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H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions. Nat Commun 2021; 12:719. [PMID: 33514712 PMCID: PMC7846766 DOI: 10.1038/s41467-021-20940-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/04/2021] [Indexed: 12/29/2022] Open
Abstract
The mechanisms underlying gene repression and silencers are poorly understood. Here we investigate the hypothesis that H3K27me3-rich regions of the genome, defined from clusters of H3K27me3 peaks, may be used to identify silencers that can regulate gene expression via proximity or looping. We find that H3K27me3-rich regions are associated with chromatin interactions and interact preferentially with each other. H3K27me3-rich regions component removal at interaction anchors by CRISPR leads to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. Cells with H3K27me3-rich regions knockout also show changes in phenotype associated with cell identity, and altered xenograft tumor growth. Finally, we observe that H3K27me3-rich regions-associated genes and long-range chromatin interactions are susceptible to H3K27me3 depletion. Our results characterize H3K27me3-rich regions and their mechanisms of functioning via looping.
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2
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Weizman E, Levy O. The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia. Commun Biol 2019; 2:282. [PMID: 31396562 PMCID: PMC6677750 DOI: 10.1038/s42003-019-0543-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Extreme weather events frequency and scale are altered due to climate change. Symbiosis between corals and their endosymbiotic-dinoflagellates (Symbiodinium) is susceptible to these events and can lead to what is known as bleaching. However, there is evidence for coral adaptive plasticity in the role of epigenetic that have acclimated to high-temperature environments. We have implemented ATAC-seq and RNA-seq to study the cnidarian-dinoflagellate model Exaptasia pallida (Aiptasia) and expose the role of chromatin-dynamics in response to thermal-stress. We have identified 1309 genomic sites that change their accessibility in response to thermal changes. Moreover, apo-symbiotic Aiptasia accessible sites were enriched with NFAT, ATF4, GATA3, SOX14, and PAX3 motifs and expressed genes related to immunological pathways. Symbiotic Aiptasia accessible sites were enriched with NKx3-1, HNF4A, IRF4 motifs and expressed genes related to oxidative-stress pathways. Our work opens a new path towards understanding thermal-stress gene regulation in association with gene activity and chromatin-dynamics.
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Affiliation(s)
- Eviatar Weizman
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
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3
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Matsushima Y, Sakamoto N, Awazu A. Insulator Activities of Nucleosome-Excluding DNA Sequences without Bound Chromatin Looping Proteins. J Phys Chem B 2019; 123:1035-1043. [DOI: 10.1021/acs.jpcb.8b10518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yuki Matsushima
- Department of Mathematical and Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Naoaki Sakamoto
- Department of Mathematical and Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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4
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Dense neural networks for predicting chromatin conformation. BMC Bioinformatics 2018; 19:372. [PMID: 30314429 PMCID: PMC6186068 DOI: 10.1186/s12859-018-2286-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022] Open
Abstract
Background DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how the DNA will fold given a distribution of bound factors, here viewed as a type of sequence, is currently an unsolved problem and several heterogeneous polymer models have shown that many features of the measured structure can be reproduced from simulations. However a model that determines the optimal connection between sequence and structure and that can rapidly assess the effects of varying either one is still lacking. Results Here we train a dense neural network to solve for the local folding of chromatin, connecting structure, represented as a contact map, to a sequence of bound chromatin factors. The network includes a convolutional filter that compresses the large number of bound chromatin factors into a single 1D sequence representation that is optimized for predicting structure. We also train a network to solve the inverse problem, namely given only structural information in the form of a contact map, predict the likely sequence of chromatin states that generated it. Conclusions By carrying out sensitivity analysis on both networks, we are able to highlight the importance of chromatin contexts and neighborhoods for regulating long-range contacts, along with critical alterations that affect contact formation. Our analysis shows that the networks have learned physical insights that are informative and intuitive about this complex polymer problem. Electronic supplementary material The online version of this article (10.1186/s12859-018-2286-z) contains supplementary material, which is available to authorized users.
