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Bernués J, Izquierdo-Boulstridge A, Reina O, Castejón L, Fernández-Castañer E, Leal N, Guerrero-Pepinosa N, Bonet-Costa C, Vujatovic O, Climent-Cantó P, Azorín F. Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation. Nucleic Acids Res 2022; 50:9212-9225. [PMID: 36039761 PMCID: PMC9458452 DOI: 10.1093/nar/gkac716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 08/01/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Post-translational modifications (PTMs) of core histones are important epigenetic determinants that correlate with functional chromatin states. However, despite multiple linker histone H1s PTMs have been identified, little is known about their genomic distribution and contribution to the epigenetic regulation of chromatin. Here, we address this question in Drosophila that encodes a single somatic linker histone, dH1. We previously reported that dH1 is dimethylated at K27 (dH1K27me2). Here, we show that dH1K27me2 is a major PTM of Drosophila heterochromatin. At mitosis, dH1K27me2 accumulates at pericentromeric heterochromatin, while, in interphase, it is also detected at intercalary heterochromatin. ChIPseq experiments show that >98% of dH1K27me2 enriched regions map to heterochromatic repetitive DNA elements, including transposable elements, simple DNA repeats and satellite DNAs. Moreover, expression of a mutated dH1K27A form, which impairs dH1K27me2, alters heterochromatin organization, upregulates expression of heterochromatic transposable elements and results in the accumulation of RNA:DNA hybrids (R-loops) in heterochromatin, without affecting H3K9 methylation and HP1a binding. The pattern of dH1K27me2 is H3K9 methylation independent, as it is equally detected in flies carrying a H3K9R mutation, and is not affected by depletion of Su(var)3-9, HP1a or Su(var)4-20. Altogether these results suggest that dH1K27me2 contributes to heterochromatin organization independently of H3K9 methylation.
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Affiliation(s)
- Jordi Bernués
- To whom correspondence should be addressed. Tel: +34 934034960;
| | - Andrea Izquierdo-Boulstridge
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lucía Castejón
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elena Fernández-Castañer
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Núria Leal
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Nancy Guerrero-Pepinosa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carles Bonet-Costa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Olivera Vujatovic
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Paula Climent-Cantó
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
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2
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Xue J, Fu Y, Fan S, Cao X, Huang W, Zhang J, Zhao Y, Chen F. Branched immunochip-integrated pairwise barcoding amplification exploring the spatial proximity of two post-translational modifications in distinct cell subpopulations. Chem Commun (Camb) 2022; 58:10020-10023. [PMID: 35983894 DOI: 10.1039/d2cc03833a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Investigating the spatial information of post-translational modifications (PTMs) in distinct cell subpopulations represents a new direction toward single-cell analysis. The specific capture of cell populations combined with PTM spatial proximity visualization making it practically challenging. Here, we develop branched immunochip-integrated pairwise barcoding amplification, termed biChip-PBA, which can perform the respective capture of cell subpopulations expressing different membrane proteins and successive PBA-based fluorescence imaging of PTM proximities. Our work may provide multilevel information for new insights into epigenetic regulation and cell function.
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Affiliation(s)
- Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Youlan Fu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Siyue Fan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Wei Huang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
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3
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Cardoso AL, Venturelli NB, da Cruz I, de Sá Patroni FM, de Moraes D, de Oliveira RA, Benavente R, Martins C. Meiotic behavior, transmission and active genes of B chromosomes in the cichlid Astatotilapia latifasciata: new clues about nature, evolution and maintenance of accessory elements. Mol Genet Genomics 2022; 297:1151-1167. [PMID: 35704117 DOI: 10.1007/s00438-022-01911-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
Abstract
Supernumerary B chromosomes (Bs) are dispensable genetic elements widespread in eukaryotes and are poorly understood mainly in relation to mechanisms of maintenance and transmission. The cichlid Astatotilapia latifasciata can harbor Bs in a range of 0 (named B -) and 1-2 (named B +). The B in A. latifasciata is rich in several classes of repetitive DNA sequences, contains protein coding genes, and affects hosts in diverse ways, including sex-biased effects. To advance in the knowledge about the mechanisms of maintenance and transmission of B chromosomes in A. latifasciata, here, we studied the meiotic behavior in males and transmission rates of A. latifasciata B chromosome. We also analyzed structurally and functionally the predicted B chromosome copies of the cell cycle genes separin-like, tubb1-like and kif11-like. We identified in the meiotic structure relative to the B chromosome the presence of proteins associated with Synaptonemal Complex organization (SMC3, SYCP1 and SYCP3) and found that the B performs self-pairing. These data suggest that isochromosome formation was a step during B chromosome evolution and this element is in a stage of diversification of the two arms keeping the self-pairing behavior to protect the A chromosome complement of negative effects of recombination. Moreover, we observed no occurrence of B-drive and confirmed the presence of cell cycle genes copies in the B chromosome and their transcription in encephalon, muscle and gonads, which can indicates beneficial effects to hosts and contribute to B maintenance.
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Affiliation(s)
- Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Natália Bortholazzi Venturelli
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Irene da Cruz
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Fábio Malta de Sá Patroni
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Rogério Antonio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, Brazil
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil.
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4
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Lapaillerie D, Lelandais B, Mauro E, Lagadec F, Tumiotto C, Miskey C, Ferran G, Kuschner N, Calmels C, Métifiot M, Rooryck C, Ivics Z, Ruff M, Zimmer C, Lesbats P, Toutain J, Parissi V. Modulation of the intrinsic chromatin binding property of HIV-1 integrase by LEDGF/p75. Nucleic Acids Res 2021; 49:11241-11256. [PMID: 34634812 PMCID: PMC8565322 DOI: 10.1093/nar/gkab886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
The stable insertion of the retroviral genome into the host chromosomes requires the association between integration complexes and cellular chromatin via the interaction between retroviral integrase and the nucleosomal target DNA. This final association may involve the chromatin-binding properties of both the retroviral integrase and its cellular cofactor LEDGF/p75. To investigate this and better understand the LEDGF/p75-mediated chromatin tethering of HIV-1 integrase, we used a combination of biochemical and chromosome-binding assays. Our study revealed that retroviral integrase has an intrinsic ability to bind and recognize specific chromatin regions in metaphase even in the absence of its cofactor. Furthermore, this integrase chromatin-binding property was modulated by the interaction with its cofactor LEDGF/p75, which redirected the enzyme to alternative chromosome regions. We also better determined the chromatin features recognized by each partner alone or within the functional intasome, as well as the chronology of efficient LEDGF/p75-mediated targeting of HIV-1 integrase to chromatin. Our data support a new chromatin-binding function of integrase acting in concert with LEDGF/p75 for the optimal association with the nucleosomal substrate. This work also provides additional information about the behavior of retroviral integration complexes in metaphase chromatin and the mechanism of action of LEDGF/p75 in this specific context.
