151
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Inhibition of G9a methyltransferase stimulates fetal hemoglobin production by facilitating LCR/γ-globin looping. Blood 2015; 126:665-72. [PMID: 25979948 DOI: 10.1182/blood-2015-02-629972] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/11/2015] [Indexed: 12/16/2022] Open
Abstract
Induction of fetal hemoglobin (HbF) production in adult erythrocytes can reduce the severity of sickle cell disease and β-thalassemia. Transcription of β-globin genes is regulated by the distant locus control region (LCR), which is brought into direct gene contact by the LDB1/GATA-1/TAL1/LMO2-containing complex. Inhibition of G9a H3K9 methyltransferase by the chemical compound UNC0638 activates fetal and represses adult β-globin gene expression in adult human hematopoietic precursor cells, but the underlying mechanisms are unclear. Here we studied UNC0638 effects on β-globin gene expression using ex vivo differentiation of CD34(+) erythroid progenitor cells from peripheral blood of healthy adult donors. UNC0638 inhibition of G9a caused dosed accumulation of HbF up to 30% of total hemoglobin in differentiated cells. Elevation of HbF was associated with significant activation of fetal γ-globin and repression of adult β-globin transcription. Changes in gene expression were associated with widespread loss of H3K9me2 in the locus and gain of LDB1 complex occupancy at the γ-globin promoters as well as de novo formation of LCR/γ-globin contacts. Our findings demonstrate that G9a establishes epigenetic conditions preventing activation of γ-globin genes during differentiation of adult erythroid progenitor cells. In this view, manipulation of G9a represents a promising epigenetic approach for treatment of β-hemoglobinopathies.
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152
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Sexton T, Cavalli G. The role of chromosome domains in shaping the functional genome. Cell 2015; 160:1049-59. [PMID: 25768903 DOI: 10.1016/j.cell.2015.02.040] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 10/23/2022]
Abstract
The genome must be highly compacted to fit within eukaryotic nuclei but must be accessible to the transcriptional machinery to allow appropriate expression of genes in different cell types and throughout developmental pathways. A growing body of work has shown that the genome, analogously to proteins, forms an ordered, hierarchical structure that closely correlates and may even be causally linked with regulation of functions such as transcription. This review describes our current understanding of how these functional genomic "secondary and tertiary structures" form a blueprint for global nuclear architecture and the potential they hold for understanding and manipulating genomic regulation.
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Affiliation(s)
- Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France.
| | - Giacomo Cavalli
- Institute of Human Genetics (IGH), 141 rue de la Cardonille, 34396 Montpellier, France.
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153
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Architectural hallmarks of the pluripotent genome. FEBS Lett 2015; 589:2905-13. [PMID: 25957773 DOI: 10.1016/j.febslet.2015.04.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 01/03/2023]
Abstract
Pluripotent stem cells (PSCs) have the ability to self-renew and are capable of generating all embryonic germ layers (Evans and Kaufman, 1981; Thomson et al., 1998). PSCs can be isolated from early embryos or may be induced via overexpression of pluripotency transcription factors in differentiated cells (Takahashi and Yamanaka, 2006). As PSCs hold great promise for regenerative medicine, the mechanisms underlying pluripotency and induction thereof are studied intensively. Pluripotency is characterized by a unique transcriptional program that is in part controlled by an exceptionally plastic regulatory chromatin landscape. In recent years, 3D genome configuration has emerged as an important regulator of transcriptional control and cellular identity (Taddei et al., 2004 [4]; Lanctot et al., 2007 [5]; Gibcus and Dekker, 2013; Misteli, 2009 [7]). Here we provide an overview of recent findings on the 3D genome organization in PSCs and discuss its putative functional role in regulation of the pluripotent state.
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154
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Aguirre LA, Alonso ME, Badía-Careaga C, Rollán I, Arias C, Fernández-Miñán A, López-Jiménez E, Aránega A, Gómez-Skarmeta JL, Franco D, Manzanares M. Long-range regulatory interactions at the 4q25 atrial fibrillation risk locus involve PITX2c and ENPEP. BMC Biol 2015; 13:26. [PMID: 25888893 PMCID: PMC4416339 DOI: 10.1186/s12915-015-0138-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/10/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Recent genome-wide association studies have uncovered genomic loci that underlie an increased risk for atrial fibrillation, the major cardiac arrhythmia in humans. The most significant locus is located in a gene desert at 4q25, approximately 170 kilobases upstream of PITX2, which codes for a transcription factor involved in embryonic left-right asymmetry and cardiac development. However, how this genomic region functionally and structurally relates to PITX2 and atrial fibrillation is unknown. RESULTS To characterise its function, we tested genomic fragments from 4q25 for transcriptional activity in a mouse atrial cardiomyocyte cell line and in transgenic mouse embryos, identifying a non-tissue-specific potentiator regulatory element. Chromosome conformation capture revealed that this region physically interacts with the promoter of the cardiac specific isoform of Pitx2. Surprisingly, this regulatory region also interacts with the promoter of the next neighbouring gene, Enpep, which we show to be expressed in regions of the developing mouse heart essential for cardiac electrical activity. CONCLUSIONS Our data suggest that de-regulation of both PITX2 and ENPEP could contribute to an increased risk of atrial fibrillation in carriers of disease-associated variants, and show the challenges that we face in the functional analysis of genome-wide disease associations.
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Affiliation(s)
- Luis A Aguirre
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - M Eva Alonso
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Claudio Badía-Careaga
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Isabel Rollán
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Cristina Arias
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Ana Fernández-Miñán
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, ctra. de Utrera km1, 41013, Seville, Spain.
| | - Elena López-Jiménez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
| | - Amelia Aránega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje de las Lagunillas s/n, 23071, Jaén, Spain.
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, ctra. de Utrera km1, 41013, Seville, Spain.
| | - Diego Franco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Paraje de las Lagunillas s/n, 23071, Jaén, Spain.
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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155
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Risca VI, Greenleaf WJ. Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet 2015; 31:357-72. [PMID: 25887733 DOI: 10.1016/j.tig.2015.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 12/15/2022]
Abstract
A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.
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Affiliation(s)
- Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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156
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Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the β-globin locus. Biosci Rep 2015; 35:BSR20140126. [PMID: 25588787 PMCID: PMC4370096 DOI: 10.1042/bsr20140126] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Enhancers are closely positioned with actively transcribed target genes by chromatin looping. Non-coding RNAs are often transcribed on active enhancers, referred to as eRNAs (enhancer RNAs). To explore the kinetics of enhancer–promoter looping and eRNA transcription during transcriptional activation, we induced the β-globin locus by chemical treatment and analysed cross-linking frequency between the β-globin gene and locus control region (LCR) and the amount of eRNAs transcribed on the LCR in a time course manner. The cross-linking frequency was increased after chemical induction but before the transcriptional activation of gene in the β-globin locus. Transcription of eRNAs was increased in concomitant with the increase in cross-linking frequency. These results show that chromatin looping and eRNA transcription precedes the transcriptional activation of gene. Concomitant occurrence of the two events suggests functional relationship between them. Chromatin looping between enhancer and promoter was generated after chemical induction but before the transcriptional activation of gene in the β-globin locus. Transcription of enhancer RNAs was increased in concomitant with the increase of chromatin looping in this locus.
