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Mitra S, Samadder A, Das P, Das S, Dasgupta M, Chakrabarti J. Decrypting ENCODEd epigenetic marks of human tRN-A-RS genes in normal, stem and cancer cell lines. J Biomol Struct Dyn 2016; 35:2759-2771. [PMID: 27659686 DOI: 10.1080/07391102.2016.1240107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Screening large-scale ENCODE data of 625 cytoplasmic transfer RNA (tRNAs) and 37 aminoacyl tRNA synthetase (AARSs) human genes, we deconstruct the array of relations between 10 histone marks affecting 15 chromatin states; their tissue specificity and variations and interchange amongst normal, cancerous and stem cells. The histone marks of RNA Pol II transcribed AARS genes share, but also contrast with that on RNA Pol III transcribed tRNA genes. tRNAs with identical/similar sequences may be in significantly varying states even within the same cell line; the chromatin scaffold, where the tRNA gene resides, is the key determinant. Hepatocellular carcinoma cell line has dominant H3K27me3, and singular clustering of other marks. Leukaemic cell line has hyperactive genes. The quiescence of the stem cells is encoded in the markers. Leaving aside the important exceptions in stem cells and elsewhere, tRNAs with cove scores above 50 have active markers and precise sets of transcription factors, and are usually well conserved compared to the low-scoring ones. Pseudo tRNAs are in heterochromatin/repressed state with anomalous exceptions in cancer cells. We motivate that Epigenetic-Phishing hacks the translation apparatus through the chromatin states governed by the histone marks of tRNA and AARS genes, and speculate on their therapeutic implications in cancer and on stem cells.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur , Kolkata 700032 , India
| | - Arpa Samadder
- b Computational & Systems Biology, Cancer Genomics, & Molecular Biophysics , University of Massachusetts , Boston , MA 02125 , USA
| | - Pijush Das
- c Structural Biology & Bioinformatics Division , Indian Institute of Chemical Biology , Kolkata 700032 , India
| | - Smarajit Das
- d Department of Genetics , University of Georgia , Athens , GA 30602 , USA
| | - Medhanjali Dasgupta
- e Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA
| | - Jayprokas Chakrabarti
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur , Kolkata 700032 , India.,f Gyanxet , BF 286 Salt Lake, Kolkata 700064 , India
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Ali T, Renkawitz R, Bartkuhn M. Insulators and domains of gene expression. Curr Opin Genet Dev 2016; 37:17-26. [PMID: 26802288 DOI: 10.1016/j.gde.2015.11.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/20/2015] [Accepted: 11/25/2015] [Indexed: 01/07/2023]
Abstract
The genomic organization into active and inactive chromatin domains imposes specific requirements for having domain boundaries to prohibit interference between the opposing activities of neighbouring domains. These boundaries provide an insulator function by binding architectural proteins that mediate long-range interactions. Among these, CTCF plays a prominent role in establishing chromatin loops (between pairs of CTCF binding sites) through recruiting cohesin. CTCF-mediated long-range interactions are integral for a multitude of topological features of interphase chromatin, such as the formation of topologically associated domains, domain insulation, enhancer blocking and even enhancer function.
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Affiliation(s)
- Tamer Ali
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, D35392 Giessen, Germany
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, D35392 Giessen, Germany.
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, D35392 Giessen, Germany
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Lupiáñez DG, Spielmann M, Mundlos S. Breaking TADs: How Alterations of Chromatin Domains Result in Disease. Trends Genet 2016; 32:225-237. [DOI: 10.1016/j.tig.2016.01.003] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 12/13/2022]
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Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C. Methods Mol Biol 2016; 1589:47-74. [PMID: 26900130 DOI: 10.1007/7651_2015_261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The chromosome conformation capture (3C) method has been invaluable in studying chromatin interactions in a population of cells at a resolution surpassing that of light microscopy, for example in the detection of functional contacts between enhancers and promoters. Recent developments in sequencing-based chromosomal contact mapping (Hi-C, 5C and 4C-Seq) have allowed researchers to interrogate pairwise chromatin interactions on a wider scale, shedding light on the three-dimensional organization of chromosomes. These methods present significant technical and bioinformatic challenges to consider at the start of the project. Here, we describe two alternative methods for Hi-C, depending on the size of the genome, and discuss the major computational approaches to convert the raw sequencing data into meaningful models of how genomes are organized.
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Molla-Herman A, Vallés AM, Ganem-Elbaz C, Antoniewski C, Huynh JR. tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription. EMBO J 2015; 34:3009-27. [PMID: 26471728 PMCID: PMC4687792 DOI: 10.15252/embj.201591006] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 09/01/2015] [Accepted: 09/04/2015] [Indexed: 02/01/2023] Open
Abstract
RNase P is a conserved endonuclease that processes the 5' trailer of tRNA precursors. We have isolated mutations in Rpp30, a subunit of RNase P, and find that these induce complete sterility in Drosophila females. Here, we show that sterility is not due to a shortage of mature tRNAs, but that atrophied ovaries result from the activation of several DNA damage checkpoint proteins, including p53, Claspin, and Chk2. Indeed, we find that tRNA processing defects lead to increased replication stress and de-repression of transposable elements in mutant ovaries. We also report that transcription of major piRNA sources collapse in mutant germ cells and that this correlates with a decrease in heterochromatic H3K9me3 marks on the corresponding piRNA-producing loci. Our data thus link tRNA processing, DNA replication, and genome defense by small RNAs. This unexpected connection reveals constraints that could shape genome organization during evolution.