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Affiliation(s)
- Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Benoît Lelandais
- Imaging and modeling unit, Computational Biology Department, Institut Pasteur, Paris, France
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Floriane Lagadec
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Camille Tumiotto
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Csaba Miskey
- Paul-Ehrlich-Institute, division of medical biotechnology, Langen, Germany
| | | | | | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Mathieu Métifiot
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | | | - Zoltan Ivics
- Paul-Ehrlich-Institute, division of medical biotechnology, Langen, Germany
| | - Marc Ruff
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale intégrative, UDS, U596 INSERM, UMR7104, CNRS, Strasbourg, France
| | - Christophe Zimmer
- Imaging and modeling unit, Computational Biology Department, Institut Pasteur, Paris, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Jérôme Toutain
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
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5
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Halsall JA, Andrews S, Krueger F, Rutledge CE, Ficz G, Reik W, Turner BM. Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle. Sci Rep 2021; 11:3009. [PMID: 33542322 PMCID: PMC7862352 DOI: 10.1038/s41598-021-82539-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Chromatin configuration influences gene expression in eukaryotes at multiple levels, from individual nucleosomes to chromatin domains several Mb long. Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions, but how remains unclear. To explore this, we used ChIP-seq and two cell types, HeLa and lymphoblastoid (LCL), to define how changes in chromatin packaging through the cell cycle influence the distributions of three transcription-associated histone modifications, H3K9ac, H3K4me3 and H3K27me3. We show that chromosome regions (bands) of 10-50 Mb, detectable by immunofluorescence microscopy of metaphase (M) chromosomes, are also present in G1 and G2. They comprise 1-5 Mb sub-bands that differ between HeLa and LCL but remain consistent through the cell cycle. The same sub-bands are defined by H3K9ac and H3K4me3, while H3K27me3 spreads more widely. We found little change between cell cycle phases, whether compared by 5 Kb rolling windows or when analysis was restricted to functional elements such as transcription start sites and topologically associating domains. Only a small number of genes showed cell-cycle related changes: at genes encoding proteins involved in mitosis, H3K9 became highly acetylated in G2M, possibly because of ongoing transcription. In conclusion, modified histone isoforms H3K9ac, H3K4me3 and H3K27me3 exhibit a characteristic genomic distribution at resolutions of 1 Mb and below that differs between HeLa and lymphoblastoid cells but remains remarkably consistent through the cell cycle. We suggest that this cell-type-specific chromosomal bar-code is part of a homeostatic mechanism by which cells retain their characteristic gene expression patterns, and hence their identity, through multiple mitoses.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Simon Andrews
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Felix Krueger
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Charlotte E Rutledge
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Bryan M Turner
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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6
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Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
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7
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Bickmore WA. Patterns in the genome. Heredity (Edinb) 2019; 123:50-57. [PMID: 31189906 DOI: 10.1038/s41437-019-0220-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/17/2019] [Accepted: 03/20/2019] [Indexed: 12/23/2022] Open
Abstract
The human genome is not randomly organised, with respect to both the linear organisation of the DNA sequence along chromosomes and to the spatial organisation of chromosomes in the cell nucleus. Here I discuss how these patterns of sequence organisation were first discovered by molecular biologists and how they relate to the patterns revealed decades earlier by cytogeneticists and manifest as chromosome bands.
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Affiliation(s)
- Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH42XU, UK.
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8
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Heinz KS, Rapp A, Casas-Delucchi CS, Lehmkuhl A, Romero-Fernández I, Sánchez A, Krämer OH, Marchal JA, Cardoso MC. DNA replication dynamics of vole genome and its epigenetic regulation. Epigenetics Chromatin 2019; 12:18. [PMID: 30871586 PMCID: PMC6416958 DOI: 10.1186/s13072-019-0262-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/07/2019] [Indexed: 01/19/2023] Open
Abstract
Background The genome of some vole rodents exhibit large blocks of heterochromatin coupled to their sex chromosomes. The DNA composition and transcriptional activity of these heterochromatin blocks have been studied, but little is known about their DNA replication dynamics and epigenetic composition. Results Here, we show prominent epigenetic marks of the heterochromatic blocks in the giant sex chromosomes of female Microtus cabrerae cells. While the X chromosomes are hypoacetylated and cytosine hypomethylated, they are either enriched for macroH2A and H3K27me3 typical for facultative heterochromatin or for H3K9me3 and HP1 beta typical for constitutive heterochromatin. Using pulse-chase replication labeling and time-lapse microscopy, we found that the heterochromatic block enriched for macroH2A/H3K27me3 of the X chromosome is replicated during mid-S-phase, prior to the heterochromatic block enriched for H3K9me3/HP1 beta, which is replicated during late S-phase. To test whether histone acetylation level regulates its replication dynamics, we induced either global hyperacetylation by pharmacological inhibition or by targeting a histone acetyltransferase to the heterochromatic region of the X chromosomes. Our data reveal that histone acetylation level affects DNA replication dynamics of the sex chromosomes’ heterochromatin and leads to a global reduction in replication fork rate genome wide. Conclusions In conclusion, we mapped major epigenetic modifications controlling the structure of the sex chromosome-associated heterochromatin and demonstrated the occurrence of differences in the molecular mechanisms controlling the replication timing of the heterochromatic blocks at the sex chromosomes in female Microtus cabrerae cells. Furthermore, we highlighted a conserved role of histone acetylation level on replication dynamics across mammalian species. Electronic supplementary material The online version of this article (10.1186/s13072-019-0262-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathrin S Heinz
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | - Alexander Rapp
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | - Corella S Casas-Delucchi
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.,Chromosome Replication Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | | | - Antonio Sánchez
- Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Oliver H Krämer
- Institute of Toxicology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | | | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.
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9
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Del Rosario BC, Kriz AJ, Del Rosario AM, Anselmo A, Fry CJ, White FM, Sadreyev RI, Lee JT. Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition. eLife 2019; 8:e42341. [PMID: 30676316 PMCID: PMC6361588 DOI: 10.7554/elife.42341] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/23/2019] [Indexed: 01/05/2023] Open
Abstract
The zinc finger CCCTC-binding protein (CTCF) carries out many functions in the cell. Although previous studies sought to explain CTCF multivalency based on sequence composition of binding sites, few examined how CTCF post-translational modification (PTM) could contribute to function. Here, we performed CTCF mass spectrometry, identified a novel phosphorylation site at Serine 224 (Ser224-P), and demonstrate that phosphorylation is carried out by Polo-like kinase 1 (PLK1). CTCF Ser224-P is chromatin-associated, mapping to at least a subset of known CTCF sites. CTCF Ser224-P accumulates during the G2/M transition of the cell cycle and is enriched at pericentric regions. The phospho-obviation mutant, S224A, appeared normal. However, the phospho-mimic mutant, S224E, is detrimental to mouse embryonic stem cell colonies. While ploidy and chromatin architecture appear unaffected, S224E mutants differentially express hundreds of genes, including p53 and p21. We have thus identified a new CTCF PTM and provided evidence of biological function.
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Affiliation(s)
- Brian C Del Rosario
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Andrea J Kriz
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
| | - Amanda M Del Rosario
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeUnited States
| | - Anthony Anselmo
- Department of Molecular BiologyMassachusetts General HospitalBostonUnited States
| | | | - Forest M White
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeUnited States
| | - Ruslan I Sadreyev
- Department of Molecular BiologyMassachusetts General HospitalBostonUnited States
| | - Jeannie T Lee
- Department of Molecular BiologyHoward Hughes Medical Institute, Massachusetts General HospitalBostonUnited States
- Department of GeneticsHarvard Medical SchoolBostonUnited States
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10
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Xie J, Chen S, Xu W, Zhao Y, Zhang D. Origination and Function of Plant Pseudogenes. PLANT SIGNALING & BEHAVIOR 2019; 14:1625698. [PMID: 31161861 PMCID: PMC6619919 DOI: 10.1080/15592324.2019.1625698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pseudogenes, nonfunctional genomic sequences derived from functional protein-coding genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Studies on the evolution and functional aspects of plant pseudogenes are limited, despite their abundance in the plant genome. To date, most researches on pseudogenes focus on mammals. Here, we summarized current knowledge on pseudogenes including the historical and recent progress, analyzes their essential roles in gene regulation in hope of further stimulating researches in plant species for understanding gene regulation and evolution.