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157
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Abstract
The different cell types of an organism share the same DNA, but during cell differentiation their genomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. These can range from large-scale folding of whole chromosomes or of smaller genomic regions, to the re-organization of local interactions between enhancers and promoters, mediated by the binding of transcription factors and chromatin looping. The higher-order organization of chromatin is also influenced by the specificity of the contacts that it makes with nuclear structures such as the lamina. Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus.
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158
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KLF1-null neonates display hydrops fetalis and a deranged erythroid transcriptome. Blood 2015; 125:2405-17. [PMID: 25724378 DOI: 10.1182/blood-2014-08-590968] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/21/2015] [Indexed: 12/14/2022] Open
Abstract
We describe a case of severe neonatal anemia with kernicterus caused by compound heterozygosity for null mutations in KLF1, each inherited from asymptomatic parents. One of the mutations is novel. This is the first described case of a KLF1-null human. The phenotype of severe nonspherocytic hemolytic anemia, jaundice, hepatosplenomegaly, and marked erythroblastosis is more severe than that present in congenital dyserythropoietic anemia type IV as a result of dominant mutations in the second zinc-finger of KLF1. There was a very high level of HbF expression into childhood (>70%), consistent with a key role for KLF1 in human hemoglobin switching. We performed RNA-seq on circulating erythroblasts and found that human KLF1 acts like mouse Klf1 to coordinate expression of many genes required to build a red cell including those encoding globins, cytoskeletal components, AHSP, heme synthesis enzymes, cell-cycle regulators, and blood group antigens. We identify novel KLF1 target genes including KIF23 and KIF11 which are required for proper cytokinesis. We also identify new roles for KLF1 in autophagy, global transcriptional control, and RNA splicing. We suggest loss of KLF1 should be considered in otherwise unexplained cases of severe neonatal NSHA or hydrops fetalis.
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159
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An autoregulatory pathway establishes the definitive chromatin conformation at the pit-1 locus. Mol Cell Biol 2015; 35:1523-32. [PMID: 25691665 DOI: 10.1128/mcb.01283-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/09/2015] [Indexed: 12/12/2022] Open
Abstract
The transcription factor Pit-1 (POU1-F1) plays a dominant role in cell lineage expansion and differentiation in the anterior pituitary. Prior studies of the mouse Pit-1 (mPit-1) gene revealed that this master regulatory locus is activated at embryonic day 13.5 (E13.5) by an early enhancer (EE), whereas its subsequent expression throughout adult life is maintained by a more distal definitive enhancer (DE). Here, we demonstrate that the sequential actions of these two enhancers are linked to corresponding shifts in their proximities to the Pit-1 promoter. We further demonstrate that the looping of the definitive enhancer to the mPit-1 promoter is critically dependent on a self-sustaining autoregulatory mechanism mediated by the Pit-1 protein. These Pit-1-dependent actions are accompanied by localized recruitment of CBP and enrichment for H3K27 acetylation within the Pit-1 locus. These data support a model in which the sequential actions of two developmentally activated enhancers are linked to a corresponding shift in higher-order chromatin structures. This shift establishes an autoregulatory circuit that maintains durable expression of Pit-1 throughout adult life.
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160
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Fang F, Xu Y, Chew KK, Chen X, Ng HH, Matsudaira P. Coactivators p300 and CBP maintain the identity of mouse embryonic stem cells by mediating long-range chromatin structure. Stem Cells 2015; 32:1805-16. [PMID: 24648406 DOI: 10.1002/stem.1705] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/25/2013] [Accepted: 12/22/2013] [Indexed: 11/07/2022]
Abstract
Master transcription factors Oct4, Sox2, and Nanog are required to maintain the pluripotency and self-renewal of embryonic stem cells (ESCs) by regulating a specific transcriptional network. A few other transcription factors have been shown to be important in ESCs by interacting with these master transcription factors; however, little is known about the transcriptional mechanisms regulated by coregulators (coactivators and corepressors). In this study, we examined the function of two highly homologous coactivators, p300 and CREB-binding protein (CBP), in ESCs. We find that these two coactivators play redundant roles in maintaining the undifferentiated state of ESCs. They are recruited by Nanog through physical interaction to Nanog binding loci, mediating the formation of long-range chromatin looping structures, which is essential to maintain ESC-specific gene expression. Further functional studies reveal that the p300/CBP binding looping fragments contain enhancer activities, suggesting that the formation of p300/CBP-mediated looping structures may recruit distal enhancers to create a concentration of factors for the transcription activation of genes that are involved in self-renewal and pluripotency. Overall, these results provide a total new insight into the transcriptional regulation mechanism of coactivators p300 and CBP in ESCs, which is important in maintaining self-renewal and pluripotency, by mediating the formation of higher order chromosome structures.
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Affiliation(s)
- Fang Fang
- Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
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161
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Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun 2015; 2:6186. [PMID: 25645053 PMCID: PMC4431651 DOI: 10.1038/ncomms7186] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022] Open
Abstract
Chromatin interactions connect distal regulatory elements to target gene promoters
guiding stimulus- and lineage-specific transcription. Few factors securing chromatin
interactions have so far been identified. Here, by integrating chromatin interaction
maps with the large collection of transcription factor-binding profiles provided by
the ENCODE project, we demonstrate that the zinc-finger protein ZNF143 preferentially occupies anchors of
chromatin interactions connecting promoters with distal regulatory elements. It
binds directly to promoters and associates with lineage-specific chromatin
interactions and gene expression. Silencing ZNF143 or modulating its DNA-binding affinity using
single-nucleotide polymorphisms (SNPs) as a surrogate of site-directed mutagenesis
reveals the sequence dependency of chromatin interactions at gene promoters. We also
find that chromatin interactions alone do not regulate gene expression. Together,
our results identify ZNF143 as a
novel chromatin-looping factor that contributes to the architectural foundation of
the genome by providing sequence specificity at promoters connected with distal
regulatory elements. Chromatin interactions can connect distal regulatory elements to
promoters via protein factors, but few such factors have been identified. Here, the
authors show that zinc-finger protein ZNF143 is a sequence-specific chromatin-looping
factor that connects promoters with distal regulatory elements.
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Affiliation(s)
- Swneke D Bailey
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada
| | - Xiaoyang Zhang
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA.,Present address: Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Kinjal Desai
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA
| | - Malika Aid
- Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Richard Cowper-Sal Lari
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Present address: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Batool Akhtar-Zaidi
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Present address: Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02142, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Benjamin Haibe-Kains
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada.,Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada. .,Ontario Institute for Cancer Research, Toronto, M5G 1L7, Ontario, Canada.