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Affiliation(s)
- Anahi Molla-Herman
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Ana Maria Vallés
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Carine Ganem-Elbaz
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Christophe Antoniewski
- GED, UPMC, CNRS UMR 7622, IBPS, Developmental Biology Laboratory (IBPS-LBD), Paris, France
| | - Jean-René Huynh
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
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Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis. Mol Cell Biol 2015; 35:2278-94. [PMID: 25918241 DOI: 10.1128/mcb.00076-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To further our understanding of the RNAi machinery within the human nucleus, we analyzed the chromatin and RNA binding of Argonaute 2 (AGO2) within human cancer cell lines. Our data indicated that AGO2 binds directly to nascent tRNA and 5S rRNA, and to the genomic loci from which these RNAs are transcribed, in a small RNA- and DICER-independent manner. AGO2 chromatin binding was not observed at non-TFIIIC-dependent RNA polymerase III (Pol III) genes or at extra-TFIIIC (ETC) sites, indicating that the interaction is specific for TFIIIC-dependent Pol III genes. A genome-wide analysis indicated that loss of AGO2 caused a global increase in mRNA expression level among genes that flank AGO2-bound tRNA genes. This effect was shown to be distinct from that of the disruption of DICER, DROSHA, or CTCF. We propose that AGO2 binding to tRNA genes has a novel and important regulatory role in human cells.
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57
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Feuerborn A, Cook PR. Why the activity of a gene depends on its neighbors. Trends Genet 2015; 31:483-90. [PMID: 26259670 DOI: 10.1016/j.tig.2015.07.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/25/2015] [Accepted: 07/15/2015] [Indexed: 11/15/2022]
Abstract
Sixty years ago, the position of a gene on a chromosome was seen to be a major determinant of gene activity; however, position effects are rarely central to current discussions of gene expression. We describe a comprehensive and simplifying view of how position in 1D sequence and 3D nuclear space underlies expression. We suggest that apparently-different regulatory motifs including enhancers, silencers, insulators, barriers, and boundaries act similarly - they are active promoters that tether target genes close to, or distant from, appropriate transcription sites or 'factories'. We also suggest that any active transcription unit regulates the firing of its neighbors - and thus can be categorized as one or other type of motif; this is consistent with expression quantitative trait loci (eQTLs) being widely dispersed.
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Affiliation(s)
- Alexander Feuerborn
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Abstract
Insulators are regulatory elements that help to organize eukaryotic chromatin via enhancer-blocking and chromatin barrier activity. Although there are several examples of transposable element (TE)-derived insulators, the contribution of TEs to human insulators has not been systematically explored. Mammalian-wide interspersed repeats (MIRs) are a conserved family of TEs that have substantial regulatory capacity and share sequence characteristics with tRNA-related insulators. We sought to evaluate whether MIRs can serve as insulators in the human genome. We applied a bioinformatic screen using genome sequence and functional genomic data from CD4(+) T cells to identify a set of 1,178 predicted MIR insulators genome-wide. These predicted MIR insulators were computationally tested to serve as chromatin barriers and regulators of gene expression in CD4(+) T cells. The activity of predicted MIR insulators was experimentally validated using in vitro and in vivo enhancer-blocking assays. MIR insulators are enriched around genes of the T-cell receptor pathway and reside at T-cell-specific boundaries of repressive and active chromatin. A total of 58% of the MIR insulators predicted here show evidence of T-cell-specific chromatin barrier and gene regulatory activity. MIR insulators appear to be CCCTC-binding factor (CTCF) independent and show a distinct local chromatin environment with marked peaks for RNA Pol III and a number of histone modifications, suggesting that MIR insulators recruit transcriptional complexes and chromatin modifying enzymes in situ to help establish chromatin and regulatory domains in the human genome. The provisioning of insulators by MIRs across the human genome suggests a specific mechanism by which TE sequences can be used to modulate gene regulatory networks.
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Hamashima K, Kanai A. Alternative genetic code for amino acids and transfer RNA revisited. Biomol Concepts 2015; 4:309-18. [PMID: 25436582 DOI: 10.1515/bmc-2013-0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 02/20/2013] [Indexed: 11/15/2022] Open
Abstract
The genetic code is highly conserved among all organisms and its evolution is thought to be strictly limited. However, an increasing number of studies have reported non-standard codes in prokaryotic and eukaryotic genomes. Most of these deviations from the standard code are attributable to tRNA changes relating to, for example, codon/anticodon base pairing and tRNA/aminoacyl-tRNA synthetase recognition. In this review, we focus on tRNA, a key molecule in the translation of the genetic code, and summarize the most recently published information on the evolutionary divergence of the tRNAs. Surprisingly, although higher eukaryotes, such as the nematode (worm), utilize the standard genetic code, newly identified nematode-specific tRNAs (nev-tRNAs) translate nucleotides in a manner that transgresses the code. Furthermore, a variety of additional functions of tRNAs, beyond their translation of the genetic code, have emerged rapidly. We also review these intriguing new aspects of tRNA, which have potential impacts on translational control, RNA silencing, antibiotic resistance, RNA biosynthesis, and transcriptional regulation.
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Functional validation of a constitutive autonomous silencer element. PLoS One 2015; 10:e0124588. [PMID: 25910277 PMCID: PMC4409358 DOI: 10.1371/journal.pone.0124588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 03/14/2015] [Indexed: 11/19/2022] Open
Abstract
Sequences of the genome that are capable of silencing gene expression are thought to play a key role in gene regulation. However, very few silencer elements capable of functioning in mammalian cells have been described, and only a fraction of these have been tested for the ability to function in an autonomous fashion. We report here the characterization and functional validation of a constitutive autonomous silencer element from the human genome called T39, and the comparison of T39 to three other putative silencer elements previously described by others. Functional analysis included one assay for enhancer-blocking insulator activity and two independent assays for silencer activity, all based on stable transfection and comparison to a neutral spacer control. In erythroid K562 cells, T39 exhibited potent silencer activity, the previously described element PRE2-S5 exhibited modest silencer activity, and the two other previously described elements exhibited no silencer activity. T39 was further found to be capable of silencing three disparate promoters, of silencing gene expression in three disparate cell lines, and of functioning as a single copy in a topology-independent manner. Of the four elements analyzed, only T39 exhibits a constitutive pattern of DNase hypersensitivity and binding by CTCF. In its native location the T39 element also exhibits a unique interaction profile with a subset of distal putative regulatory elements. Taken together, these studies validate T39 as a constitutive autonomous silencer, identify T39 as a defined control for future studies of other regulatory elements such as insulators, and provide a basic chromatin profile for one highly potent silencer element.
