genetics toolbox for dissecting quantitative traits.
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Affiliation(s)
- Richard Mott
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom; ,
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