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5
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Farré P, Emberly E. A maximum-entropy model for predicting chromatin contacts. PLoS Comput Biol 2018; 14:e1005956. [PMID: 29401453 PMCID: PMC5814105 DOI: 10.1371/journal.pcbi.1005956] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/15/2018] [Accepted: 01/04/2018] [Indexed: 11/19/2022] Open
Abstract
The packaging of DNA inside a nucleus shows complex structure stabilized by a host of DNA-bound factors. Both the distribution of these factors and the contacts between different genomic locations of the DNA can now be measured on a genome-wide scale. This has advanced the development of models aimed at predicting the conformation of DNA given only the locations of bound factors-the chromatin folding problem. Here we present a maximum-entropy model that is able to predict a contact map representation of structure given a sequence of bound factors. Non-local effects due to the sequence neighborhood around contacting sites are found to be important for making accurate predictions. Lastly, we show that the model can be used to infer a sequence of bound factors given only a measurement of structure. This opens up the possibility for efficiently predicting sequence regions that may play a role in generating cell-type specific structural differences.
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Affiliation(s)
- Pau Farré
- Department of Physics, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, Burnaby, BC V5A1S6, Canada
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6
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Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Towards quantitative analysis of gene regulation by enhancers. Epigenomics 2017; 9:1219-1231. [PMID: 28799793 DOI: 10.2217/epi-2017-0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
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Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Stefjord Todolli
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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7
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Abstract
Chromosomes are folded into cells in a nonrandom fashion, with particular genetic loci occupying distinct spatial regions. This observation raises the question of whether the spatial organization of a chromosome governs its functions, such as recombination or transcription. We consider this general question in the specific context of mating-type switching in budding yeast, which is a model system for homologous recombination. Mating-type switching is induced by a DNA double-strand break (DSB) at the MAT locus on chromosome III, followed by homologous recombination between the cut MAT locus and one of two donor loci (HMLα and HMRa), located on the same chromosome. Previous studies have suggested that in MATa cells after the DSB is induced chromosome III undergoes refolding, which directs the MAT locus to recombine with HMLα. Here, we propose a quantitative model of mating-type switching predicated on the assumption of DSB-induced chromosome refolding, which also takes into account the previously measured stochastic dynamics and polymer nature of yeast chromosomes. Using quantitative fluorescence microscopy, we measure changes in the distance between the donor (HMLα) and MAT loci after the DSB and find agreement with the theory. Predictions of the theory also agree with measurements of changes in the use of HMLα as the donor, when we perturb the refolding of chromosome III. These results establish refolding of yeast chromosome III as a key driving force in MAT switching and provide an example of a cell regulating the spatial organization of its chromosome so as to direct homology search during recombination.
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8
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Haberle V, Lenhard B. Promoter architectures and developmental gene regulation. Semin Cell Dev Biol 2016; 57:11-23. [PMID: 26783721 DOI: 10.1016/j.semcdb.2016.01.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 01/03/2023]
Abstract
Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation. Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development. This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.
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Affiliation(s)
- Vanja Haberle
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK; Department of Biology, University of Bergen, Thormøhlensgate 53A, N-5008 Bergen, Norway
| | - Boris Lenhard
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.
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9
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Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res 2015; 26:70-84. [PMID: 26518482 PMCID: PMC4691752 DOI: 10.1101/gr.196006.115] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/26/2015] [Indexed: 01/06/2023]
Abstract
Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina E Khrameeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia; Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia
| | | | - Ilya M Flyamer
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Pavel Kos
- Physics Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Mikhaleva
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, RAS, 123182 Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, RAS, 123182 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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10
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Imakaev MV, Fudenberg G, Mirny LA. Modeling chromosomes: Beyond pretty pictures. FEBS Lett 2015; 589:3031-6. [PMID: 26364723 DOI: 10.1016/j.febslet.2015.09.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/03/2015] [Indexed: 10/23/2022]
Abstract
Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data-driven ensembles, and two classes of de novo models: structural ensembles and mechanistic ensembles. Finally, we highlight specific questions mechanistic ensembles can address.