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61
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Kowarz E, Löscher D, Marschalek R. Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines. Biotechnol J 2015; 10:647-53. [PMID: 25650551 DOI: 10.1002/biot.201400821] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/13/2015] [Accepted: 02/03/2015] [Indexed: 01/02/2023]
Abstract
Stable gene expression in mammalian cells is a prerequisite for many in vitro and in vivo experiments. However, either the integration of plasmids into mammalian genomes or the use of retro-/lentiviral systems have intrinsic limitations. The use of transposable elements, e.g. the Sleeping Beauty system (SB), circumvents most of these drawbacks (integration sites, size limitations) and allows the quick generation of stable cell lines. The integration process of SB is catalyzed by a transposase and the handling of this gene transfer system is easy, fast and safe. Here, we report our improvements made to the existing SB vector system and present two new vector types for robust constitutive or inducible expression of any gene of interest. Both types are available in 16 variants with different selection marker (puromycin, hygromycin, blasticidin, neomycin) and fluorescent protein expression (GFP, RFP, BFP) to fit most experimental requirements. With this system it is possible to generate cell lines from stable transfected cells quickly and reliably in a medium-throughput setting (three to five days). Cell lines robustly express any gene-of-interest, either constitutively or tightly regulated by doxycycline. This allows many laboratory experiments to speed up generation of data in a rapid and robust manner.
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Affiliation(s)
- Eric Kowarz
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
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62
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Kononenko AV, Lee NCO, Liskovykh M, Masumoto H, Earnshaw WC, Larionov V, Kouprina N. Generation of a conditionally self-eliminating HAC gene delivery vector through incorporation of a tTAVP64 expression cassette. Nucleic Acids Res 2015; 43:e57. [PMID: 25712097 PMCID: PMC4482055 DOI: 10.1093/nar/gkv124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/07/2015] [Indexed: 11/25/2022] Open
Abstract
Human artificial chromosome (HAC)-based vectors represent an alternative technology for gene delivery and expression with a potential to overcome the problems caused by virus-based vectors. The recently developed alphoidtetO-HAC has an advantage over other HAC vectors because it can be easily eliminated from cells by inactivation of the HAC kinetochore via binding of chromatin modifiers, tTA or tTS, to its centromeric tetO sequences. This provides a unique control for phenotypes induced by genes loaded into the HAC. The alphoidtetO-HAC elimination is highly efficient when a high level of chromatin modifiers as tetR fusion proteins is achieved following transfection of cells by a retrovirus vector. However, such vectors are potentially mutagenic and might want to be avoided under some circumstances. Here, we describe a novel system that allows verification of phenotypic changes attributed to expression of genes from the HAC without a transfection step. We demonstrated that a single copy of tTAVP64 carrying four tandem repeats of the VP16 domain constitutively expressed from the HAC is capable to generate chromatin changes in the HAC kinetochore that are not compatible with its function. To adopt the alphoidtetO-HAC for routine gene function studies, we constructed a new TAR-BRV- tTAVP64 cloning vector that allows a selective isolation of a gene of interest from genomic DNA in yeast followed by its direct transfer to bacterial cells and subsequent loading into the loxP site of the alphoidtetO-HAC in hamster CHO cells from where the HAC may be MMCT-transferred to the recipient human cells.
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Affiliation(s)
- Artem V Kononenko
- Developmental Therapeutic Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nicholas C O Lee
- Developmental Therapeutic Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mikhail Liskovykh
- Developmental Therapeutic Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Vladimir Larionov
- Developmental Therapeutic Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Natalay Kouprina
- Developmental Therapeutic Branch, National Cancer Institute, Bethesda, MD 20892, USA
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Abstract
tRNAs are widely believed to segregate into two classes, I and II. Computational analysis of eukaryotic tRNA entries in Genomic tRNA Database, however, leads to new, albeit paradoxical, presence of more than a thousand class-I tRNAs with uncharacteristic long variable arms (V-arms), like in class-II. Out of 62,202 tRNAs from 69 eukaryotes, as many as 1431 class-I tRNAs have these novel extended V-arms, and we refer to them as paradoxical tRNAs (pxtRNAs). A great majority of these 1431 pxtRNA genes are located in intergenic regions, about 18% embedded in introns of genes or ESTs, and just one in 3'UTR. A check on the conservations of 2D and 3D base pairs for each position of these pxtRNAs reveals a few variations, but they seem to have almost all the known features (already known identity and conserved elements of tRNA). Analyses of the A-Box and B-Box of these pxtRNA genes in eukaryotes display salient deviations from the previously annotated conserved features of the standard promoters, whereas the transcription termination signals are just canonical and non-canonical runs of thymidine, similar to the ones in standard tRNA genes. There is just one such pxtRNA(ProAGG) gene in the entire human genome, and the availability of data allows epigenetic analysis of this human pxtRNA(ProAGG) in three different cell lines, H1 hESC, K562, and NHEK, to assess the level of its expression. Histone acetylation and methylation of this lone pxtRNA(ProAGG) gene in human differ from that of the nine standard human tRNA(ProAGG) genes. The V-arm nucleotide sequences and their secondary structures in pxtRNA differ from that of class-II tRNA. Considering these differences, hypotheses of alternative splicing, non-canonical intron and gene transfer are examined to partially improve the Cove scores of these pxtRNAs and to critically question their antecedence and novelty.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Arpa Samadder
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Pijush Das
- b Cancer Biology & Inflammatory Disorder Division , Indian Institute of Chemical Biology , Kolkata , India
| | - Smarajit Das
- c Department of Medical Biochemistry and Cell Biology , Institute of Biomedicine, University of Gothenburg , Gothenburg , Sweden
| | - Jayprokas Chakrabarti
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India.,d Gyanxet, BF 286 Salt Lake, Kolkata , India
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64
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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65
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Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet 2014; 16:98-112. [DOI: 10.1038/nrg3861] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Wang J, Lawry ST, Cohen AL, Jia S. Chromosome boundary elements and regulation of heterochromatin spreading. Cell Mol Life Sci 2014; 71:4841-52. [PMID: 25192661 PMCID: PMC4234687 DOI: 10.1007/s00018-014-1725-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 11/29/2022]
Abstract
Chromatin is generally classified as euchromatin or heterochromatin, each with distinct histone modifications, compaction levels, and gene expression patterns. Although the proper formation of heterochromatin is essential for maintaining genome integrity and regulating gene expression, heterochromatin can also spread into neighboring regions in a sequence-independent manner, leading to the inactivation of genes. Because the distance of heterochromatin spreading is stochastic, the formation of boundaries, which block the spreading of heterochromatin, is critical for maintaining stable gene expression patterns. Here we review the current understanding of the mechanisms underlying heterochromatin spreading and boundary formation.