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Affiliation(s)
- Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Sisi Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Weijie Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Yiyang Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- CONTACT Deqiang Zhang National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
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Megadomains and superloops form dynamically but are dispensable for X-chromosome inactivation and gene escape. Nat Commun 2018; 9:5004. [PMID: 30479398 PMCID: PMC6258728 DOI: 10.1038/s41467-018-07446-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 10/24/2018] [Indexed: 01/17/2023] Open
Abstract
The mammalian inactive X-chromosome (Xi) is structurally distinct from all other chromosomes and serves as a model for how the 3D genome is organized. The Xi shows weakened topologically associated domains and is instead organized into megadomains and superloops directed by the noncoding loci, Dxz4 and Firre. Their functional significance is presently unclear, though one study suggests that they permit Xi genes to escape silencing. Here, we find that megadomains do not precede Xist expression or Xi gene silencing. Deleting Dxz4 disrupts the sharp megadomain border, whereas deleting Firre weakens intra-megadomain interactions. However, deleting Dxz4 and/or Firre has no impact on Xi silencing and gene escape. Nor does it affect Xi nuclear localization, stability, or H3K27 methylation. Additionally, ectopic integration of Dxz4 and Xist is not sufficient to form megadomains on autosomes. We conclude that Dxz4 and megadomains are dispensable for Xi silencing and escape from X-inactivation. The mammalian inactive X-chromosome (Xi) is organized into megadomains and superloops directed by the noncoding loci, Dxz4 and Firre. Here the authors provide evidence that megadomains do not precede Xist expression or Xi gene silencing, and suggest that Dxz4, Firre, and megadomains are dispensable for Xi silencing and escape from X-inactivation.
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12
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Szydlowski NA, Go JS, Hu YS. Chromatin imaging and new technologies for imaging the nucleome. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1442. [PMID: 30456928 DOI: 10.1002/wsbm.1442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulated emission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global and sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Nicole A Szydlowski
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Jane S Go
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
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13
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Yuan H, Zhang X, Zhang Q, Wang Y, Wang S, Li Y, Zhang Y, Jing J, Qiu J, Wang Z, Leng L. Comparative transcriptome profiles of Lindian chicken eyelids identify melanin genes controlling eyelid pigmentation. Br Poult Sci 2018; 60:15-22. [PMID: 30421986 DOI: 10.1080/00071668.2018.1544414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
1. During the long history of chicken domestication, eyelid colour, like skin colour and shank colour, has been one of the physical traits of Chinese indigenous chickens that influence consumer buying behaviour. In China, the Lindian chicken, which has coloured feathers, is renowned for the appetizing flavour of its meat and eggs, and its eyelid colours vary from deep (black) to light shades (light yellow). 2. To investigate genes involved in eyelid colour, the expression profiles of black and light-yellow eyelids of Lindian chickens were analysed with transcriptome sequencing. 3. A total of 13 466 genes were detected in the eyelids, among which 14 were differentially expressed. Among these differentially expressed genes (DEGs), three key genes, premelanosome protein (PMEL), dopachrome tautomerase (DCT), and tyrosinase (TYR), encoded proteins that positively regulate melanogenesis and melanin deposition. PMEL, DCT and TYR were expressed much more strongly in the black eyelids than in the light-yellow eyelids. A Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that tyrosine metabolism and melanogenesis genes were significantly enriched among these DEGs (corrected P < 0.05). 4. In conclusion, melanin may be one of the main factors involved in Lindian chicken eyelid colour. Furthermore, these results provide a valuable resource for the future study of the physical traits of Lindian chicken.
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Affiliation(s)
- H Yuan
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - X Zhang
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - Q Zhang
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - Y Wang
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - S Wang
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - Y Li
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - Y Zhang
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - J Jing
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - J Qiu
- a Key Laboratory of Chicken Genetics and Breeding and Rural Affairs , Ministry of Agriculture , Harbin , Heilongjiang , China
| | - Z Wang
- b Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province , Harbin , Heilongjiang , China
| | - L Leng
- c College of Animal Science and Technology , Northeast Agricultural University , Harbin , Heilongjiang , China
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14
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Liu D, Skomorovska Y, Song J, Bowler E, Harris R, Ravasz M, Bai S, Ayati M, Tamai K, Koyuturk M, Yuan X, Wang Z, Wang Y, Ewing R. ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1. Cancer Biol Ther 2018; 20:90-100. [PMID: 30148686 PMCID: PMC6292503 DOI: 10.1080/15384047.2018.1507256] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/22/2018] [Accepted: 07/29/2018] [Indexed: 12/23/2022] Open
Abstract
Background: Epithelial-to-mesenchymal transition (EMT) is a key step in the transformation of epithelial cells into migratory and invasive tumour cells. Intricate positive and negative regulatory processes regulate EMT. Many oncogenic signalling pathways can induce EMT, but the specific mechanisms of how this occurs, and how this process is controlled are not fully understood. Methods: RNA-Seq analysis, computational analysis of protein networks and large-scale cancer genomics datasets were used to identify ELF3 as a negative regulator of the expression of EMT markers. Western blotting coupled to siRNA as well as analysis of tumour/normal colorectal cancer panels was used to investigate the expression and function of ELF3. Results: RNA-Seq analysis of colorectal cancer cells expressing mutant and wild-type β-catenin and analysis of colorectal cancer cells expressing inducible mutant RAS showed that ELF3 expression is reduced in response to oncogenic signalling and antagonizes Wnt and RAS oncogenic signalling pathways. Analysis of gene-expression patterns across The Cancer Genome Atlas (TCGA) and protein localization in colorectal cancer tumour panels showed that ELF3 expression is anti-correlated with β-catenin and markers of EMT and correlates with better clinical prognosis. Conclusions: ELF3 is a negative regulator of the EMT transcription factor (EMT-TF) ZEB1 through its function as an antagonist of oncogenic signalling.
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Affiliation(s)
- D Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Y Skomorovska
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - J Song
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - E Bowler
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - R Harris
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - M Ravasz
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Bai
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - M Ayati
- Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - K Tamai
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - M Koyuturk
- Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - X Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Z Wang
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Y Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - R.M. Ewing
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
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Zaidi SK, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS. Mitotic Gene Bookmarking: An Epigenetic Program to Maintain Normal and Cancer Phenotypes. Mol Cancer Res 2018; 16:1617-1624. [PMID: 30002192 DOI: 10.1158/1541-7786.mcr-18-0415] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/24/2018] [Accepted: 06/22/2018] [Indexed: 01/06/2023]
Abstract
Reconfiguration of nuclear structure and function during mitosis presents a significant challenge to resume the next cell cycle in the progeny cells without compromising structural and functional identity of the cells. Equally important is the requirement for cancer cells to retain the transformed phenotype, that is, unrestricted proliferative potential, suppression of cell phenotype, and activation of oncogenic pathways. Mitotic gene bookmarking retention of key regulatory proteins that include sequence-specific transcription factors, chromatin-modifying factors, and components of RNA Pol (RNAP) I and II regulatory machineries at gene loci on mitotic chromosomes plays key roles in coordinate control of cell phenotype, growth, and proliferation postmitotically. There is growing recognition that three distinct protein types, mechanistically, play obligatory roles in mitotic gene bookmarking: (i) Retention of phenotypic transcription factors on mitotic chromosomes is essential to sustain lineage commitment; (ii) Select chromatin modifiers and posttranslational histone modifications/variants retain competency of mitotic chromatin for gene reactivation as cells exit mitosis; and (iii) Functional components of RNAP I and II transcription complexes (e.g., UBF and TBP, respectively) are retained on genes poised for reactivation immediately following mitosis. Importantly, recent findings have identified oncogenes that are associated with target genes on mitotic chromosomes in cancer cells. The current review proposes that mitotic gene bookmarking is an extensively utilized epigenetic mechanism for stringent control of proliferation and identity in normal cells and hypothesizes that bookmarking plays a pivotal role in maintenance of tumor phenotypes, that is, unrestricted proliferation and compromised control of differentiation. Mol Cancer Res; 16(11); 1617-24. ©2018 AACR.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Jeffrey A Nickerson
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Anthony N Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont.