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Affiliation(s)
- Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data. BMC Bioinformatics 2015; 16:171. [PMID: 26001583 PMCID: PMC4492175 DOI: 10.1186/s12859-015-0584-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
Background A variety of DNA binding proteins are involved in regulating and shaping the packing of chromatin. They aid the formation of loops in the DNA that function to isolate different structural domains. A recent experimental technique, Hi-C, provides a method for determining the frequency of such looping between all distant parts of the genome. Given that the binding locations of many chromatin associated proteins have also been measured, it has been possible to make estimates for their influence on the long-range interactions as measured by Hi-C. However, a challenge in this analysis is the predominance of non-specific contacts that mask out the specific interactions of interest. Results We show that transforming the Hi-C contact frequencies into free energies gives a natural method for separating out the distance dependent non-specific interactions. In particular we apply Principal Component Analysis (PCA) to the transformed free energy matrix to identify the dominant modes of interaction. PCA identifies systematic effects as well as high frequency spatial noise in the Hi-C data which can be filtered out. Thus it can be used as a data driven approach for normalizing Hi-C data. We assess this PCA based normalization approach, along with several other normalization schemes, by fitting the transformed Hi-C data using a pairwise interaction model that takes as input the known locations of bound chromatin factors. The result of fitting is a set of predictions for the coupling energies between the various chromatin factors and their effect on the energetics of looping. We show that the quality of the fit can be used as a means to determine how much PCA filtering should be applied to the Hi-C data. Conclusions We find that the different normalizations of the Hi-C data vary in the quality of fit to the pairwise interaction model. PCA filtering can improve the fit, and the predicted coupling energies lead to biologically meaningful insights for how various chromatin bound factors influence the stability of DNA loops in chromatin. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0584-2) contains supplementary material, which is available to authorized users.
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12
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Cubeñas-Potts C, Corces VG. Architectural proteins, transcription, and the three-dimensional organization of the genome. FEBS Lett 2015; 589:2923-30. [PMID: 26008126 DOI: 10.1016/j.febslet.2015.05.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/07/2015] [Accepted: 05/09/2015] [Indexed: 12/20/2022]
Abstract
Architectural proteins mediate interactions between distant sequences in the genome. Two well-characterized functions of architectural protein interactions include the tethering of enhancers to promoters and bringing together Polycomb-containing sites to facilitate silencing. The nature of which sequences interact genome-wide appears to be determined by the orientation of the architectural protein binding sites as well as the number and identity of architectural proteins present. Ultimately, long range chromatin interactions result in the formation of loops within the chromatin fiber. In this review, we discuss data suggesting that architectural proteins mediate long range chromatin interactions that both facilitate and hinder neighboring interactions, compartmentalizing the genome into regions of highly interacting chromatin domains.
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Affiliation(s)
- Caelin Cubeñas-Potts
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, USA.
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13
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Doyle B, Fudenberg G, Imakaev M, Mirny LA. Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput Biol 2014; 10:e1003867. [PMID: 25340767 PMCID: PMC4207457 DOI: 10.1371/journal.pcbi.1003867] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/20/2014] [Indexed: 11/29/2022] Open
Abstract
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site. In eukaryotes, enhancers directly contact promoters over large genomic distances to regulate gene expression. Characterizing the principles underlying these long-range enhancer-promoter contacts is crucial for a full understanding of gene expression. Recent experimental mapping of chromosomal interactions by the Hi-C method shows an intricate network of local looping interactions surrounding enhancers and promoters. We model a region of chromatin fiber as a long polymer and study how the formation of loops between certain regulatory elements can insulate or facilitate enhancer-promoter interactions. We find 2–5 fold insulation or facilitation, depending on the location of looping elements relative to an enhancer-promoter pair. These effects originate from the polymer nature of chromatin, without requiring additional mechanisms beyond the formation of a chromatin loop. Our findings suggest that loop-mediated gene regulation by elements in the vicinity of an enhancer-promoter pair can be understood as an allosteric effect. This highlights the complex effects that local chromatin organization can have on gene regulation.