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
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67
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Schoborg T, Labrador M. Expanding the roles of chromatin insulators in nuclear architecture, chromatin organization and genome function. Cell Mol Life Sci 2014; 71:4089-113. [PMID: 25012699 PMCID: PMC11113341 DOI: 10.1007/s00018-014-1672-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/31/2014] [Accepted: 06/23/2014] [Indexed: 01/08/2023]
Abstract
Of the numerous classes of elements involved in modulating eukaryotic chromosome structure and function, chromatin insulators arguably remain the most poorly understood in their contribution to these processes in vivo. Indeed, our view of chromatin insulators has evolved dramatically since their chromatin boundary and enhancer blocking properties were elucidated roughly a quarter of a century ago as a result of recent genome-wide, high-throughput methods better suited to probing the role of these elements in their native genomic contexts. The overall theme that has emerged from these studies is that chromatin insulators function as general facilitators of higher-order chromatin loop structures that exert both physical and functional constraints on the genome. In this review, we summarize the result of recent work that supports this idea as well as a number of other studies linking these elements to a diverse array of nuclear processes, suggesting that chromatin insulators exert master control over genome organization and behavior.
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Affiliation(s)
- Todd Schoborg
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
- Present Address: Laboratory of Molecular Machines and Tissue Architecture, Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Dr Rm 2122, Bethesda, MD 20892 USA
| | - Mariano Labrador
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
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68
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Wang Q, Nowak CM, Korde A, Oh DH, Dassanayake M, Donze D. Compromised RNA polymerase III complex assembly leads to local alterations of intergenic RNA polymerase II transcription in Saccharomyces cerevisiae. BMC Biol 2014; 12:89. [PMID: 25348158 PMCID: PMC4228148 DOI: 10.1186/s12915-014-0089-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/17/2014] [Indexed: 12/26/2022] Open
Abstract
Background Assembled RNA polymerase III (Pol III) complexes exert local effects on chromatin processes, including influencing transcription of neighboring RNA polymerase II (Pol II) transcribed genes. These properties have been designated as ‘extra-transcriptional’ effects of the Pol III complex. Previous coding sequence microarray studies using Pol III factor mutants to determine global effects of Pol III complex assembly on Pol II promoter activity revealed only modest effects that did not correlate with the proximity of Pol III complex binding sites. Results Given our recent results demonstrating that tDNAs block progression of intergenic Pol II transcription, we hypothesized that extra-transcriptional effects within intergenic regions were not identified in the microarray study. To reconsider global impacts of Pol III complex binding, we used RNA sequencing to compare transcriptomes of wild type versus Pol III transcription factor TFIIIC depleted mutants. The results reveal altered intergenic Pol II transcription near TFIIIC binding sites in the mutant strains, where we observe readthrough of upstream transcripts that normally terminate near these sites, 5′- and 3′-extended transcripts, and de-repression of adjacent genes and intergenic regions. Conclusions The results suggest that effects of assembled Pol III complexes on transcription of neighboring Pol II promoters are of greater magnitude than previously appreciated, that such effects influence expression of adjacent genes at transcriptional start site and translational levels, and may explain a function of the conserved ETC sites in yeast. The results may also be relevant to synthetic biology efforts to design a minimal yeast genome. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0089-x) contains supplementary material, which is available to authorized users.
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Snider CE, Stephens AD, Kirkland JG, Hamdani O, Kamakaka RT, Bloom K. Dyskerin, tRNA genes, and condensin tether pericentric chromatin to the spindle axis in mitosis. ACTA ACUST UNITED AC 2014; 207:189-99. [PMID: 25332162 PMCID: PMC4210444 DOI: 10.1083/jcb.201405028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pericentric enrichment of condensin on budding yeast chromosomes, which contributes to chromatin compaction and mitotic spindle structure and integrity, is mediated by condensin interaction with tRNA genes and the tRNA-interacting protein dyskerin. Condensin is enriched in the pericentromere of budding yeast chromosomes where it is constrained to the spindle axis in metaphase. Pericentric condensin contributes to chromatin compaction, resistance to microtubule-based spindle forces, and spindle length and variance regulation. Condensin is clustered along the spindle axis in a heterogeneous fashion. We demonstrate that pericentric enrichment of condensin is mediated by interactions with transfer ribonucleic acid (tRNA) genes and their regulatory factors. This recruitment is important for generating axial tension on the pericentromere and coordinating movement between pericentromeres from different chromosomes. The interaction between condensin and tRNA genes in the pericentromere reveals a feature of yeast centromeres that has profound implications for the function and evolution of mitotic segregation mechanisms.