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16
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Raccaud M, Suter DM. Transcription factor retention on mitotic chromosomes: regulatory mechanisms and impact on cell fate decisions. FEBS Lett 2017; 592:878-887. [PMID: 28862742 DOI: 10.1002/1873-3468.12828] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/14/2017] [Accepted: 08/24/2017] [Indexed: 12/21/2022]
Abstract
During mitosis, gene transcription stops, and the bulk of DNA-binding proteins are excluded from condensed chromosomes. While most gene-specific transcription factors are largely evicted from mitotic chromosomes, a subset remains bound to specific and non-specific DNA sites. Here, we review the current knowledge on the mechanisms leading to the retention of a subset of transcription factors on mitotic chromosomes and discuss the implications in gene expression regulation and their potential as an epigenetic mechanism controlling stem cell self-renewal and differentiation.
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Affiliation(s)
- Mahé Raccaud
- UPSUTER, Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland
| | - David M Suter
- UPSUTER, Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland
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17
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Festuccia N, Gonzalez I, Navarro P. The Epigenetic Paradox of Pluripotent ES Cells. J Mol Biol 2016; 429:1476-1503. [PMID: 27988225 DOI: 10.1016/j.jmb.2016.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022]
Abstract
The propagation and maintenance of gene expression programs are at the foundation of the preservation of cell identity. A large and complex set of epigenetic mechanisms enables the long-term stability and inheritance of transcription states. A key property of authentic epigenetic regulation is being independent from the instructive signals used for its establishment. This makes epigenetic regulation, particularly epigenetic silencing, extremely robust and powerful to lock regulatory states and stabilise cell identity. In line with this, the establishment of epigenetic silencing during development restricts cell potency and maintains the cell fate choices made by transcription factors (TFs). However, how more immature cells that have not yet established their definitive fate maintain their transitory identity without compromising their responsiveness to signalling cues remains unclear. A paradigmatic example is provided by pluripotent embryonic stem (ES) cells derived from a transient population of cells of the blastocyst. Here, we argue that ES cells represent an interesting "epigenetic paradox": even though they are captured in a self-renewing state characterised by extremely efficient maintenance of their identity, which is a typical manifestation of robust epigenetic regulation, they seem not to heavily rely on classical epigenetic mechanisms. Indeed, self-renewal strictly depends on the TFs that previously instructed their undifferentiated identity and relies on a particular signalling-dependent chromatin state where repressive chromatin marks play minor roles. Although this "epigenetic paradox" may underlie their exquisite responsiveness to developmental cues, it suggests that alternative mechanisms to faithfully propagate gene regulatory states might be prevalent in ES cells.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France.
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18
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The loading of condensin in the context of chromatin. Curr Genet 2016; 63:577-589. [PMID: 27909798 DOI: 10.1007/s00294-016-0669-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 11/24/2016] [Accepted: 11/25/2016] [Indexed: 12/23/2022]
Abstract
The packaging of DNA into chromosomes is a ubiquitous process that enables living organisms to structure and transmit their genome accurately through cell divisions. In the three kingdoms of life, the architecture and dynamics of chromosomes rely upon ring-shaped SMC (Structural Maintenance of Chromosomes) condensin complexes. To understand how condensin rings organize chromosomes, it is essential to decipher how they associate with chromatin filaments. Here, we use recent evidence to discuss the role played by nucleosomes and transcription factors in the loading of condensin at transcribed genes. We propose a model whereby cis-acting features nestled in the promoters of active genes synergistically attract condensin rings and promote their association with DNA.
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19
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Wiersma M, Bussiere M, Halsall JA, Turan N, Slany R, Turner BM, Nightingale KP. Protein kinase Msk1 physically and functionally interacts with the KMT2A/MLL1 methyltransferase complex and contributes to the regulation of multiple target genes. Epigenetics Chromatin 2016; 9:52. [PMID: 27895715 PMCID: PMC5106815 DOI: 10.1186/s13072-016-0103-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET domain-catalysed methylation of H3K4. It is essential for normal embryonic development and haematopoiesis and frequently mutated in cancer. The catalytic properties and targeting of KMT2A/MLL1 depend on the proteins with which it complexes and the post-translational protein modifications which some of these proteins put in place, though detailed mechanisms remain unclear. RESULTS KMT2A/MLL1 (both native and FLAG-tagged) and Msk1 (RPS6KA5) co-immunoprecipitated in various cell types. KMT2A/MLL1 and Msk1 knockdown demonstrated that the great majority of genes whose activity changed on KTM2A/MLL1 knockdown, responded comparably to Msk1 knockdown, as did levels of H3K4 methylation and H3S10 phosphorylation at KTM2A target genes HoxA4, HoxA5. Knockdown experiments also showed that KMT2A/MLL1 is required for the genomic targeting of Msk1, but not vice versa. CONCLUSION The KMT2A/MLL1 complex is associated with, and functionally dependent upon, the kinase Msk1, part of the MAP kinase signalling pathway. We propose that Msk1-catalysed phosphorylation at H3 serines 10 and 28, supports H3K4 methylation by the KMT2A/MLL1 complex both by making H3 a more attractive substrate for its SET domain, and improving target gene accessibility by prevention of HP1- and Polycomb-mediated chromatin condensation.
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Affiliation(s)
- Maaike Wiersma
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Marianne Bussiere
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
- Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 22f, Box 2404, 3001 Louvain, Belgium
| | - John A. Halsall
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Nil Turan
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Robert Slany
- Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Bryan M. Turner
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Karl P. Nightingale
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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20
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Zheng D, Ye W, Song Q, Han F, Zhang T, Chen ZJ. Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton. PLANT PHYSIOLOGY 2016; 172:1760-1771. [PMID: 27637746 PMCID: PMC5100776 DOI: 10.1104/pp.16.01210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/12/2016] [Indexed: 05/06/2023]
Abstract
Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for analyzing individual genes. Here, we comparatively analyzed immunostained metaphase chromosomes and ChIP-seq of individual genes, which revealed a chromatin basis for biased homoeologous gene expression in polyploids. We examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homeologs as in the A homeologs. Consistent with the cytological observation, ChIP-seq analysis showed that more D homeologs with biased H3K4me3 levels than A homeologs with biased modifications correlated with the greater number of the genes with D-biased expression than that with A-biased expression in most homeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes, which correlate with known translocations and may affect the local chromatin structure and expression levels for the genes involved. This example of genome-wide histone modifications that determine expression bias of homeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species, including many important crops.
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Affiliation(s)
- Dewei Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (D.Z., W.Y., T.Z., Z.J.C.)
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas, Austin, Texas 78712 (Q.S., Z.J.C.); and
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (F.H.)
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (D.Z., W.Y., T.Z., Z.J.C.)
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas, Austin, Texas 78712 (Q.S., Z.J.C.); and
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (F.H.)
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (D.Z., W.Y., T.Z., Z.J.C.)
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas, Austin, Texas 78712 (Q.S., Z.J.C.); and
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (F.H.)
| | - Fangpu Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (D.Z., W.Y., T.Z., Z.J.C.)
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas, Austin, Texas 78712 (Q.S., Z.J.C.); and
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (F.H.)
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (D.Z., W.Y., T.Z., Z.J.C.)
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas, Austin, Texas 78712 (Q.S., Z.J.C.); and
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (F.H.)
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (D.Z., W.Y., T.Z., Z.J.C.);
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas, Austin, Texas 78712 (Q.S., Z.J.C.); and
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (F.H.)