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Affiliation(s)
- Boryana Doyle
- Program for Research in Mathematics, Engineering and Science for High School Students, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Undergraduate Research Opportunities Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Maxim Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Leonid A. Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, United States of America
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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14
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Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells. Proc Natl Acad Sci U S A 2014; 111:E4449-57. [PMID: 25288735 DOI: 10.1073/pnas.1410764111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic gene regulation involves complex patterns of long-range DNA-looping interactions between enhancers and promoters, but how these specific interactions are achieved is poorly understood. Models that posit other DNA loops--that aid or inhibit enhancer-promoter contact--are difficult to test or quantitate rigorously in eukaryotic cells. Here, we use the well-characterized DNA-looping proteins Lac repressor and phage λ CI to measure interactions between pairs of long DNA loops in E. coli cells in the three possible topological arrangements. We find that side-by-side loops do not affect each other. Nested loops assist each other's formation consistent with their distance-shortening effect. In contrast, alternating loops, where one looping element is placed within the other DNA loop, inhibit each other's formation, thus providing clear support for the loop domain model for insulation. Modeling shows that combining loop assistance and loop interference can provide strong specificity in long-range interactions.
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15
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Vogelmann J, Le Gall A, Dejardin S, Allemand F, Gamot A, Labesse G, Cuvier O, Nègre N, Cohen-Gonsaud M, Margeat E, Nöllmann M. Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila genome. PLoS Genet 2014; 10:e1004544. [PMID: 25165871 PMCID: PMC4148193 DOI: 10.1371/journal.pgen.1004544] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 06/17/2014] [Indexed: 11/18/2022] Open
Abstract
Chromatin insulators are genetic elements implicated in the organization of chromatin and the regulation of transcription. In Drosophila, different insulator types were characterized by their locus-specific composition of insulator proteins and co-factors. Insulators mediate specific long-range DNA contacts required for the three dimensional organization of the interphase nucleus and for transcription regulation, but the mechanisms underlying the formation of these contacts is currently unknown. Here, we investigate the molecular associations between different components of insulator complexes (BEAF32, CP190 and Chromator) by biochemical and biophysical means, and develop a novel single-molecule assay to determine what factors are necessary and essential for the formation of long-range DNA interactions. We show that BEAF32 is able to bind DNA specifically and with high affinity, but not to bridge long-range interactions (LRI). In contrast, we show that CP190 and Chromator are able to mediate LRI between specifically-bound BEAF32 nucleoprotein complexes in vitro. This ability of CP190 and Chromator to establish LRI requires specific contacts between BEAF32 and their C-terminal domains, and dimerization through their N-terminal domains. In particular, the BTB/POZ domains of CP190 form a strict homodimer, and its C-terminal domain interacts with several insulator binding proteins. We propose a general model for insulator function in which BEAF32/dCTCF/Su(HW) provide DNA specificity (first layer proteins) whereas CP190/Chromator are responsible for the physical interactions required for long-range contacts (second layer). This network of organized, multi-layer interactions could explain the different activities of insulators as chromatin barriers, enhancer blockers, and transcriptional regulators, and suggest a general mechanism for how insulators may shape the organization of higher-order chromatin during cell division.
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Affiliation(s)
- Jutta Vogelmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Antoine Le Gall
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Stephanie Dejardin
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Frederic Allemand
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Adrien Gamot
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université de Toulouse, Toulouse; France
| | - Gilles Labesse
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Olivier Cuvier
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université de Toulouse, Toulouse; France
| | - Nicolas Nègre
- Laboratoire Diversité, Génomes & Interactions Microorganismes-Insectes, INRA UMR1333, Université de Montpellier 2, Montpellier, France
| | - Martin Cohen-Gonsaud
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Emmanuel Margeat
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Marcelo Nöllmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
- * E-mail:
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16
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Jost D, Carrivain P, Cavalli G, Vaillant C. Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains. Nucleic Acids Res 2014; 42:9553-61. [PMID: 25092923 PMCID: PMC4150797 DOI: 10.1093/nar/gku698] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin folding and epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation and its relation to epigenetics.
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Affiliation(s)
- Daniel Jost
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Pascal Carrivain
- Institute of Human Genetics, CNRS UPR 1142, Montpellier 34000, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR 1142, Montpellier 34000, France
| | - Cédric Vaillant
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
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17
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Maksimenko O, Kyrchanova O, Bonchuk A, Stakhov V, Parshikov A, Georgiev P. Highly conserved ENY2/Sus1 protein binds to Drosophila CTCF and is required for barrier activity. Epigenetics 2014; 9:1261-70. [PMID: 25147918 DOI: 10.4161/epi.32086] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chromatin insulators affect interactions between promoters and enhancers/silencers and function as barriers for the spreading of repressive chromatin. Drosophila insulator protein dCTCF marks active promoters and boundaries of many histone H3K27 trimethylation domains associated with repressed chromatin. In particular, dCTCF binds to such boundaries between the parasegment-specific regulatory domains of the Bithorax complex. Here we demonstrate that the evolutionarily conserved protein ENY2 is recruited to the zinc-finger domain of dCTCF and is required for the barrier activity of dCTCF-dependent insulators in transgenic lines. Inactivation of ENY2 by RNAi in BG3 cells leads to the spreading of H3K27 trimethylation and Pc protein at several dCTCF boundaries. The results suggest that evolutionarily conserved ENY2 is responsible for barrier activity mediated by the dCTCF protein.