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162
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Visser M, Palstra RJ, Kayser M. Allele-specific transcriptional regulation of IRF4 in melanocytes is mediated by chromatin looping of the intronic rs12203592 enhancer to the IRF4 promoter. Hum Mol Genet 2015; 24:2649-61. [PMID: 25631878 DOI: 10.1093/hmg/ddv029] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/24/2015] [Indexed: 01/07/2023] Open
Abstract
The majority of significant single-nucleotide polymorphisms (SNPs) identified with genome-wide association studies are located in non-coding regions of the genome; it is therefore possible that they are involved in transcriptional regulation of a nearby gene rather than affecting an encoded protein's function. Previously, it was demonstrated that the SNP rs12203592, located in intron 4 of the IRF4 gene, is strongly associated with human skin pigmentation and modulates an enhancer element that controls expression of IRF4. In our study, we investigated the allele-specific effect of rs12203592 on IRF4 expression in epidermal skin samples and in melanocytic cells from donors of different skin color. We focused on the characteristics and activity of the enhancer, and on long-range chromatin interactions in melanocytic cells homozygous and heterozygous for rs12203592. We found that, irrespective of the trans-activating environment, IRF4 transcription is strongly correlated with the allelic status of rs12203592, the activity of the rs12203592 enhancer and that the chromatin features depend on the rs12203592 genotype. Furthermore, we demonstrate that the rs12203592 enhancer physically interacts with the IRF4 promoter through an allele-dependent chromatin loop, and suggest that subsequent allele-specific activation of IRF4 transcription is stabilized by another allele-specific loop from the rs12203592 enhancer to an additional regulatory element in IRF4. We conclude that the non-coding SNP rs12203592 is located in a regulatory region and affects a wide range of enhancer characteristics, resulting into modulation of the enhancer's activity, its interaction with the IRF4 promoter and subsequent allele-specific transcription of IRF4. Our findings provide another example of a non-coding SNP affecting skin color by modulating enhancer-mediated transcriptional regulation.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Robert-Jan Palstra
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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163
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de Almeida CR, Hendriks RW, Stadhouders R. Dynamic Control of Long-Range Genomic Interactions at the Immunoglobulin κ Light-Chain Locus. Adv Immunol 2015; 128:183-271. [DOI: 10.1016/bs.ai.2015.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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164
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R. Caré B, Emeriau PE, Cortini R, Victor JM. Chromatin epigenomic domain folding: size matters. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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165
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Iarovaia OV, Ioudinkova ES, Petrova NV, Dolgushin KV, Kovina AV, Nefedochkina AV, Vassetzky YS, Razin SV. Evolution of α- and β-globin genes and their regulatory systems in light of the hypothesis of domain organization of the genome. BIOCHEMISTRY (MOSCOW) 2014; 79:1141-50. [PMID: 25539999 DOI: 10.1134/s0006297914110017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The α- and β-globin gene domains are a traditional model for study of the domain organization of the eucaryotic genome because these genes encode hemoglobin, a physiologically important protein. The α-globin and β-globin gene domains are organized in completely different ways, while the expression of globin genes is tightly coordinated, which makes it extremely interesting to study the origin of these genes and the evolution of their regulatory systems. In this review, the organization of the α- and β-globin gene domains and their genomic environment in different taxonomic groups are comparatively analyzed. A new hypothesis of possible evolutionary pathways for segregated α- and β-globin gene domains of warm-blooded animals is proposed.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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166
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Gushchanskaya ES, Artemov AV, Ulyanov SV, Penin AA, Logacheva MD, Razin SV, Gavrilov AA. Spatial organization of housekeeping genes in interphase nuclei. Mol Biol 2014. [DOI: 10.1134/s0026893314060053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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167
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Deng W, Rupon JW, Krivega I, Breda L, Motta I, Jahn KS, Reik A, Gregory PD, Rivella S, Dean A, Blobel GA. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 2014; 158:849-860. [PMID: 25126789 DOI: 10.1016/j.cell.2014.05.050] [Citation(s) in RCA: 302] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 04/26/2014] [Accepted: 05/29/2014] [Indexed: 01/17/2023]
Abstract
Distal enhancers commonly contact target promoters via chromatin looping. In erythroid cells, the locus control region (LCR) contacts β-type globin genes in a developmental stage-specific manner to stimulate transcription. Previously, we induced LCR-promoter looping by tethering the self-association domain (SA) of Ldb1 to the β-globin promoter via artificial zinc fingers. Here, we show that targeting the SA to a developmentally silenced embryonic globin gene in adult murine erythroblasts triggers its transcriptional reactivation. This activity depends on the LCR, consistent with an LCR-promoter looping mechanism. Strikingly, targeting the SA to the fetal γ-globin promoter in primary adult human erythroblasts increases γ-globin promoter-LCR contacts, stimulating transcription to approximately 85% of total β-globin synthesis, with a reciprocal reduction in adult β-globin expression. Our findings demonstrate that forced chromatin looping can override a stringent developmental gene expression program and suggest a novel approach to control the balance of globin gene transcription for therapeutic applications.
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Affiliation(s)
- Wulan Deng
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Transcription Imaging Consortium, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jeremy W Rupon
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Breda
- Division of Hematology-Oncology, Department of Pediatrics, Weill Cornell Medical College, New York, NY 10021, USA
| | - Irene Motta
- Division of Hematology-Oncology, Department of Pediatrics, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kristen S Jahn
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | | | - Stefano Rivella
- Division of Hematology-Oncology, Department of Pediatrics, Weill Cornell Medical College, New York, NY 10021, USA; Division of Hematology-Oncology, Department of Cell and Biology Development, Weill Cornell Medical College, New York, NY 10021, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Kolovos P, van de Werken HJ, Kepper N, Zuin J, Brouwer RW, Kockx CE, Wendt KS, van IJcken WF, Grosveld F, Knoch TA. Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics Chromatin 2014; 7:10. [PMID: 25031611 PMCID: PMC4100494 DOI: 10.1186/1756-8935-7-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/28/2014] [Indexed: 11/26/2022] Open
Abstract
Background Significant efforts have recently been put into the investigation of the spatial organization and the chromatin-interaction networks of genomes. Chromosome conformation capture (3C) technology and its derivatives are important tools used in this effort. However, many of these have limitations, such as being limited to one viewpoint, expensive with moderate to low resolution, and/or requiring a large sequencing effort. Techniques like Hi-C provide a genome-wide analysis. However, it requires massive sequencing effort with considerable costs. Here we describe a new technique termed Targeted Chromatin Capture (T2C), to interrogate large selected regions of the genome. T2C provides an unbiased view of the spatial organization of selected loci at superior resolution (single restriction fragment resolution, from 2 to 6 kbp) at much lower costs than Hi-C due to the lower sequencing effort. Results We applied T2C on well-known model regions, the mouse β-globin locus and the human H19/IGF2 locus. In both cases we identified all known chromatin interactions. Furthermore, we compared the human H19/IGF2 locus data obtained from different chromatin conformation capturing methods with T2C data. We observed the same compartmentalization of the locus, but at a much higher resolution (single restriction fragments vs. the common 40 kbp bins) and higher coverage. Moreover, we compared the β-globin locus in two different biological samples (mouse primary erythroid cells and mouse fetal brain), where it is either actively transcribed or not, to identify possible transcriptional dependent interactions. We identified the known interactions in the β-globin locus and the same topological domains in both mouse primary erythroid cells and in mouse fetal brain with the latter having fewer interactions probably due to the inactivity of the locus. Furthermore, we show that interactions due to the important chromatin proteins, Ldb1 and Ctcf, in both tissues can be analyzed easily to reveal their role on transcriptional interactions and genome folding. Conclusions T2C is an efficient, easy, and affordable with high (restriction fragment) resolution tool to address both genome compartmentalization and chromatin-interaction networks for specific genomic regions at high resolution for both clinical and non-clinical research.