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Making Sense of the Tangle: Insights into Chromatin Folding and Gene Regulation. Genes (Basel) 2016; 7:genes7100071. [PMID: 27669308 PMCID: PMC5083910 DOI: 10.3390/genes7100071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/10/2016] [Accepted: 09/07/2016] [Indexed: 01/03/2023] Open
Abstract
Proximity ligation assays such as circularized chromosome conformation capture and high-throughput chromosome capture assays have shed light on the structural organization of the interphase genome. Functional topologically associating domains (TADs) that constitute the building blocks of genomic organization are disrupted and reconstructed during the cell cycle. Epigenetic memory, as well as the sequence of chromosomes, regulate TAD reconstitution. Sub-TAD domains that are invariant across cell types have been identified, and contacts between these domains, rather than looping, are speculated to drive chromatin folding. Replication domains are established simultaneously with TADs during the cell cycle and the two correlate well in terms of characteristic features, such as lamin association and histone modifications. CCCTC-binding factor (CTCF) and cohesin cooperate across different cell types to regulate genes and genome organization. CTCF elements that demarcate TAD boundaries are commonly disrupted in cancer and promote oncogene activation. Chromatin looping facilitates interactions between distant promoters and enhancers, and the resulting enhanceosome complex promotes gene expression. Deciphering the chromatin tangle requires comprehensive integrative analyses of DNA- and protein-dependent factors that regulate genomic organization.
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22
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Davie JR, Xu W, Delcuve GP. Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing. Biochem Cell Biol 2016; 94:1-11. [DOI: 10.1139/bcb-2015-0065] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is often stated as a mark of transcriptionally active promoters. However, closer study of the positioning of H3K4me3 shows the mark locating primarily after the first exon at the 5′ splice site and overlapping with a CpG island in mammalian cells. There are several enzyme complexes that are involved in the placement of the H3K4me3 mark, including multiple protein complexes containing SETD1A, SETD1B, and MLL1 enzymes (writers). CXXC1, which is associated with SETD1A and SETD1B, target these enzymes to unmethylated CpG islands. Lysine demethylases (KDM5 family members, erasers) demethylate H3K4me3. The H3K4me3 mark is recognized by several proteins (readers), including lysine acetyltransferase complexes, chromatin remodelers, and RNA bound proteins involved in pre-mRNA splicing. Interestingly, attenuation of H3K4me3 impacts pre-mRNA splicing, and inhibition of pre-mRNA splicing attenuates H3K4me3.
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Affiliation(s)
- James R. Davie
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Wayne Xu
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Genevieve P. Delcuve
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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Domaschenz R, Livernois AM, Rao S, Ezaz T, Deakin JE. Immunofluorescent staining reveals hypermethylation of microchromosomes in the central bearded dragon, Pogona vitticeps. Mol Cytogenet 2015; 8:104. [PMID: 26719769 PMCID: PMC4696178 DOI: 10.1186/s13039-015-0208-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/18/2015] [Indexed: 11/18/2022] Open
Abstract
Background Studies of model organisms have demonstrated that DNA cytosine methylation and histone modifications are key regulators of gene expression in biological processes. Comparatively little is known about the presence and distribution of epigenetic marks in non-model amniotes such as non-avian reptiles whose genomes are typically packaged into chromosomes of distinct size classes. Studies of chicken karyotypes have associated the gene-richness and high GC content of microchromosomes with a distinct epigenetic landscape. To determine whether this is likely to be a common feature of amniote microchromosomes, we have analysed the distribution of epigenetic marks using immunofluorescence on metaphase chromosomes of the central bearded dragon (Pogona vitticeps). This study is the first to study the distribution of epigenetic marks on non-avian reptile chromosomes. Results We observed an enrichment of DNA cytosine methylation, active modifications H3K4me2 and H3K4me3, as well as the repressive mark H3K27me3 in telomeric regions on macro and microchromosomes. Microchromosomes were hypermethylated compared to macrochromosomes, as they are in chicken. However, differences between macro- and microchromosomes for histone modifications associated with actively transcribed or repressed DNA were either less distinct or not detectable. Conclusions Hypermethylation of microchromosomes compared to macrochromosomes is a shared feature between P. vitticeps and avian species. The lack of the clear distinction between macro- and microchromosome staining patterns for active and repressive histone modifications makes it difficult to determine at this stage whether microchrosome hypermethylation is correlated with greater gene density as it is in aves, or associated with the greater GC content of P. vitticeps microchromosomes compared to macrochromosomes.
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Affiliation(s)
- Renae Domaschenz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.,Present address: John Curtin School of Medical Research, The Australian National University, Canberra, ACT Australia
| | | | - Sudha Rao
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, ACT 2601 Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia
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Schellhaus AK, De Magistris P, Antonin W. Nuclear Reformation at the End of Mitosis. J Mol Biol 2015; 428:1962-85. [PMID: 26423234 DOI: 10.1016/j.jmb.2015.09.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 12/17/2022]
Abstract
Cells have developed highly sophisticated ways to accurately pass on their genetic information to the daughter cells. In animal cells, which undergo open mitosis, the nuclear envelope breaks down at the beginning of mitosis and the chromatin massively condenses to be captured and segregated by the mitotic spindle. These events have to be reverted in order to allow the reformation of a nucleus competent for DNA transcription and replication, as well as all other nuclear processes occurring in interphase. Here, we summarize our current knowledge of how, in animal cells, the highly compacted mitotic chromosomes are decondensed at the end of mitosis and how a nuclear envelope, including functional nuclear pore complexes, reassembles around these decondensing chromosomes.
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Affiliation(s)
| | - Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany.
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25
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Terrenoire E, Halsall JA, Turner BM. Immunolabelling of human metaphase chromosomes reveals the same banded distribution of histone H3 isoforms methylated at lysine 4 in primary lymphocytes and cultured cell lines. BMC Genet 2015; 16:44. [PMID: 25925961 PMCID: PMC4417270 DOI: 10.1186/s12863-015-0200-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/14/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Using metaphase spreads from human lymphoblastoid cell lines, we previously showed how immunofluorescence microscopy could define the distribution of histone modifications across metaphase chromosomes. We showed that different histone modifications gave consistent and clearly defined immunofluorescent banding patterns. However, it was not clear to what extent these higher level distributions were influenced by long-term growth in culture, or by the specific functional associations of individual histone modifications. RESULTS Metaphase chromosome spreads from human lymphocytes stimulated to grow in short-term culture, were immunostained with antibodies to histone H3 mono- or tri-methylated at lysine 4 (H3K4me1, H3K4me3). Chromosomes were identified on the basis of morphology and reverse DAPI (rDAPI) banding. Both antisera gave the same distinctive immunofluorescent staining pattern, with unstained heterochromatic regions and a banded distribution along the chromosome arms. Karyotypes were prepared, showing the reproducibility of banding between sister chromatids, homologue pairs and from one metaphase spread to another. At the light microscope level, we detect no difference between the banding patterns along chromosomes from primary lymphocytes and lymphoblastoid cell lines adapted to long-term growth in culture. CONCLUSIONS The distribution of H3K4me3 is the same across metaphase chromosomes from human primary lymphocytes and LCL, showing that higher level distribution is not altered by immortalization or long-term culture. The two modifications H3K4me1 (enriched in gene enhancer regions) and H3K4me3 (enriched in gene promoter regions) show the same distributions across human metaphase chromosomes, showing that functional differences do not necessarily cause modifications to differ in their higher-level distributions.
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Affiliation(s)
- Edith Terrenoire
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Mindelsohn Way, Edgbaston, Birmingham, B15 2TG, UK.
- Present address : Service de Génétique, CHU de Tours, 2 Boulevard Tonnellé, 37044, Tours, Cedex 09, France.
| | - John A Halsall
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Bryan M Turner
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Farré M, Robinson TJ, Ruiz-Herrera A. An Integrative Breakage Model of genome architecture, reshuffling and evolution: The Integrative Breakage Model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity. Bioessays 2015; 37:479-88. [PMID: 25739389 DOI: 10.1002/bies.201400174] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 12/23/2022]
Abstract
Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the study of genome evolution. The analysis of the high-level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders.