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Affiliation(s)
- Oksana Maksimenko
- Laboratory of Gene Expression Regulation in Development; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Olga Kyrchanova
- Group of Transcriptional Regulation; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Artem Bonchuk
- Group of Transcriptional Regulation; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Viacheslav Stakhov
- Laboratory of Gene Expression Regulation in Development; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Alexander Parshikov
- Department of the Control of Genetic Processes; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
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18
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Lhoumaud P, Hennion M, Gamot A, Cuddapah S, Queille S, Liang J, Micas G, Morillon P, Urbach S, Bouchez O, Severac D, Emberly E, Zhao K, Cuvier O. Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes. EMBO J 2014; 33:1599-613. [PMID: 24916307 DOI: 10.15252/embj.201385965] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chromosomal domains in Drosophila are marked by the insulator-binding proteins (IBPs) dCTCF/Beaf32 and cofactors that participate in regulating long-range interactions. Chromosomal borders are further enriched in specific histone modifications, yet the role of histone modifiers and nucleosome dynamics in this context remains largely unknown. Here, we show that IBP depletion impairs nucleosome dynamics specifically at the promoters and coding sequence of genes flanked by IBP binding sites. Biochemical purification identifies the H3K36 histone methyltransferase NSD/dMes-4 as a novel IBP cofactor, which specifically co-regulates the chromatin accessibility of hundreds of genes flanked by dCTCF/Beaf32. NSD/dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-dependent H3K36 trimethylation, nucleosome positioning, and RNA splicing. Our results unveil a model for how IBPs regulate nucleosome dynamics and gene expression through NSD/dMes-4, which may regulate H3K27me3 spreading. Our data uncover how IBPs dynamically regulate chromatin organization depending on distinct cofactors.
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Affiliation(s)
- Priscillia Lhoumaud
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Magali Hennion
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Adrien Gamot
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Suresh Cuddapah
- Systems Biology Center, National Heart, Lung and Blood Institute National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sophie Queille
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Jun Liang
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Gael Micas
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Pauline Morillon
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Serge Urbach
- Mass-Spectrometry Facility, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Olivier Bouchez
- UMR444-Laboratoire de Génétique Cellulaire & GeT-PlaGe, INRA Genotoul, Auzeville, Toulouse, France
| | - Dany Severac
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Eldon Emberly
- Physics Department, Simon Fraser University (SFU), Burnaby, BC, Canada
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute National Institutes of Health (NIH), Bethesda, MD, USA
| | - Olivier Cuvier
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
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19
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Longpre KM, Kinstlinger NS, Mead EA, Wang Y, Thekkumthala AP, Carreno KA, Hot A, Keefer JM, Tully L, Katz LS, Pietrzykowski AZ. Seasonal variation of urinary microRNA expression in male goats (Capra hircus) as assessed by next generation sequencing. Gen Comp Endocrinol 2014; 199:1-15. [PMID: 24457251 DOI: 10.1016/j.ygcen.2014.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 12/03/2013] [Accepted: 01/08/2014] [Indexed: 01/09/2023]
Abstract
Testosterone plays a key role in preparation of a male domesticated goat (Capra hircus) to breeding season including changes in the urogenital tract of a male goat (buck). microRNAs are important regulators of cellular metabolism, differentiation and function. They are powerful intermediaries of hormonal activity in the body, including the urogenital tract. We investigated seasonal changes in expression of microRNAs in goat buck urine and their potential consequences using next generation sequencing (microRNA-Seq). We determined the location of each microRNA gene in the goat genome. Testosterone was measured by radioimmunoassay and the androgen receptor binding sites (ARBS) in the promoters of the microRNA genes were determined by MatInspector. The overall impact of regulated microRNAs on cellular physiology was assessed by mirPath. We observed high testosterone levels during the breeding season and changes in the expression of forty microRNAs. Nineteen microRNAs were upregulated, while twenty-one were downregulated. We identified several ARBS in the promoters of regulated microRNAs. Notably, the mostly inhibited microRNA, miR-1246, has a unique set of several gene copy variants associated with a cluster of androgen receptor binding sites. Concomitant changes in regulated microRNA expression could promote transcription, proliferation and differentiation of urogenital tract cells. Together, these findings indicate that in a domesticated goat (Capra hircus), there are specific changes in the microRNA expression profile in buck urine during breeding season, which could be attributable to high testosterone levels during breeding, and could help in preparation of the urogenital tract for high metabolic demands of that season.