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Affiliation(s)
- Petros Kolovos
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Harmen Jg van de Werken
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Nick Kepper
- Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Jessica Zuin
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Rutger Ww Brouwer
- Center for Biomics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Christel Em Kockx
- Center for Biomics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Wilfred Fj van IJcken
- Center for Biomics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Tobias A Knoch
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
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169
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Schwarzer W, Spitz F. The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains. Curr Opin Genet Dev 2014; 27:74-82. [PMID: 24907448 DOI: 10.1016/j.gde.2014.03.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 02/06/2023]
Abstract
Specificity and precision of expression are essential for the genes that regulate developmental processes. The specialized cis-acting modules, such as enhancers, that define gene expression patterns can be distributed across large regions, raising questions about the nature of the mechanisms that underline their action. Recent data has exposed the structural 3D context in which these long-range enhancers are operating. Here, we present how these studies shed new light on principles driving long-distance regulatory relationships. We discuss the molecular mechanisms that enable and accompany the action of long-range acting elements and the integration of multiple distributed regulatory inputs into the coherent and specific regulatory programs that are key to embryonic development.
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Affiliation(s)
- Wibke Schwarzer
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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170
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Tai PWL, Zaidi SK, Wu H, Grandy RA, Montecino MM, van Wijnen AJ, Lian JB, Stein GS, Stein JL. The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. J Cell Physiol 2014; 229:711-27. [PMID: 24242872 PMCID: PMC3996806 DOI: 10.1002/jcp.24508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 12/31/2022]
Abstract
Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology.
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Affiliation(s)
- Phillip W. L. Tai
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Sayyed K. Zaidi
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Hai Wu
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Rodrigo A. Grandy
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Martin M. Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
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171
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Chang KH, Fang X, Wang H, Huang A, Cao H, Yang Y, Bonig H, Stamatoyannopoulos JA, Papayannopoulou T. Epigenetic modifications and chromosome conformations of the beta globin locus throughout development. Stem Cell Rev Rep 2014; 9:397-407. [PMID: 22374078 DOI: 10.1007/s12015-012-9355-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human embryonic stem cells provide an alternative to using human embryos for studying developmentally regulated gene expression. The co-expression of high levels of embryonic ε and fetal γ globin by the hESC-derived erythroblasts allows the interrogation of ε globin regulation at the transcriptional and epigenetic level which could only be attained previously by studying cell lines or transgenic mice. In this study, we compared the histone modifications across the β globin locus of the undifferentiated hESCs and hESC-, FL-, and mobilized PB CD34(+) cells-derived erythroblasts, which have distinct globin expression patterns corresponding to their developmental stages. We demonstrated that the histone codes employed by the β globin locus are conserved throughout development. Furthermore, in spite of the close proximity of the ε globin promoter, as compared to the β or γ globin promoter, with the LCR, a chromatin loop was also formed between the LCR and the active ε globin promoter, similar to the loop that forms between the β or γ globin promoters and the LCR, in contrary to the previously proposed tracking mechanism.
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Affiliation(s)
- Kai-Hsin Chang
- Department of Medicine, Division of Hematology, University of Washington, NE Pacific St, Box 357710, Seattle, WA 98195, USA
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172
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Zielke T, Saumweber H. Dissection of open chromatin domain formation by site-specific recombination in Drosophila. J Cell Sci 2014; 127:2365-75. [PMID: 24639466 DOI: 10.1242/jcs.147546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Drosophila polytene interphase chromosomes provide an ideal test system to study the rules that define the structure of chromatin domains. We established a transgenic condensed chromatin domain cassette for the insertion of large pieces of DNA by site-specific recombination. Insertion of this cassette into open chromatin generated a condensed domain, visible as an extra band on polytene chromosomes. Site-specific recombination of DNA sequence variants into this ectopic band allowed us to compare their capacity for open chromatin formation by cytogenetic methods. We demonstrate that the 61C7-8 interband DNA maintains its open chromatin conformation and epigenetic state at an ectopic position. By deletion analysis, we mapped the sequences essential for open chromatin formation to a 490-bp fragment in the proximal part of the 17-kb interband sequence. This fragment overlaps binding sites for the chromatin protein Chriz (also known as Chro), the histone kinase Jil-1 and the boundary element protein CP190. It also overlaps a promoter region that locates between the Rev1 and Med30 transcription units.
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Affiliation(s)
- Thomas Zielke
- Humboldt University Berlin Institute of Biology, Cytogenetics Group, Chausseestrasse 117, 10115, Berlin, Germany
| | - Harald Saumweber
- Humboldt University Berlin Institute of Biology, Cytogenetics Group, Chausseestrasse 117, 10115, Berlin, Germany
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173
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Ball AR, Chen YY, Yokomori K. Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:191-202. [PMID: 24269489 PMCID: PMC3951616 DOI: 10.1016/j.bbagrm.2013.11.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/09/2013] [Accepted: 11/14/2013] [Indexed: 12/16/2022]
Abstract
Cohesins are conserved and essential Structural Maintenance of Chromosomes (SMC) protein-containing complexes that physically interact with chromatin and modulate higher-order chromatin organization. Cohesins mediate sister chromatid cohesion and cellular long-distance chromatin interactions affecting genome maintenance and gene expression. Discoveries of mutations in cohesin's subunits and its regulator proteins in human developmental disorders, so-called "cohesinopathies," reveal crucial roles for cohesins in development and cellular growth and differentiation. In this review, we discuss the latest findings concerning cohesin's functions in higher-order chromatin architecture organization and gene regulation and new insight gained from studies of cohesinopathies. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Alexander R Ball
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Yen-Yun Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA.
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174
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Wood AM, Garza-Gongora AG, Kosak ST. A Crowdsourced nucleus: understanding nuclear organization in terms of dynamically networked protein function. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:178-90. [PMID: 24412853 PMCID: PMC3954575 DOI: 10.1016/j.bbagrm.2014.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/30/2013] [Accepted: 01/02/2014] [Indexed: 01/14/2023]
Abstract
The spatial organization of the nucleus results in a compartmentalized structure that affects all aspects of nuclear function. This compartmentalization involves genome organization as well as the formation of nuclear bodies and plays a role in many functions, including gene regulation, genome stability, replication, and RNA processing. Here we review the recent findings associated with the spatial organization of the nucleus and reveal that a common theme for nuclear proteins is their ability to participate in a variety of functions and pathways. We consider this multiplicity of function in terms of Crowdsourcing, a recent phenomenon in the world of information technology, and suggest that this model provides a novel way to synthesize the many intersections between nuclear organization and function. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Ashley M Wood
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Arturo G Garza-Gongora
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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175
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Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F. Functional and topological characteristics of mammalian regulatory domains. Genome Res 2014; 24:390-400. [PMID: 24398455 PMCID: PMC3941104 DOI: 10.1101/gr.163519.113] [Citation(s) in RCA: 312] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/19/2013] [Indexed: 01/04/2023]
Abstract
Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene regulatory activities along the mouse genome, using hundreds of insertions of a regulatory sensor. We found that enhancers distribute their activities along broad regions and not in a gene-centric manner, defining large regulatory domains. Remarkably, these domains correlate strongly with the recently described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within large domains. These findings support a model of genomic organization where TADs confine regulatory activities to specific but large regulatory domains, contributing to the establishment of specific gene expression profiles.