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Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, Barcelona, Spain
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Çelik S. Understanding the complexity of antigen retrieval of DNA methylation for immunofluorescence-based measurement and an approach to challenge. J Immunol Methods 2014; 416:1-16. [PMID: 25435341 DOI: 10.1016/j.jim.2014.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/31/2014] [Accepted: 11/21/2014] [Indexed: 12/28/2022]
Abstract
Cytosine methylation (5-methylcytosine, 5meC) in the CpG-rich regions of the mammalian genome is an important epigenetic mechanism playing roles in transcription regulation and genomic stability. The abnormalities in DNA methylation can occur in various types of cancer and some genetic diseases. The measurement of DNA methylation is therefore important and there is a range of methodologies used to detect DNA methylation. Many methods based on bisulfite treatment appeared with a lack of specificity after recent discoveries of various modifications of methylated cytosine, however there are new treatments developed to overcome this limitation. Immunofluorescence is currently known to be able to specifically detect DNA methylation as it uses different antibodies against 5meC and its derivatives, but it is a semi-quantitative method. Immunofluorescence protocols commonly include fixation of cells followed by permeabilisation, antigen retrieval, and treatments with antibodies. Establishing the strategy for antigen retrieval of immunofluorescence is important to unmask epitopes (i.e. 5meC) from other proteins, and therefore to access the antigen of interest. There are many approaches used for antigen retrieval induced by acid, enzyme and/or heat. The selection of antigen retrieval method can depend on a variety of such antigen-based or cell-based conditions, since the dynamic structure of DNA and chromatin accounts for the complexity of involved proteins to mask the epitope. This review aims to specifically focus on the complexity of in situ detection of DNA methylation by immunofluorescence-based methods using antigen retrieval with the current understanding of DNA methylation mechanism, and suggests conditions for antigenic retrieval of 5meC epitope.
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Affiliation(s)
- Selcen Çelik
- Human Reproduction and Development Unit, Kolling Institute for Medical Research, Sydney Medical School, University of Sydney, Sydney 2065, Australia.
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28
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Dekker J. Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics Chromatin 2014; 7:25. [PMID: 25435919 PMCID: PMC4247682 DOI: 10.1186/1756-8935-7-25] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/15/2014] [Indexed: 01/19/2023] Open
Abstract
Genetic and epigenetic inheritance through mitosis is critical for dividing cells to maintain their state. This process occurs in the context of large-scale re-organization of chromosome conformation during prophase leading to the formation of mitotic chromosomes, and during the reformation of the interphase nucleus during telophase and early G1. This review highlights how recent studies over the last 5 years employing chromosome conformation capture combined with classical models of chromosome organization based on decades of microscopic observations, are providing new insights into the three-dimensional organization of chromatin inside the interphase nucleus and within mitotic chromosomes. One striking observation is that interphase genome organization displays cell type-specific features that are related to cell type-specific gene expression, whereas mitotic chromosome folding appears universal and tissue invariant. This raises the question of whether or not there is a need for an epigenetic memory for genome folding. Herein, the two different folding states of mammalian genomes are reviewed and then models are discussed wherein instructions for cell type-specific genome folding are locally encoded in the linear genome and transmitted through mitosis, e.g., as open chromatin sites with or without continuous binding of transcription factors. In the next cell cycle these instructions are used to re-assemble protein complexes on regulatory elements which then drive three-dimensional folding of the genome from the bottom up through local action and self-assembly into higher order levels of cell type-specific organization. In this model, no explicit epigenetic memory for cell type-specific chromosome folding is required.
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Affiliation(s)
- Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103 USA
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29
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Abstract
Poised (bivalent) chromatin is defined by the simultaneous presence of histone modifications associated with both gene activation and repression. This epigenetic feature was first observed at promoters of lineage-specific regulatory genes in embryonic stem cells in culture. More recent work has shown that, in vivo, mammalian germ cells maintain poised chromatin at promoters of many genes that regulate somatic development, and that they retain this state from fetal stages through meiosis and gametogenesis. We hypothesize that the poised chromatin state is essential for germ cell identity and function. We propose three roles for poised chromatin in the mammalian germ line: prevention of DNA methylation, maintenance of germ cell identity and preparation for totipotency. We discuss these roles in the context of recently proposed models for germline potency and epigenetic inheritance.
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Affiliation(s)
- Bluma J Lesch
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - David C Page
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02142, USA Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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30
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Khan WA, Rogan PK, Knoll JHM. Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes. Mol Cytogenet 2014; 7:70. [PMID: 25520753 PMCID: PMC4269072 DOI: 10.1186/s13039-014-0070-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Condensation differences along the lengths of homologous, mitotic metaphase chromosomes are well known. This study reports molecular cytogenetic data showing quantifiable localized differences in condensation between homologs that are related to differences in accessibility (DA) of associated DNA probe targets. Reproducible DA was observed for ~10% of locus-specific, short (1.5-5 kb) single copy DNA probes used in fluorescence in situ hybridization. RESULTS Fourteen probes (from chromosomes 1, 5, 9, 11, 15, 17, 22) targeting genic and intergenic regions were developed and hybridized to cells from 10 individuals with cytogenetically-distinguishable homologs. Differences in hybridization between homologs were non-random for 8 genomic regions (RGS7, CACNA1B, GABRA5, SNRPN, HERC2, PMP22:IVS3, ADORA2B:IVS1, ACR) and were not unique to known imprinted domains or specific chromosomes. DNA probes within CCNB1, C9orf66, ADORA2B:Promoter-Ex1, PMP22:IVS4-Ex 5, and intergenic region 1p36.3 showed no DA (equivalent accessibility), while OPCML showed unbiased DA. To pinpoint probe locations, we performed 3D-structured illumination microscopy (3D-SIM). This showed that genomic regions with DA had 3.3-fold greater volumetric, integrated probe intensities and broad distributions of probe depths along axial and lateral axes of the 2 homologs, compared to a low copy probe target (NOMO1) with equivalent accessibility. Genomic regions with equivalent accessibility were also enriched for epigenetic marks of open interphase chromatin (DNase I HS, H3K27Ac, H3K4me1) to a greater extent than regions with DA. CONCLUSIONS This study provides evidence that DA is non-random and reproducible; it is locus specific, but not unique to known imprinted regions or specific chromosomes. Non-random DA was also shown to be heritable within a 2 generation family. DNA probe volume and depth measurements of hybridized metaphase chromosomes further show locus-specific chromatin accessibility differences by super-resolution 3D-SIM. Based on these data and the analysis of interphase epigenetic marks of genomic intervals with DA, we conclude that there are localized differences in compaction of homologs during mitotic metaphase and that these differences may arise during or preceding metaphase chromosome compaction. Our results suggest new directions for locus-specific structural analysis of metaphase chromosomes, motivated by the potential relationship of these findings to underlying epigenetic changes established during interphase.