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Affiliation(s)
- Kristy M Longpre
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Noah S Kinstlinger
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Edward A Mead
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Yongping Wang
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Austin P Thekkumthala
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Katherine A Carreno
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Azra Hot
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Jennifer M Keefer
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Luke Tully
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Larry S Katz
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA
| | - Andrzej Z Pietrzykowski
- Rutgers University, Department of Animal Sciences, 67 Poultry Farm Lane, New Brunswick, NJ 08901, USA.
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20
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Kyrchanova O, Georgiev P. Chromatin insulators and long-distance interactions in Drosophila. FEBS Lett 2013; 588:8-14. [PMID: 24211836 DOI: 10.1016/j.febslet.2013.10.039] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 10/25/2013] [Accepted: 10/25/2013] [Indexed: 12/31/2022]
Abstract
Data on long-distance enhancer-mediated activation of gene promoters and complex regulation of gene expression by multiple enhancers have prompted the hypothesis that the action of enhancers is restricted by insulators. Studies with transgenic lines have shown that insulators are responsible for establishing proper local interactions between regulatory elements, but not for defining independent transcriptional domains that restrict the activity of enhancers. It has also become apparent that enhancer blocking is only one of several functional activities of known insulator proteins, which also contribute to the organization of chromosome architecture and the integrity of regulatory elements.
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Affiliation(s)
- Olga Kyrchanova
- Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia.
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21
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Effective blocking of the white enhancer requires cooperation between two main mechanisms suggested for the insulator function. PLoS Genet 2013; 9:e1003606. [PMID: 23861668 PMCID: PMC3701704 DOI: 10.1371/journal.pgen.1003606] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 05/20/2013] [Indexed: 11/24/2022] Open
Abstract
Chromatin insulators block the action of transcriptional enhancers when interposed between an enhancer and a promoter. In this study, we examined the role of chromatin loops formed by two unrelated insulators, gypsy and Fab-7, in their enhancer-blocking activity. To test for this activity, we selected the white reporter gene that is activated by the eye-specific enhancer. The results showed that one copy of the gypsy or Fab-7 insulator failed to block the eye enhancer in most of genomic sites, whereas a chromatin loop formed by two gypsy insulators flanking either the eye enhancer or the reporter completely blocked white stimulation by the enhancer. However, strong enhancer blocking was achieved due not only to chromatin loop formation but also to the direct interaction of the gypsy insulator with the eye enhancer, which was confirmed by the 3C assay. In particular, it was observed that Mod(mdg4)-67.2, a component of the gypsy insulator, interacted with the Zeste protein, which is critical for the eye enhancer–white promoter communication. These results suggest that efficient enhancer blocking depends on the combination of two factors: chromatin loop formation by paired insulators, which generates physical constraints for enhancer–promoter communication, and the direct interaction of proteins recruited to an insulator and to the enhancer–promoter pair. The mechanism underlying enhancer blocking by insulators is unclear. Current models suggest that insulator proteins block enhancers either by formation of chromatin loops or by direct interaction with protein complexes bound to the enhancers and promoters. Here, we tested the role of a chromatin loop in blocking the activity of two Drosophila insulators, gypsy and Fab-7. Both insulators failed to effectively block the interaction between the eye enhancer and the white promoter at most of genomic sites. Insertion of an additional gypsy copy either upstream of the eye enhancer or downstream from the white gene led to complete blocking of the enhancer–promoter communication. In contrast, flanking of the eye enhancer by Fab-7 insulators only weakly improved enhancer blocking. Such a difference in enhancer blocking may be explained by finding that Mod(mdg4)-67.2, a component of gypsy insulator, directly interacts with the Zeste protein, which is critical for enhancer–promoter communication in the white gene.