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Affiliation(s)
- Orsolya Symmons
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Veli Vural Uslu
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Taro Tsujimura
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sandra Ruf
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sonya Nassari
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Wibke Schwarzer
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Laurence Ettwiller
- Centre for Organismal Studies, University of Heidelberg, 69111 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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176
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Williams RL, Starmer J, Mugford JW, Calabrese JM, Mieczkowski P, Yee D, Magnuson T. fourSig: a method for determining chromosomal interactions in 4C-Seq data. Nucleic Acids Res 2014; 42:e68. [PMID: 24561615 PMCID: PMC4005674 DOI: 10.1093/nar/gku156] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-Seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-Seq experiments generate large, complicated data sets and it is imperative that signal is properly distinguished from noise. Currently, there are a limited number of methods for analyzing 4C-Seq data. Here, we present a new method, fourSig, which in addition to being precise and simple to use also includes a new feature that prioritizes detected interactions. Our results demonstrate the efficacy of fourSig with previously published and novel 4C-Seq data sets and show that our significance prioritization correlates with the ability to reproducibly detect interactions among replicates.
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Affiliation(s)
- Rex L Williams
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA, Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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177
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Yun WJ, Kim YW, Kang Y, Lee J, Dean A, Kim A. The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription. Nucleic Acids Res 2014; 42:4283-93. [PMID: 24470145 PMCID: PMC3985645 DOI: 10.1093/nar/gku072] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
TAL1 is a key hematopoietic transcription factor that binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. The complex mediates long-range interaction between the β-globin locus control region (LCR) and active globin genes, and although TAL1 is one of the two DNA-binding complex members, its role is unclear. To explore the role of TAL1 in transcription activation of the human γ-globin genes, we reduced the expression of TAL1 in erythroid K562 cells using lentiviral short hairpin RNA, compromising its association in the β-globin locus. In the TAL1 knockdown cells, the γ-globin transcription was reduced to 35% and chromatin looping of the Gγ-globin gene with the LCR was disrupted with decreased occupancy of the complex member Ldb1 and LMO2 in the locus. However, GATA-1 binding, DNase I hypersensitive site formation and several histone modifications were largely maintained across the β-globin locus. In addition, overexpression of TAL1 increased the γ-globin transcription and increased interaction frequency between the Gγ-globin gene and LCR. These results indicate that TAL1 plays a critical role in chromatin loop formation between the γ-globin genes and LCR, which is a critical step for the transcription of the γ-globin genes.
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Affiliation(s)
- Won Ju Yun
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Pusan 609-735, Korea and Laboratory of Cellular and Developmental Biology, NIDDK, NIH, Bethesda, MD 20892, USA
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178
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Gavrilov AA, Chetverina HV, Chermnykh ES, Razin SV, Chetverin AB. Quantitative analysis of genomic element interactions by molecular colony technique. Nucleic Acids Res 2013; 42:e36. [PMID: 24369423 PMCID: PMC3950710 DOI: 10.1093/nar/gkt1322] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde-cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA-protein complex cannot be stabilized by formaldehyde cross-linking.
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Affiliation(s)
- Alexey A Gavrilov
- Group of Genome Spatial Organization, Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia, Laboratory of Viral RNA Biochemistry, Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia, Laboratory of Cell Proliferation Problems, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow 119334, Russia, Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, Moscow 119334, Russia and Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
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179
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Bian Q, Khanna N, Alvikas J, Belmont AS. β-Globin cis-elements determine differential nuclear targeting through epigenetic modifications. ACTA ACUST UNITED AC 2013; 203:767-83. [PMID: 24297746 PMCID: PMC3857487 DOI: 10.1083/jcb.201305027] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multiple cis-elements surrounding the β-globin gene locus combine to target this locus to the nuclear periphery through at least two different epigenetic marks. Increasing evidence points to nuclear compartmentalization as a contributing mechanism for gene regulation, yet mechanisms for compartmentalization remain unclear. In this paper, we use autonomous targeting of bacterial artificial chromosome (BAC) transgenes to reveal cis requirements for peripheral targeting. Three peripheral targeting regions (PTRs) within an HBB BAC bias a competition between pericentric versus peripheral heterochromatin targeting toward the nuclear periphery, which correlates with increased H3K9me3 across the β-globin gene cluster and locus control region. Targeting to both heterochromatin compartments is dependent on Suv39H-mediated H3K9me3 methylation. In different chromosomal contexts, PTRs confer no targeting, targeting to pericentric heterochromatin, or targeting to the periphery. A combination of fluorescent in situ hybridization, BAC transgenesis, and knockdown experiments reveals that peripheral tethering of the endogenous HBB locus depends both on Suv39H-mediated H3K9me3 methylation over hundreds of kilobases surrounding HBB and on G9a-mediated H3K9me2 methylation over flanking sequences in an adjacent lamin-associated domain. Our results demonstrate that multiple cis-elements regulate the overall balance of specific epigenetic marks and peripheral gene targeting.
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Affiliation(s)
- Qian Bian
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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180
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de Laat W, Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 2013; 502:499-506. [PMID: 24153303 DOI: 10.1038/nature12753] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 09/02/2013] [Indexed: 12/26/2022]
Abstract
How a complex animal can arise from a fertilized egg is one of the oldest and most fascinating questions of biology, the answer to which is encoded in the genome. Body shape and organ development, and their integration into a functional organism all depend on the precise expression of genes in space and time. The orchestration of transcription relies mostly on surrounding control sequences such as enhancers, millions of which form complex regulatory landscapes in the non-coding genome. Recent research shows that high-order chromosome structures make an important contribution to enhancer functionality by triggering their physical interactions with target genes.
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Affiliation(s)
- Wouter de Laat
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
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181
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Chetverina D, Aoki T, Erokhin M, Georgiev P, Schedl P. Making connections: insulators organize eukaryotic chromosomes into independent cis-regulatory networks. Bioessays 2013; 36:163-72. [PMID: 24277632 DOI: 10.1002/bies.201300125] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Insulators play a central role in subdividing the chromosome into a series of discrete topologically independent domains and in ensuring that enhancers and silencers contact their appropriate target genes. In this review we first discuss the general characteristics of insulator elements and their associated protein factors. A growing collection of insulator proteins have been identified including a family of proteins whose expression is developmentally regulated. We next consider several unexpected discoveries that require us to completely rethink how insulators function (and how they can best be assayed). These discoveries also require a reevaluation of how insulators might restrict or orchestrate (by preventing or promoting) interactions between regulatory elements and their target genes. We conclude by connecting these new insights into the mechanisms of insulator action to dynamic changes in the three-dimensional topology of the chromatin fiber and the generation of specific patterns of gene activity during development and differentiation.