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Affiliation(s)
- Wahab A Khan
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Peter K Rogan
- />Departments of Biochemistry and Computer Science, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Joan HM Knoll
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
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Mitosis gives a brief window of opportunity for a change in gene transcription. PLoS Biol 2014; 12:e1001914. [PMID: 25072650 PMCID: PMC4114836 DOI: 10.1371/journal.pbio.1001914] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/17/2014] [Indexed: 12/22/2022] Open
Abstract
In mitotic nuclei transplant experiments, many genes undergo major changes in gene expression. This supports the idea that mitosis facilitates new cell fate decisions during normal development. Cell differentiation is remarkably stable but can be reversed by somatic cell nuclear transfer, cell fusion, and iPS. Nuclear transfer to amphibian oocytes provides a special opportunity to test transcriptional reprogramming without cell division. We show here that, after nuclear transfer to amphibian oocytes, mitotic chromatin is reprogrammed up to 100 times faster than interphase nuclei. We find that, as cells traverse mitosis, their genes pass through a temporary phase of unusually high responsiveness to oocyte reprogramming factors (mitotic advantage). Mitotic advantage is not explained by nuclear penetration, DNA modifications, histone acetylation, phosphorylation, methylation, nor by salt soluble chromosomal proteins. Our results suggest that histone H2A deubiquitination may account, at least in part, for the acquisition of mitotic advantage. They support the general principle that a temporary access of cytoplasmic factors to genes during mitosis may facilitate somatic cell nuclear reprogramming and the acquisition of new cell fates in normal development. Cells are dividing very actively at a time in development when new gene expression and new cell lineages arise. At mitosis, most transcription factors are temporarily displaced from chromosomes. We show that, after transplantation to oocytes, somatic cell nuclei that have been synchronized in mitosis can be reprogrammed to pluripotency gene expression up to 100 times faster than interphase nuclei. We find that, as cells traverse mitosis, their genes pass through a temporary phase of unusually high responsiveness to oocyte reprogramming factors (mitotic advantage). Many other genes in the genome have also shown a mitotic advantage, which affects the rate rather than the final level of transcriptional enhancement. This is attributable to a chromatin state rather than to more rapid passage of reprogramming factors through the nuclear membrane. Histone H2A deubiquitination at mitosis is required for the acquisition of mitotic advantage. Our results support the general principle that a temporary access of cytoplasmic factors to genes during mitosis facilitates somatic cell nuclear reprogramming and the acquisition of new cell fates in normal development.
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32
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He S, Yan S, Wang P, Zhu W, Wang X, Shen Y, Shao K, Xin H, Li S, Li L. Comparative analysis of genome-wide chromosomal histone modification patterns in maize cultivars and their wild relatives. PLoS One 2014; 9:e97364. [PMID: 24819606 PMCID: PMC4018347 DOI: 10.1371/journal.pone.0097364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/19/2014] [Indexed: 01/09/2023] Open
Abstract
Recent advances demonstrate that epigenome changes can also cause phenotypic diversity and can be heritable across generations, indicating that they may play an important role in evolutionary processes. In this study, we analyzed the chromosomal distribution of several histone modifications in five elite maize cultivars (B73, Mo17, Chang7-2, Zheng58, ZD958) and their two wild relatives (Zea mays L. ssp. parviglumis and Zea nicaraguensis) using a three-dimensional (3D) epigenome karyotyping approach by combining immunostaining and 3D reconstruction with deconvolution techniques. The distribution of these histone modifications along chromosomes demonstrated that the histone modification patterns are conserved at the chromosomal level and have not changed significantly following domestication. The comparison of histone modification patterns between metaphase chromosomes and interphase nuclei showed that some of the histone modifications were retained as the cell progressed from interphase into metaphase, although remodelling existed. This study will increase comprehension of the function of epigenetic modifications in the structure and evolution of the maize genome.
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Affiliation(s)
- Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- State Key Laboratory of Cotton Biology, College of Life Sciences, Henan University, Kaifeng, China
- * E-mail: (LL); (SH)
| | - Shihan Yan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Pu Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wei Zhu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, China
| | - Xiangwu Wang
- School of Physics and Electronics, Henan University, Kaifeng, China
| | - Yao Shen
- State Key Laboratory of Cotton Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Kejia Shao
- State Key Laboratory of Cotton Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, China
| | - Shaohua Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, China
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (LL); (SH)
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Zaidi SK, Grandy RA, Lopez-Camacho C, Montecino MM, van Wijnen AJ, Lian JB, Stein JL, Stein GS. Bookmarking target genes in mitosis: a shared epigenetic trait of phenotypic transcription factors and oncogenes? Cancer Res 2014; 74:420-5. [PMID: 24408924 PMCID: PMC3996803 DOI: 10.1158/0008-5472.can-13-2837] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The regulatory information for phenotype, proliferation, and growth of normal and tumor cells must be maintained through genome replication in the S phase and cell division during mitosis. Epigenetic mechanisms that include DNA methylation, posttranslational modifications of histones, selective utilization of histone variants, and inheritable RNA molecules play pivotal roles in maintaining cellular identity through mitotic divisions. Recent studies demonstrate that mitotic occupancy of genes, which are determinants of cell fate, growth, and proliferation, by lineage-restricted transcription factors is a key epigenetic mechanism for retention and transmission of cellular expression memory. Evidence is emerging for the presence of distinct transcriptional regulatory microenvironments in mitotic chromosomes in which the genes bookmarked for reactivation postmitotically reside. Importantly, some oncoproteins are present in mitotic microenvironments where they occupy target genes during mitosis and may contribute to perpetuating the transformed phenotype. We discuss emerging regulatory implications of epigenetically bookmarking genes during mitosis for physiologic control as well as for the onset and progression of cancer.
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Affiliation(s)
- Sayyed K. Zaidi
- Vermont Cancer Center and Department of Biochemistry, University of Vermont, Burlington VT
| | - Rodrigo A. Grandy
- Vermont Cancer Center and Department of Biochemistry, University of Vermont, Burlington VT
| | - Cesar Lopez-Camacho
- Vermont Cancer Center and Department of Biochemistry, University of Vermont, Burlington VT
| | - Martin M. Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - Andre J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jane B. Lian
- Vermont Cancer Center and Department of Biochemistry, University of Vermont, Burlington VT
| | - Janet L. Stein
- Vermont Cancer Center and Department of Biochemistry, University of Vermont, Burlington VT
| | - Gary S. Stein
- Vermont Cancer Center and Department of Biochemistry, University of Vermont, Burlington VT
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Turner BM. Nucleosome signalling; an evolving concept. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:623-6. [PMID: 24412235 DOI: 10.1016/j.bbagrm.2014.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/02/2014] [Indexed: 11/16/2022]
Abstract
The nucleosome core particle is the first stage of DNA packaging in virtually all eukaryotes. It both organises nuclear DNA and protects it from adventitious binding of transcription factors and the consequent deregulation of gene expression. Both properties are essential to allow the genome expansion characteristic of complex eukaryotes. The nucleosome is a flexible structure in vivo, allowing selective relaxation of its intrinsically inhibitory effects in response to external signals. Structural changes are brought about by dedicated remodelling enzymes and by posttranslational modifications of the core histones. Histone modifications occasionally alter nucleosome structure directly, but their more usual roles are to act as receptors on the nucleosome surface that are recognised by specific protein domains. The bound proteins, in turn, affect nucleosome structure and function. This strategy enormously expands the signalling capacity of the nucleosome and its ability to influence both the initiation and elongation stages of transcription. The enzymes responsible for placing and removing histone modifications, and the modification-binding proteins themselves, are ubiquitous, numerous and conserved amongst eukaryotes. Like the nucleosome, they date back to the earliest eukaryotes and may have played integral and essential roles in eukaryotic evolution. The present properties and epigenetic functions of the nucleosome reflect its evolutionary past and the selective pressures to which it has responded and can be better understood in this context. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Bryan M Turner
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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35
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Epigenetics of eu- and heterochromatin in inverted and conventional nuclei from mouse retina. Chromosome Res 2013; 21:535-54. [PMID: 23996328 DOI: 10.1007/s10577-013-9375-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 12/20/2022]
Abstract
To improve light propagation through the retina, the rod nuclei of nocturnal mammals are uniquely changed compared to the nuclei of other cells. In particular, the main classes of chromatin are segregated in them and form regular concentric shells in order; inverted in comparison to conventional nuclei. A broad study of the epigenetic landscape of the inverted and conventional mouse retinal nuclei indicated several differences between them and several features of general interest for the organization of the mammalian nuclei. In difference to nuclei with conventional architecture, the packing density of pericentromeric satellites and LINE-rich chromatin is similar in inverted rod nuclei; euchromatin has a lower packing density in both cases. A high global chromatin condensation in rod nuclei minimizes the structural difference between active and inactive X chromosome homologues. DNA methylation is observed primarily in the chromocenter, Dnmt1 is primarily associated with the euchromatic shell. Heterochromatin proteins HP1-alpha and HP1-beta localize in heterochromatic shells, whereas HP1-gamma is associated with euchromatin. For most of the 25 studied histone modifications, we observed predominant colocalization with a certain main chromatin class. Both inversions in rod nuclei and maintenance of peripheral heterochromatin in conventional nuclei are not affected by a loss or depletion of the major silencing core histone modifications in respective knock-out mice, but for different reasons. Maintenance of peripheral heterochromatin appears to be ensured by redundancy both at the level of enzymes setting the epigenetic code (writers) and the code itself, whereas inversion in rods rely on the absence of the peripheral heterochromatin tethers (absence of code readers).