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22
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Kyrchanova O, Leman D, Parshikov A, Fedotova A, Studitsky V, Maksimenko O, Georgiev P. New properties of Drosophila scs and scs' insulators. PLoS One 2013; 8:e62690. [PMID: 23638134 PMCID: PMC3634774 DOI: 10.1371/journal.pone.0062690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/25/2013] [Indexed: 11/18/2022] Open
Abstract
Insulators are defined as a class of regulatory elements that delimit independent transcriptional domains within eukaryotic genomes. The first insulators to be identified were scs and scs', which flank the domain including two heat shock 70 genes. Zw5 and BEAF bind to scs and scs', respectively, and are responsible for the interaction between these insulators. Using the regulatory regions of yellow and white reporter genes, we have found that the interaction between scs and scs' improves the enhancer-blocking activity of the weak scs' insulator. The sequences of scs and scs' insulators include the promoters of genes that are strongly active in S2 cells but not in the eyes, in which the enhancer-blocking activity of these insulators has been extensively examined. Only the promoter of the Cad87A gene located at the end of the scs insulator drives white expression in the eyes, and the white enhancer can slightly stimulate this promoter. The scs insulator contains polyadenylation signals that may be important for preventing transcription through the insulator. As shown previously, scs and scs' can insulate transcription of the white transgene from the enhancing effects of the surrounding genome, a phenomenon known as the chromosomal position effect (CPE). After analyzing many independent transgenic lines, we have concluded that transgenes carrying the scs insulator are rarely inserted into genomic regions that stimulate the white reporter expression in the eyes.
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Affiliation(s)
- Olga Kyrchanova
- Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Leman
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Parshikov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Fedotova
- Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vasily Studitsky
- School of Biology, Moscow State University, Moscow, Russia
- Department of Pharmacology, UMDNJ–Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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23
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Abstract
Enhancers are regulatory DNA sequences that activate transcription over long distances. Recent studies revealed a widespread role of distant activation in eukaryotic gene regulation and in development of various human diseases, including cancer. Genomic and gene-targeted studies of enhancer action revealed novel mechanisms of transcriptional activation over a distance. They include formation of stable, inactive DNA-protein complexes at the enhancer and target promoter before activation, facilitated distant communication by looping of the spacer chromatin-covered DNA, and promoter activation by mechanisms that are different from classic recruiting. These studies suggest the similarity between the looping mechanisms involved in enhancer action on DNA in bacteria and in chromatin of higher organisms.
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24
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Junier I, Dale RK, Hou C, Képès F, Dean A. CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus. Nucleic Acids Res 2012; 40:7718-27. [PMID: 22705794 PMCID: PMC3439919 DOI: 10.1093/nar/gks536] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the three-dimensional folding of a 1 Mbp region of human chromosome 11 containing the β-globin genes by integrating looping interactions of the CCCTC-binding insulator protein CTCF determined comprehensively by chromosome conformation capture (3C) into a polymer model of chromatin. We find that CTCF-mediated cell type-specific interactions in erythroid cells are organized to favor contacts known to occur in vivo between the β-globin locus control region (LCR) and genes. In these cells, the modeled β-globin domain folds into a globule with the LCR and the active globin genes on the periphery. In contrast, in non-erythroid cells, the globule is less compact with few but dominant CTCF interactions driving the genes away from the LCR. This leads to a decrease in contact frequencies that can exceed 1000-fold depending on the stiffness of the chromatin and the exact position of the genes. Our findings show that an ensemble of CTCF contacts functionally affects spatial distances between control elements and target genes contributing to chromosomal organization required for transcription.
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Affiliation(s)
- Ivan Junier
- Epigenomics Project and institute of Systems and Synthetic Biology, Genopole®, CNRS, University of Evry, 5 rue Henri Desbrueres, Evry F-91030, Institute of Complex Systems, Paris, France.
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