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Affiliation(s)
- Chloe E Snider
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrew D Stephens
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jacob G Kirkland
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Omar Hamdani
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Rohinton T Kamakaka
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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70
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Matylla-Kulinska K, Tafer H, Weiss A, Schroeder R. Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:591-600. [PMID: 25045147 PMCID: PMC4233971 DOI: 10.1002/wrna.1243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/15/2014] [Accepted: 04/22/2014] [Indexed: 12/19/2022]
Abstract
The human genome is scattered with repetitive sequences, and the ENCODE project revealed that 60–70% of the genomic DNA is transcribed into RNA. As a consequence, the human transcriptome contains a large portion of repeat-derived RNAs (repRNAs). Here, we present a hypothesis for the evolution of novel functional repeat-derived RNAs from non-coding RNAs (ncRNAs) by retrotransposition. Upon amplification, the ncRNAs can diversify in sequence and subsequently evolve new activities, which can result in novel functions. Non-coding transcripts derived from highly repetitive regions can therefore serve as a reservoir for the evolution of novel functional RNAs. We base our hypothetical model on observations reported for short interspersed nuclear elements derived from 7SL RNA and tRNAs, α satellites derived from snoRNAs and SL RNAs derived from U1 small nuclear RNA. Furthermore, we present novel putative human repeat-derived ncRNAs obtained by the comparison of the Dfam and Rfam databases, as well as several examples in other species. We hypothesize that novel functional ncRNAs can derive also from other repetitive regions and propose Genomic SELEX as a tool for their identification.
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Affiliation(s)
- Katarzyna Matylla-Kulinska
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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71
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Cohen AL, Jia S. Noncoding RNAs and the borders of heterochromatin. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:835-47. [PMID: 25044367 DOI: 10.1002/wrna.1249] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 04/30/2014] [Accepted: 05/21/2014] [Indexed: 11/08/2022]
Abstract
Eukaryotic genomes contain long stretches of repetitive DNA sequences, which are the preferred sites for the assembly of heterochromatin structures. The formation of heterochromatin results in highly condensed chromosomal domains that limit the accessibility of DNA to the transcription and recombination machinery to maintain genome stability. Heterochromatin has the tendency to spread, and the formation of boundaries that block heterochromatin spreading is required to maintain stable gene expression patterns. Recent work has suggested that noncoding RNAs (ncRNAs) are involved in regulating boundary formation in addition to their well-established roles in chromatin regulation. Here, we present a review of our current understanding of the involvement of ncRNA at the boundaries of heterochromatin, highlighting their mechanisms of action in different settings.
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Affiliation(s)
- Allison L Cohen
- Department of Biological Sciences, Columbia University, New York, NY, USA
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72
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Scott KC. Transcription and ncRNAs: at the cent(rome)re of kinetochore assembly and maintenance. Chromosome Res 2014; 21:643-51. [PMID: 24190519 DOI: 10.1007/s10577-013-9387-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Centromeres are sites of chromosomal spindle attachment during mitosis and meiosis. Centromeres are defined, in part, by a distinct chromatin landscape in which histone H3 is replaced by the conserved histone H3 variant, CENP-A. Sequences competent for centromere formation and function vary among organisms and are typically composed of repetitive DNA. It is unclear how such diverse genomic signals are integrated with the epigenetic mechanisms that govern CENP-A incorporation at a single locus on each chromosome. Recent work highlights the intriguing possibility that the transcriptional properties of centromeric core DNA contribute to centromere identity and maintenance through cell division. Moreover, core-derived noncoding RNAs (ncRNAs) have emerged as active participants in the regulation and control of centromere activity in plants and mammals. This paper reviews the transcriptional properties of eukaryotic centromeres and discusses the known roles of core-derived ncRNAs in chromatin integrity, kinetochore assembly, and centromere activity.
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Affiliation(s)
- Kristin C Scott
- Duke Institute for Genome Science and Policy, Duke University, DUMC, Durham, NC, 27708, USA,
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73
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Van Bortle K, Nichols MH, Li L, Ong CT, Takenaka N, Qin ZS, Corces VG. Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol 2014; 15:R82. [PMID: 24981874 PMCID: PMC4226948 DOI: 10.1186/gb-2014-15-5-r82] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/30/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Chromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains. The borders of these domains are highly enriched for architectural proteins with characterized roles in insulator function. However, a majority of architectural protein binding sites localize within topological domains, suggesting sites associated with domain borders represent a functionally different subclass of these regulatory elements. How topologically associating domains are established and what differentiates border-associated from non-border architectural protein binding sites remain unanswered questions. RESULTS By mapping the genome-wide target sites for several Drosophila architectural proteins, including previously uncharacterized profiles for TFIIIC and SMC-containing condensin complexes, we uncover an extensive pattern of colocalization in which architectural proteins establish dense clusters at the borders of topological domains. Reporter-based enhancer-blocking insulator activity as well as endogenous domain border strength scale with the occupancy level of architectural protein binding sites, suggesting co-binding by architectural proteins underlies the functional potential of these loci. Analyses in mouse and human stem cells suggest that clustering of architectural proteins is a general feature of genome organization, and conserved architectural protein binding sites may underlie the tissue-invariant nature of topologically associating domains observed in mammals. CONCLUSIONS We identify a spectrum of architectural protein occupancy that scales with the topological structure of chromosomes and the regulatory potential of these elements. Whereas high occupancy architectural protein binding sites associate with robust partitioning of topologically associating domains and robust insulator function, low occupancy sites appear reserved for gene-specific regulation within topological domains.
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Affiliation(s)
- Kevin Van Bortle
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Michael H Nichols
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Li Li
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Chin-Tong Ong
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Naomi Takenaka
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
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74
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Darrow EM, Chadwick BP. A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse. Nucleic Acids Res 2014; 42:6421-35. [PMID: 24753417 PMCID: PMC4041453 DOI: 10.1093/nar/gku280] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 01/08/2023] Open
Abstract
The human genome contains numerous large tandem repeats, many of which remain poorly characterized. Here we report a novel transfer RNA (tRNA) tandem repeat on human chromosome 1q23.3 that shows extensive copy number variation with 9-43 repeat units per allele and displays evidence of meiotic and mitotic instability. Each repeat unit consists of a 7.3 kb GC-rich sequence that binds the insulator protein CTCF and bears the chromatin hallmarks of a bivalent domain in human embryonic stem cells. A tRNA containing tandem repeat composed of at least three 7.6-kb GC-rich repeat units reside within a syntenic region of mouse chromosome 1. However, DNA sequence analysis reveals that, with the exception of the tRNA genes that account for less than 6% of a repeat unit, the remaining 7.2 kb is not conserved with the notable exception of a 24 base pair sequence corresponding to the CTCF binding site, suggesting an important role for this protein at the locus.