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Affiliation(s)
- Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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182
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Three fingers on the switch: Krüppel-like factor 1 regulation of γ-globin to β-globin gene switching. Curr Opin Hematol 2013; 20:193-200. [PMID: 23474875 DOI: 10.1097/moh.0b013e32835f59ba] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Krüppel-like factor 1 (KLF1) regulates most aspects of erythropoiesis. Many years ago, transgenic mouse studies implicated KLF1 in the control of the human γ-globin to β-globin switch. In this review, we will integrate these initial studies with recent developments in human genetics to discuss our present understanding of how KLF1 and its target genes direct the switch. RECENT FINDINGS Recent studies have shown that human mutations in KLF1 are common and mostly asymptomatic, but lead to significant increases in levels of fetal hemoglobin (HbF) (α2γ2) and adult HbA2 (α2δ2). Genome-wide association studies (GWAS) have demonstrated that three primary loci are associated with increased HbF levels in the population: the β-globin locus itself, the BCL11A locus, and a site between MYB and HBS1L. We discuss evidence that KLF1 directly regulates BCL11A, MYB and other genes, which are involved directly or indirectly in γ-globin silencing, thus providing a link between GWAS and KLF1 in hemoglobin switching. SUMMARY KLF1 regulates the γ-globin to β-globin genetic switch by many mechanisms. Firstly, it facilitates formation of an active chromatin hub (ACH) at the β-globin gene cluster. Specifically, KLF1 conscripts the adult-stage β-globin gene to replace the γ-globin gene within the ACH in a stage-specific manner. Secondly, KLF1 acts as a direct activator of genes that encode repressors of γ-globin gene expression. Finally, KLF1 is a regulator of many components of the cell cycle machinery. We suggest that dysregulation of these genes leads to cell cycle perturbation and 'erythropoietic stress' leading to indirect upregulation of HbF.
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183
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Epigenetic control of cytokine gene expression: regulation of the TNF/LT locus and T helper cell differentiation. Adv Immunol 2013; 118:37-128. [PMID: 23683942 DOI: 10.1016/b978-0-12-407708-9.00002-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Epigenetics encompasses transient and heritable modifications to DNA and nucleosomes in the native chromatin context. For example, enzymatic addition of chemical moieties to the N-terminal "tails" of histones, particularly acetylation and methylation of lysine residues in the histone tails of H3 and H4, plays a key role in regulation of gene transcription. The modified histones, which are physically associated with gene regulatory regions that typically occur within conserved noncoding sequences, play a functional role in active, poised, or repressed gene transcription. The "histone code" defined by these modifications, along with the chromatin-binding acetylases, deacetylases, methylases, demethylases, and other enzymes that direct modifications resulting in specific patterns of histone modification, shows considerable evolutionary conservation from yeast to humans. Direct modifications at the DNA level, such as cytosine methylation at CpG motifs that represses promoter activity, are another highly conserved epigenetic mechanism of gene regulation. Furthermore, epigenetic modifications at the nucleosome or DNA level can also be coupled with higher-order intra- or interchromosomal interactions that influence the location of regulatory elements and that can place them in an environment of specific nucleoprotein complexes associated with transcription. In the mammalian immune system, epigenetic gene regulation is a crucial mechanism for a range of physiological processes, including the innate host immune response to pathogens and T cell differentiation driven by specific patterns of cytokine gene expression. Here, we will review current findings regarding epigenetic regulation of cytokine genes important in innate and/or adaptive immune responses, with a special focus upon the tumor necrosis factor/lymphotoxin locus and cytokine-driven CD4+ T cell differentiation into the Th1, Th2, and Th17 lineages.
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184
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Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1161-74. [PMID: 23938249 DOI: 10.1016/j.bbagrm.2013.08.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 02/06/2023]
Abstract
Ever since the discovery of DNA methylation at cytosine residues, the role of this so called fifth base has been extensively studied and debated. Until recently, the majority of DNA methylation studies focused on the analysis of CpG islands associated to promoter regions. However, with the upcoming possibilities to study DNA methylation in a genome-wide context, this epigenetic mark can now be studied in an unbiased manner. As a result, recent studies have shown that not only promoters but also intragenic and intergenic regions are widely modulated during physiological processes and disease. In particular, it is becoming increasingly clear that DNA methylation in the gene body is not just a passive witness of gene transcription but it seems to be actively involved in multiple gene regulation processes. In this review we discuss the potential role of intragenic DNA methylation in alternative promoter usage, regulation of short and long non-coding RNAs, alternative RNA processing, as well as enhancer activity. Furthermore, we summarize how the intragenic DNA methylome is modified both during normal cell differentiation and neoplastic transformation.
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185
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Pourfarzad F, Aghajanirefah A, de Boer E, Ten Have S, Bryn van Dijk T, Kheradmandkia S, Stadhouders R, Thongjuea S, Soler E, Gillemans N, von Lindern M, Demmers J, Philipsen S, Grosveld F. Locus-specific proteomics by TChP: targeted chromatin purification. Cell Rep 2013; 4:589-600. [PMID: 23911284 DOI: 10.1016/j.celrep.2013.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/01/2013] [Accepted: 07/07/2013] [Indexed: 12/20/2022] Open
Abstract
Here, we show that transcription factors bound to regulatory sequences can be identified by purifying these unique sequences directly from mammalian cells in vivo. Using targeted chromatin purification (TChP), a double-pull-down strategy with a tetracycline-sensitive "hook" bound to a specific promoter, we identify transcription factors bound to the repressed γ-globin gene-associated regulatory regions. After validation of the binding, we show that, in human primary erythroid cells, knockdown of a number of these transcription factors induces γ-globin gene expression. Reactivation of γ-globin gene expression ameliorates the symptoms of β-thalassemia and sickle cell disease, and these factors provide potential targets for the development of therapeutics for treating these patients.
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Affiliation(s)
- Farzin Pourfarzad
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands; Center for Biomedical Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, the Netherlands
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186
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Valdes-Quezada C, Arriaga-Canon C, Fonseca-Guzmán Y, Guerrero G, Recillas-Targa F. CTCF demarcates chicken embryonic α-globin gene autonomous silencing and contributes to adult stage-specific gene expression. Epigenetics 2013; 8:827-38. [PMID: 23880533 DOI: 10.4161/epi.25472] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Genomic loci composed of more than one gene are frequently subjected to differential gene expression, with the chicken α-globin domain being a clear example. In the present study we aim to understand the globin switching mechanisms responsible for the epigenetic silencing of the embryonic π gene and the transcriptional activation of the adult α(D) and α(A) genes at the genomic domain level. In early stages, we describe a physical contact between the embryonic π gene and the distal 3' enhancer that is lost later during development. We show that such a level of regulation is achieved through the establishment of a DNA hypermethylation sub-domain that includes the embryonic gene and the adjacent genomic sequences. The multifunctional CCCTCC-binding factor (CTCF), which is located upstream of the α(D) gene promoter, delimits this sub-domain and creates a transition between the inactive sub-domain and the active sub-domain, which includes the adult α(D) gene. In avian-transformed erythroblast HD3 cells that are induced to differentiate, we found active DNA demethylation of the adult α(D) promoter, coincident with the incorporation of 5-hydroxymethylcytosine (5hmC) and concomitant with adult gene transcriptional activation. These results suggest that autonomous silencing of the embryonic π gene is needed to facilitate an optimal topological conformation of the domain. This model proposes that CTCF is contributing to a specific chromatin configuration that is necessary for differential α-globin gene expression during development.