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Halley-Stott RP, Gurdon JB. Epigenetic memory in the context of nuclear reprogramming and cancer. Brief Funct Genomics 2013; 12:164-73. [PMID: 23585580 PMCID: PMC3662891 DOI: 10.1093/bfgp/elt011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epigenetic memory represents a natural mechanism whereby the identity of a cell is maintained through successive cell cycles, allowing the specification and maintenance of differentiation during development and in adult cells. Cancer is a loss or reversal of the stable differentiated state of adult cells and may be mediated in part by epigenetic changes. The identity of somatic cells can also be reversed experimentally by nuclear reprogramming. Nuclear reprogramming experiments reveal the mechanisms required to activate embryonic gene expression in adult cells and thus provide insight into the reversal of epigenetic memory. In this article, we will introduce epigenetic memory and the mechanisms by which it may operate. We limit our discussion primarily to the context of nuclear reprogramming and briefly discuss the relevance of memory and reprogramming to cancer biology.
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Affiliation(s)
- Richard P Halley-Stott
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN United Kingdom
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Reliable detection of epigenetic histone marks and nuclear proteins in tissue cryosections. Chromosome Res 2012; 20:849-58. [DOI: 10.1007/s10577-012-9318-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 10/27/2022]
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The adjustable nucleosome: an epigenetic signaling module. Trends Genet 2012; 28:436-44. [PMID: 22633123 DOI: 10.1016/j.tig.2012.04.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/04/2012] [Accepted: 04/23/2012] [Indexed: 11/23/2022]
Abstract
This review examines the proposition that the nucleosome, in addition to its role as a DNA packaging device, is a signaling module through which changing environmental and metabolic conditions can influence genomic functions. The role of enzyme-catalyzed post-translational modifications of the core histones is critically assessed, leading to the conclusion that they play varied, often crucial and sometimes causative roles in this signaling process.
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Lindeman L, Andersen I, Reiner A, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P. Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Dev Cell 2011; 21:993-1004. [DOI: 10.1016/j.devcel.2011.10.008] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 08/12/2011] [Accepted: 10/11/2011] [Indexed: 12/29/2022]
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Moreno PA, Vélez PE, Martínez E, Garreta LE, Díaz N, Amador S, Tischer I, Gutiérrez JM, Naik AK, Tobar F, García F. The human genome: a multifractal analysis. BMC Genomics 2011; 12:506. [PMID: 21999602 PMCID: PMC3277318 DOI: 10.1186/1471-2164-12-506] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 10/14/2011] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Several studies have shown that genomes can be studied via a multifractal formalism. Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. Here we investigate the possibility that the human genome shows a similar behavior to that observed in the nematode. RESULTS We report here multifractality in the human genome sequence. This behavior correlates strongly on the presence of Alu elements and to a lesser extent on CpG islands and (G+C) content. In contrast, no or low relationship was found for LINE, MIR, MER, LTRs elements and DNA regions poor in genetic information. Gene function, cluster of orthologous genes, metabolic pathways, and exons tended to increase their frequencies with ranges of multifractality and large gene families were located in genomic regions with varied multifractality. Additionally, a multifractal map and classification for human chromosomes are proposed. CONCLUSIONS Based on these findings, we propose a descriptive non-linear model for the structure of the human genome, with some biological implications. This model reveals 1) a multifractal regionalization where many regions coexist that are far from equilibrium and 2) this non-linear organization has significant molecular and medical genetic implications for understanding the role of Alu elements in genome stability and structure of the human genome. Given the role of Alu sequences in gene regulation, genetic diseases, human genetic diversity, adaptation and phylogenetic analyses, these quantifications are especially useful.
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Affiliation(s)
- Pedro A Moreno
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Santiago de Cali, Colombia
| | - Patricia E Vélez
- Profesora del Departamento de Biología, FACNED, Universidad del Cauca, Popayán, Colombia
- Escuela de Ciencias Básicas. Facultad de Salud, Universidad del Valle, Santiago de Cali, Colombia
| | - Ember Martínez
- Departamento de Sistemas, Universidad del Cauca, Popayán, Colombia
| | - Luis E Garreta
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Santiago de Cali, Colombia
| | - Néstor Díaz
- Departamento de Sistemas, Universidad del Cauca, Popayán, Colombia
| | - Siler Amador
- Departamento de Sistemas, Universidad del Cauca, Popayán, Colombia
| | - Irene Tischer
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Santiago de Cali, Colombia
| | - José M Gutiérrez
- Instituto de Física de Cantabria, Universidad de Cantabria-CSIC, Santander, España
| | | | - Fabián Tobar
- Escuela de Ciencias Básicas. Facultad de Salud, Universidad del Valle, Santiago de Cali, Colombia
| | - Felipe García
- Escuela de Ciencias Básicas. Facultad de Salud, Universidad del Valle, Santiago de Cali, Colombia
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Gostissa M, Alt FW, Chiarle R. Mechanisms that promote and suppress chromosomal translocations in lymphocytes. Annu Rev Immunol 2011; 29:319-50. [PMID: 21219174 DOI: 10.1146/annurev-immunol-031210-101329] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recurrent chromosomal translocations are characteristic features of many types of cancers, especially lymphomas and leukemias. Several basic mechanistic factors are required for the generation of most translocations. First, DNA double-strand breaks (DSBs) must be present simultaneously at the two participating loci. Second, the two broken loci must either be in proximity or be moved into proximity to be joined. Finally, cellular DNA repair pathways must be available to join the two broken loci to complete the translocation. These mechanistic factors can vary in different normal and mutant cells and, as a result, substantially influence the frequency at which particular translocations are generated in a given cell type. Ultimately, however, appearance of recurrent oncogenic translocations in tumors is, in most cases, strongly influenced by selection for the translocated oncogene during the tumorigenesis process. In this review, we discuss in depth the factors and pathways that contribute to the generation of translocations in lymphocytes and other cell types. We also discuss recent findings regarding mechanisms that underlie the appearance of recurrent translocations in tumors.
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Affiliation(s)
- Monica Gostissa
- Howard Hughes Medical Institute, Immune Disease Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Massachusetts 02115, USA
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Abstract
The mechanisms limiting clonal T-cell expansion in response to cytokines to cells that have recognised cognate antigen via their T-cell receptor are incompletely understood. A study by Rawlings et al identifies one such mechanism that functions, unexpectedly, through chromatin compaction and involves a subunit of condensin — a complex better known for restructuring chromosomes in mitosis.
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Affiliation(s)
- Andrew J Wood
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, CA, USA
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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