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Affiliation(s)
- Emily M Darrow
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Brian P Chadwick
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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75
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Heger P, Wiehe T. New tools in the box: An evolutionary synopsis of chromatin insulators. Trends Genet 2014; 30:161-71. [DOI: 10.1016/j.tig.2014.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 01/19/2023]
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76
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Ong CT, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 2014; 15:234-46. [PMID: 24614316 DOI: 10.1038/nrg3663] [Citation(s) in RCA: 703] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome is organized in the three-dimensional nuclear space in a specific manner that is both a cause and a consequence of its function. This organization is partly established by a special class of architectural proteins, of which CCCTC-binding factor (CTCF) is the best characterized. Although CTCF has been assigned various roles that are often contradictory, new results now help to draw a unifying model to explain the many functions of this protein. CTCF creates boundaries between topologically associating domains in chromosomes and, within these domains, facilitates interactions between transcription regulatory sequences. Thus, CTCF links the architecture of the genome to its function.
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Affiliation(s)
- Chin-Tong Ong
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, Georgia 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, Georgia 30322, USA
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77
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Cuartero S, Fresán U, Reina O, Planet E, Espinàs ML. Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function. EMBO J 2014; 33:637-47. [PMID: 24502977 DOI: 10.1002/embj.201386001] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Insulators are DNA-protein complexes that play a central role in chromatin organization and regulation of gene expression. In Drosophila different proteins, dCTCF, Su(Hw), and BEAF bind to specific subsets of insulators most of them having in common CP190. It has been shown that there are a number of CP190-binding sites that are not shared with any other known insulator protein, suggesting that other proteins could cooperate with CP190 to regulate insulator activity. Here we report on the identification of two previously uncharacterized proteins as CP190-interacting proteins, that we have named Ibf1 and Ibf2. These proteins localize at insulator bodies and associate with chromatin at CP190-binding sites throughout the genome. We also show that Ibf1 and Ibf2 are DNA-binding proteins that form hetero-oligomers that mediate CP190 binding to chromatin. Moreover, Ibf1 and Ibf2 are necessary for insulator activity in enhancer-blocking assays and Ibf2 null mutation cause a homeotic phenotype. Taken together our data reveal a novel pathway of CP190 recruitment to chromatin that is required for insulator activity.
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Affiliation(s)
- Sergi Cuartero
- Institute of Molecular Biology of Barcelona IBMB-CSIC, and Institute for Research in Biomedicine IRB, Barcelona, Spain
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78
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Kouprina N, Tomilin AN, Masumoto H, Earnshaw WC, Larionov V. Human artificial chromosome-based gene delivery vectors for biomedicine and biotechnology. Expert Opin Drug Deliv 2014; 11:517-35. [DOI: 10.1517/17425247.2014.882314] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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79
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Atkinson TJ, Halfon MS. Regulation of gene expression in the genomic context. Comput Struct Biotechnol J 2014; 9:e201401001. [PMID: 24688749 PMCID: PMC3962188 DOI: 10.5936/csbj.201401001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/10/2013] [Accepted: 12/29/2013] [Indexed: 11/22/2022] Open
Abstract
Metazoan life is dependent on the proper temporal and spatial control of gene expression within the many cells-essentially all with the identical genome-that make up the organism. While much is understood about how individual gene regulatory elements function, many questions remain about how they interact to maintain correct regulation globally throughout the genome. In this review we summarize the basic features and functions of the crucial regulatory elements promoters, enhancers, and insulators and discuss some of the ways in which proper interactions between these elements is realized. We focus in particular on the role of core promoter sequences and propose explanations for some of the contradictory results seen in experiments aimed at understanding insulator function. We suggest that gene regulation depends on local genomic context and argue that more holistic in vivo investigations that take into account multiple local features will be necessary to understand how genome-wide gene regulation is maintained.
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Affiliation(s)
- Taylor J Atkinson
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
- Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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80
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Rodriguez A, Bjerling P. The links between chromatin spatial organization and biological function. Biochem Soc Trans 2013; 41:1634-9. [PMID: 24256267 PMCID: PMC3836414 DOI: 10.1042/bst20130213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 02/06/2023]
Abstract
During the last few years, there has been a rapid increase in our knowledge of how chromatin is organized inside the nucleus. Techniques such as FISH (fluorescence in situ hybridization) have proved that chromosomes organize themselves in so-called CTs (chromosome territories). In addition, newly developed 3C (chromatin conformation capture) techniques have revealed that certain chromosomal regions tend to interact with adjacent regions on either the same chromosome or adjacent chromosomes, and also that regions in close proximity are replicated simultaneously. Furthermore, transcriptionally repressed or active areas occupy different nuclear compartments. Another new technique, named DamID (DNA adenine methyltransferase identification), has strengthened the notion that transcriptionally repressed genes are often found in close association with the nuclear membrane, whereas transcriptionally active regions are found in the more central regions of the nucleus. However, in response to various stimuli, transcriptionally repressed regions are known to relocalize from the nuclear lamina to the interior of the nucleus, leading to a concomitant up-regulation of otherwise silenced genes. Taken together, these insights are of great interest for the relationship between chromosomal spatial organization and genome function. In the present article, we review recent advances in this field with a focus on mammalian cells and the eukaryotic model organism Schizosaccharomyces pombe.