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Affiliation(s)
- Christian Valdes-Quezada
- Instituto de Fisiología Celular; Departamento de Genética Molecular; Universidad Nacional Autónoma de México; México D.F., México
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187
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Wei Z, Huang D, Gao F, Chang WH, An W, Coetzee GA, Wang K, Lu W. Biological implications and regulatory mechanisms of long-range chromosomal interactions. J Biol Chem 2013; 288:22369-77. [PMID: 23779110 DOI: 10.1074/jbc.r113.485292] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Development of high-throughput sequencing-based methods has enabled us to examine nuclear architecture at unprecedented resolution, allowing further examination of the function of long-range chromosomal interactions. Here, we review methods used to investigate novel long-range chromosomal interactions and genome-wide organization of chromatin. We further discuss transcriptional activation and silencing in relation to organization and positioning of gene loci and regulation of chromatin organization through protein complexes and noncoding RNAs.
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Affiliation(s)
- Zong Wei
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
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188
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Harmston N, Lenhard B. Chromatin and epigenetic features of long-range gene regulation. Nucleic Acids Res 2013; 41:7185-99. [PMID: 23766291 PMCID: PMC3753629 DOI: 10.1093/nar/gkt499] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The precise regulation of gene transcription during metazoan development is controlled by a complex system of interactions between transcription factors, histone modifications and modifying enzymes and chromatin conformation. Developments in chromosome conformation capture technologies have revealed that interactions between regions of chromatin are pervasive and highly cell-type specific. The movement of enhancers and promoters in and out of higher-order chromatin structures within the nucleus are associated with changes in expression and histone modifications. However, the factors responsible for mediating these changes and determining enhancer:promoter specificity are still not completely known. In this review, we summarize what is known about the patterns of epigenetic and chromatin features characteristic of elements involved in long-range interactions. In addition, we review the insights into both local and global patterns of chromatin interactions that have been revealed by the latest experimental and computational methods.
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Affiliation(s)
- Nathan Harmston
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London W12 0NN, UK, Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK and Department of Informatics, University of Bergen, Thromøhlensgate 55, N-5008 Bergen, Norway
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189
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Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res 2013; 41:e132. [PMID: 23671339 PMCID: PMC3711450 DOI: 10.1093/nar/gkt373] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of long-range genomic interactions, via the generation of ligation products between DNA sequences, which are closely juxtaposed in vivo. These interactions involve promoter regions, enhancers and other regulatory and structural elements of chromosomes and can reveal key details of the regulation of gene expression. 3C-seq is a variant of the method for the detection of interactions between one chosen genomic element (viewpoint) and the rest of the genome. We present r3Cseq, an R/Bioconductor package designed to perform 3C-seq data analysis in a number of different experimental designs. The package reads a common aligned read input format, provides data normalization, allows the visualization of candidate interaction regions and detects statistically significant chromatin interactions, thus greatly facilitating hypothesis generation and the interpretation of experimental results. We further demonstrate its use on a series of real-world applications.
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Affiliation(s)
- Supat Thongjuea
- Computational Biology Unit, Uni Computing, Uni Research AS, N-5020 Bergen, Norway
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190
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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 2013; 14:390-403. [PMID: 23657480 DOI: 10.1038/nrg3454] [Citation(s) in RCA: 752] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.
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191
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Holwerda SJB, de Laat W. CTCF: the protein, the binding partners, the binding sites and their chromatin loops. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120369. [PMID: 23650640 PMCID: PMC3682731 DOI: 10.1098/rstb.2012.0369] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CTCF has it all. The transcription factor binds to tens of thousands of genomic sites, some tissue-specific, others ultra-conserved. It can act as a transcriptional activator, repressor and insulator, and it can pause transcription. CTCF binds at chromatin domain boundaries, at enhancers and gene promoters, and inside gene bodies. It can attract many other transcription factors to chromatin, including tissue-specific transcriptional activators, repressors, cohesin and RNA polymerase II, and it forms chromatin loops. Yet, or perhaps therefore, CTCF's exact function at a given genomic site is unpredictable. It appears to be determined by the associated transcription factors, by the location of the binding site relative to the transcriptional start site of a gene, and by the site's engagement in chromatin loops with other CTCF-binding sites, enhancers or gene promoters. Here, we will discuss genome-wide features of CTCF binding events, as well as locus-specific functions of this remarkable transcription factor.
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Affiliation(s)
| | - Wouter de Laat
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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192
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Schönheit J, Kuhl C, Gebhardt M, Klett F, Riemke P, Scheller M, Huang G, Naumann R, Leutz A, Stocking C, Priller J, Andrade-Navarro M, Rosenbauer F. PU.1 Level-Directed Chromatin Structure Remodeling at the Irf8 Gene Drives Dendritic Cell Commitment. Cell Rep 2013; 3:1617-28. [DOI: 10.1016/j.celrep.2013.04.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 11/23/2012] [Accepted: 04/08/2013] [Indexed: 01/22/2023] Open
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193
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Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res 2013; 23:777-88. [PMID: 23482648 PMCID: PMC3638134 DOI: 10.1101/gr.152140.112] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 03/07/2013] [Indexed: 11/24/2022]
Abstract
Regulatory elements recruit transcription factors that modulate gene expression distinctly across cell types, but the relationships among these remains elusive. To address this, we analyzed matched DNase-seq and gene expression data for 112 human samples representing 72 cell types. We first defined more than 1800 clusters of DNase I hypersensitive sites (DHSs) with similar tissue specificity of DNase-seq signal patterns. We then used these to uncover distinct associations between DHSs and promoters, CpG islands, conserved elements, and transcription factor motif enrichment. Motif analysis within clusters identified known and novel motifs in cell-type-specific and ubiquitous regulatory elements and supports a role for AP-1 regulating open chromatin. We developed a classifier that accurately predicts cell-type lineage based on only 43 DHSs and evaluated the tissue of origin for cancer cell types. A similar classifier identified three sex-specific loci on the X chromosome, including the XIST lincRNA locus. By correlating DNase I signal and gene expression, we predicted regulated genes for more than 500K DHSs. Finally, we introduce a web resource to enable researchers to use these results to explore these regulatory patterns and better understand how expression is modulated within and across human cell types.
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Affiliation(s)
- Nathan C. Sheffield
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27710, USA
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27710, USA
| | - Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Lingyun Song
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27710, USA
| | - Alexias Safi
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27710, USA
| | | | - Boris Lenhard
- Bergen Center for Computational Science and Sars Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
- Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; and MRC Clinical Sciences Centre, London W12 0NN, United Kingdom
| | - Gregory E. Crawford
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27710, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina 27710, USA
| | - Terrence S. Furey
- Department of Genetics and Department of Biology, Carolina Center for Genome Sciences, Linberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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194
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Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell 2013; 49:773-82. [PMID: 23473598 DOI: 10.1016/j.molcel.2013.02.011] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/17/2012] [Accepted: 02/06/2013] [Indexed: 12/21/2022]
Abstract
Mammalian genomes encode genetic information in their linear sequence, but appropriate expression of their genes requires chromosomes to fold into complex three-dimensional structures. Transcriptional control involves the establishment of physical connections among genes and regulatory elements, both along and between chromosomes. Recent technological innovations in probing the folding of chromosomes are providing new insights into the spatial organization of genomes and its role in gene regulation. It is emerging that folding of large complex chromosomes involves a hierarchy of structures, from chromatin loops that connect genes and enhancers to larger chromosomal domains and nuclear compartments. The larger these structures are along this hierarchy, the more stable they are within cells, while becoming more stochastic between cells. Here, we review the experimental and theoretical data on this hierarchy of structures and propose a key role for the recently discovered topologically associating domains.