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Key Words
- chromatin
- fission yeast
- heterochromatin
- nuclear organization
- transcriptional regulation
- 3c, chromosome conformation capture
- 4c, circularized chromosome conformation capture
- 5c, carbon copy chromosome conformation capture
- cenp, centromere protein
- chip, chromatin immunoprecipitation
- ct, chromosome territory
- dam, dna adenine methyltansferase
- damid, dna adenine methyltransferase identification
- fish, fluorescence in situ hybridization
- hic, genome-wide chromosome conformation capture
- inm, inner nuclear membrane
- lad, lamina-associated domain
- lem, lap2/emerin/man1
- mps, massive parallel sequencing
- nad, nucleoli-associated domain
- nm, nuclear membrane
- onm, outer nuclear membrane
- tfiiic, transcription factor iiic
- tor, time of replication
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Affiliation(s)
- Alejandro Rodriguez
- *Department of Medical Biochemistry and Microbiology (IMBIM), Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
| | - Pernilla Bjerling
- *Department of Medical Biochemistry and Microbiology (IMBIM), Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
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81
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Fujioka M, Sun G, Jaynes JB. The Drosophila eve insulator Homie promotes eve expression and protects the adjacent gene from repression by polycomb spreading. PLoS Genet 2013; 9:e1003883. [PMID: 24204298 PMCID: PMC3814318 DOI: 10.1371/journal.pgen.1003883] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/29/2013] [Indexed: 12/18/2022] Open
Abstract
Insulators can block the action of enhancers on promoters and the spreading of repressive chromatin, as well as facilitating specific enhancer-promoter interactions. However, recent studies have called into question whether the activities ascribed to insulators in model transgene assays actually reflect their functions in the genome. The Drosophila even skipped (eve) gene is a Polycomb (Pc) domain with a Pc-group response element (PRE) at one end, flanked by an insulator, an arrangement also seen in other genes. Here, we show that this insulator has three major functions. It blocks the spreading of the eve Pc domain, preventing repression of the adjacent gene, TER94. It prevents activation of TER94 by eve regulatory DNA. It also facilitates normal eve expression. When Homie is deleted in the context of a large transgene that mimics both eve and TER94 regulation, TER94 is repressed. This repression depends on the eve PRE. Ubiquitous TER94 expression is “replaced” by expression in an eve pattern when Homie is deleted, and this effect is reversed when the PRE is also removed. Repression of TER94 is attributable to spreading of the eve Pc domain into the TER94 locus, accompanied by an increase in histone H3 trimethylation at lysine 27. Other PREs can functionally replace the eve PRE, and other insulators can block PRE-dependent repression in this context. The full activity of the eve promoter is also dependent on Homie, and other insulators can promote normal eve enhancer-promoter communication. Our data suggest that this is not due to preventing promoter competition, but is likely the result of the insulator organizing a chromosomal conformation favorable to normal enhancer-promoter interactions. Thus, insulator activities in a native context include enhancer blocking and enhancer-promoter facilitation, as well as preventing the spread of repressive chromatin. Insulators are specialized DNA elements that can separate the genome into functional units. Most of the current thinking about these elements comes from studies done with model transgenes. Studies of insulators within the specialized Hox gene complexes have suggested that model transgenes can reflect the normal functions of these elements in their native context. However, recent genome-wide studies have called this into question. This work analyzes the native function of an insulator that resides between the Drosophila genes eve and TER94, which are expressed in very different patterns. Also, the eve gene is a Polycomb (Pc) domain, a specialized type of chromatin that is found in many places throughout the genome. We show that this insulator has three major functions. It blocks the spreading of the eve Pc domain, preventing repression of TER94. It prevents activation of TER94 by eve regulatory DNA. It also facilitates normal eve expression. Each of these activities are consistent with those seen with model transgenes, and other known insulators can provide these functions in this context. This work provides a novel and convincing example of the normal role of insulators in regulating the eukaryotic genome, as well as providing insights into their mechanisms of action.
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Affiliation(s)
- Miki Fujioka
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Guizhi Sun
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - James B. Jaynes
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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82
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Wallace HA, Bosco G. Condensins and 3D Organization of the Interphase Nucleus. CURRENT GENETIC MEDICINE REPORTS 2013; 1:219-229. [PMID: 24563825 DOI: 10.1007/s40142-013-0024-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Condensins are conserved multi-subunit protein complexes that participate in eukaryotic genome organization. Well known for their role in mitotic chromosome condensation, condensins have recently emerged as integral components of diverse interphase processes. Recent evidence shows that condensins are involved in chromatin organization, gene expression, and DNA repair and indicates similarities between the interphase and mitotic functions of condensin. Recent work has enhanced our knowledge of how chromatin architecture is dynamically regulated by condensin to impact essential cellular processes.
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Affiliation(s)
- Heather A Wallace
- Department of Genetics, Geisel School of Medicine at Dartmouth, 609 Vail, HB 7400, Hanover, NH 03755, USA
| | - Giovanni Bosco
- Department of Genetics, Geisel School of Medicine at Dartmouth, 609 Vail, HB 7400, Hanover, NH 03755, USA
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83
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Poly(ADP-ribosyl)ation regulates insulator function and intrachromosomal interactions in Drosophila. Cell 2013; 155:148-59. [PMID: 24055367 DOI: 10.1016/j.cell.2013.08.052] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/29/2013] [Accepted: 08/23/2013] [Indexed: 11/20/2022]
Abstract
Insulators mediate inter- and intrachromosomal contacts to regulate enhancer-promoter interactions and establish chromosome domains. The mechanisms by which insulator activity can be regulated to orchestrate changes in the function and three-dimensional arrangement of the genome remain elusive. Here, we demonstrate that Drosophila insulator proteins are poly(ADP-ribosyl)ated and that mutation of the poly(ADP-ribose) polymerase (Parp) gene impairs their function. This modification is not essential for DNA occupancy of insulator DNA-binding proteins dCTCF and Su(Hw). However, poly(ADP-ribosyl)ation of K566 in CP190 promotes protein-protein interactions with other insulator proteins, association with the nuclear lamina, and insulator activity in vivo. Consistent with these findings, the nuclear clustering of CP190 complexes is disrupted in Parp mutant cells. Importantly, poly(ADP-ribosyl)ation facilitates intrachromosomal interactions between insulator sites measured by 4C. These data suggest that the role of insulators in organizing the three-dimensional architecture of the genome may be modulated by poly(ADP-ribosyl)ation.