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Affiliation(s)
- Johan H Gibcus
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
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195
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Cagliero C, Grand RS, Jones MB, Jin DJ, O'Sullivan JM. Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription. Nucleic Acids Res 2013; 41:6058-71. [PMID: 23632166 PMCID: PMC3695519 DOI: 10.1093/nar/gkt325] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) -binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci.
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Affiliation(s)
- Cedric Cagliero
- Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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196
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Kim YW, Kim A. Histone acetylation contributes to chromatin looping between the locus control region and globin gene by influencing hypersensitive site formation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:963-9. [PMID: 23607989 DOI: 10.1016/j.bbagrm.2013.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 03/27/2013] [Accepted: 04/11/2013] [Indexed: 01/19/2023]
Abstract
Chromatin loops are formed between enhancers and promoters and between insulators to regulate gene transcription in the eukaryotic genome. These transcription regulatory elements forming loops have highly acetylated histones. To understand the correlation between histone acetylation and chromatin loop formation, we inhibited the expression of histone acetyltransferase CBP and p300 in erythroid K562 cells and analyzed the chromatin structure of the β-globin locus. The proximity between the locus control region (LCR) and the active (G)γ-globin gene was decreased in the β-globin locus when histones were hypoacetylated by the double knockdown of CBP and p300. Sensitivity to DNase I and binding of erythroid specific activators were reduced in the hypoacetylated LCR hypersensitive sites (HSs) and gene promoter. Interestingly, the chromatin loop between HS5 and 3'HS1 was formed regardless of the hypoacetylation of the β-globin locus. CTCF binding was maintained at HS5 and 3'HS1 in the hypoacetylated locus. Thus, these results indicate that histone acetylation contributes to chromatin looping through the formation of HSs in the LCR and gene promoter. However, looping between insulators appears to be independent from histone acetylation.
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Affiliation(s)
- Yea Woon Kim
- Department of Molecular Biology, Pusan National University, Busan, South Korea
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197
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Gavrilov AA, Golov AK, Razin SV. Actual ligation frequencies in the chromosome conformation capture procedure. PLoS One 2013; 8:e60403. [PMID: 23555968 PMCID: PMC3608588 DOI: 10.1371/journal.pone.0060403] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/25/2013] [Indexed: 11/19/2022] Open
Abstract
Chromosome conformation capture (3C) and derivative experimental procedures are used to estimate the spatial proximity between different genomic elements, thus providing information about the 3D organization of genomic domains and whole genomes within the nucleus. All C-methods are based on the proximity ligation-the preferential ligation of joined DNA fragments obtained upon restriction enzyme digestion of in vivo cross-linked chromatin. Here, using the mouse beta-globin genes in erythroid cells as a model, we estimated the actual frequencies of ligation between the fragments bearing the promoter of the major beta-globin gene and its distant enhancers and showed that the number of ligation products produced does not exceed 1% of all fragments subjected to the ligation. Although this low yield of 3C ligation products may be explained entirely by technical issues, it may as well reflect a low frequency of interaction between DNA regulatory elements in vivo.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.
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198
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Abstract
We present a strategy to examine the chromatin conformation of individual loci in specific cell types during Drosophila embryogenesis. Regulatory DNA is tagged with binding sites (lacO) for LacI, which is used to immunoprecipitate the tagged chromatin from specific cell types. We applied this approach to Distalless (Dll), a gene required for limb development in Drosophila. We show that the local chromatin conformation at Dll depends on the cell type: in cells that express Dll, the 5' regulatory region is in close proximity to the Dll promoter. In Dll-nonexpressing cells this DNA is in a more extended configuration. In addition, transcriptional activators and repressors are bound to Dll regulatory DNA in a cell type-specific manner. The pattern of binding by GAGA factor and the variant histone H2Av suggest that they play a role in the regulation of Dll chromatin conformation in expressing and nonexpressing cell types, respectively.
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199
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Krijger PHL, de Laat W. Identical cells with different 3D genomes; cause and consequences? Curr Opin Genet Dev 2013; 23:191-6. [PMID: 23415810 DOI: 10.1016/j.gde.2012.12.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
Abstract
The mammalian genome is folded into topological domains, chromosomal units that probably serve to spatially accommodate enhancer-promoter interactions and control gene expression levels across cell populations. Longer-range contacts beyond topological domains are also formed, but only in subpopulations of cells. We propose a model (dog-on-a-lead model) to understand the principles behind and consequences of cell-specific remote DNA contacts and speculate that cell-specific genome topologies can cause variegated gene expression among otherwise identical cells.
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Affiliation(s)
- Peter H L Krijger
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Urecht, The Netherlands
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200
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Regulatory elements associated with paternally-expressed genes in the imprinted murine Angelman/Prader-Willi syndrome domain. PLoS One 2013; 8:e52390. [PMID: 23390487 PMCID: PMC3563663 DOI: 10.1371/journal.pone.0052390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 11/13/2012] [Indexed: 11/19/2022] Open
Abstract
The Angelman/Prader-Willi syndrome (AS/PWS) domain contains at least 8 imprinted genes regulated by a bipartite imprinting center (IC) associated with the SNRPN gene. One component of the IC, the PWS-IC, governs the paternal epigenotype and expression of paternal genes. The mechanisms by which imprinting and expression of paternal genes within the AS/PWS domain – such as MKRN3 and NDN – are regulated by the PWS-IC are unclear. The syntenic region in the mouse is organized and imprinted similarly to the human domain with the murine PWS-IC defined by a 6 kb interval within the Snrpn locus that includes the promoter. To identify regulatory elements that may mediate PWS-IC function, we mapped the location and allele-specificity of DNase I hypersensitive (DH) sites within the PWS-IC in brain cells, then identified transcription factor binding sites within a subset of these DH sites. Six major paternal-specific DH sites were detected in the Snrpn gene, five of which map within the 6 kb PWS-IC. We postulate these five DH sites represent functional components of the murine PWS-IC. Analysis of transcription factor binding within multiple DH sites detected nuclear respiratory factors (NRF's) and YY1 specifically on the paternal allele. NRF's and YY1 were also detected in the paternal promoter region of the murine Mrkn3 and Ndn genes. These results suggest that NRF's and YY1 may facilitate PWS-IC function and coordinately regulate expression of paternal genes. The presence of NRF's also suggests a link between transcriptional regulation within the AS/PWS domain and regulation of respiration. 3C analyses indicated Mkrn3 lies in close proximity to the PWS-IC on the paternal chromosome, evidence that the PWS-IC functions by allele-specific interaction with its distal target genes. This could occur by allele-specific co-localization of the PWS-IC and its target genes to transcription factories containing NRF's and YY1.
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