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84
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Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells. Mol Cell Biol 2013; 33:4504-16. [PMID: 24043305 DOI: 10.1128/mcb.00545-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells.
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85
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Phillips-Cremins JE, Corces VG. Chromatin insulators: linking genome organization to cellular function. Mol Cell 2013; 50:461-74. [PMID: 23706817 DOI: 10.1016/j.molcel.2013.04.018] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A growing body of evidence suggests that insulators have a primary role in orchestrating the topological arrangement of higher-order chromatin architecture. Insulator-mediated long-range interactions can influence the epigenetic status of the genome and, in certain contexts, may have important effects on gene expression. Here we discuss higher-order chromatin organization as a unifying mechanism for diverse insulator actions across the genome.
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86
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Good PD, Kendall A, Ignatz-Hoover J, Miller EL, Pai DA, Rivera SR, Carrick B, Engelke DR. Silencing near tRNA genes is nucleosome-mediated and distinct from boundary element function. Gene 2013; 526:7-15. [PMID: 23707796 PMCID: PMC3745993 DOI: 10.1016/j.gene.2013.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 01/22/2023]
Abstract
Transfer RNA (tRNA) genes and other RNA polymerase III transcription units are dispersed in high copy throughout nuclear genomes, and can antagonize RNA polymerase II transcription in their immediate chromosomal locus. Previous work in Saccharomyces cerevisiae found that this local silencing required subnuclear clustering of the tRNA genes near the nucleolus. Here we show that the silencing also requires nucleosome participation, though the nature of the nucleosome interaction appears distinct from other forms of transcriptional silencing. Analysis of an extensive library of histone amino acid substitutions finds a large number of residues that affect the silencing, both in the histone N-terminal tails and on the nucleosome disk surface. The residues on the disk surfaces involved are largely distinct from those affecting other regulatory phenomena. Consistent with the large number of histone residues affecting tgm silencing, survey of chromatin modification mutations shows that several enzymes known to affect nucleosome modification and positioning are also required. The enzymes include an Rpd3 deacetylase complex, Hos1 deacetylase, Glc7 phosphatase, and the RSC nucleosome remodeling activity, but not multiple other activities required for other silencing forms or boundary element function at tRNA gene loci. Models for communication between the tRNA gene transcription complexes and local chromatin are discussed.
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Affiliation(s)
- Paul D. Good
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Ann Kendall
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | | | - Erin L. Miller
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Dave A. Pai
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Sara R. Rivera
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - Brian Carrick
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - David R. Engelke
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA
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87
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Ritland Politz JC, Scalzo D, Groudine M. Something silent this way forms: the functional organization of the repressive nuclear compartment. Annu Rev Cell Dev Biol 2013; 29:241-70. [PMID: 23834025 PMCID: PMC3999972 DOI: 10.1146/annurev-cellbio-101512-122317] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The repressive compartment of the nucleus is comprised primarily of telomeric and centromeric regions, the silent portion of ribosomal RNA genes, the majority of transposable element repeats, and facultatively repressed genes specific to different cell types. This compartment localizes into three main regions: the peripheral heterochromatin, perinucleolar heterochromatin, and pericentromeric heterochromatin. Both chromatin remodeling proteins and transcription of noncoding RNAs are involved in maintenance of repression in these compartments. Global reorganization of the repressive compartment occurs at each cell division, during early development, and during terminal differentiation. Differential action of chromatin remodeling complexes and boundary element looping activities are involved in mediating these organizational changes. We discuss the evidence that heterochromatin formation and compartmentalization may drive nuclear organization.
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Affiliation(s)
| | - David Scalzo
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Mark Groudine
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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88
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Li G, Zhou L. Genome-wide identification of chromatin transitional regions reveals diverse mechanisms defining the boundary of facultative heterochromatin. PLoS One 2013; 8:e67156. [PMID: 23840609 PMCID: PMC3696093 DOI: 10.1371/journal.pone.0067156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/14/2013] [Indexed: 11/18/2022] Open
Abstract
Due to the self-propagating nature of the heterochromatic modification H3K27me3, chromatin barrier activities are required to demarcate the boundary and prevent it from encroaching into euchromatic regions. Studies in Drosophila and vertebrate systems have revealed several important chromatin barrier elements and their respective binding factors. However, epigenomic data indicate that the binding of these factors are not exclusive to chromatin boundaries. To gain a comprehensive understanding of facultative heterochromatin boundaries, we developed a two-tiered method to identify the Chromatin Transitional Region (CTR), i.e. the nucleosomal region that shows the greatest transition rate of the H3K27me3 modification as revealed by ChIP-Seq. This approach was applied to identify CTRs in Drosophila S2 cells and human HeLa cells. Although many insulator proteins have been characterized in Drosophila, less than half of the CTRs in S2 cells are associated with known insulator proteins, indicating unknown mechanisms remain to be characterized. Our analysis also revealed that the peak binding of insulator proteins are usually 1–2 nucleosomes away from the CTR. Comparison of CTR-associated insulator protein binding sites vs. those in heterochromatic region revealed that boundary-associated binding sites are distinctively flanked by nucleosome destabilizing sequences, which correlates with significant decreased nucleosome density and increased binding intensities of co-factors. Interestingly, several subgroups of boundaries have enhanced H3.3 incorporation but reduced nucleosome turnover rate. Our genome-wide study reveals that diverse mechanisms are employed to define the boundaries of facultative heterochromatin. In both Drosophila and mammalian systems, only a small fraction of insulator protein binding sites co-localize with H3K27me3 boundaries. However, boundary-associated insulator binding sites are distinctively flanked by nucleosome destabilizing sequences, which correlates with significantly decreased nucleosome density and increased binding of co-factors.
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Affiliation(s)
- Guangyao Li
- Graduate Program in Genetics and Genomics, University of Florida Genetics Institute; Department of Molecular Genetics and Microbiology & University of Florida Shands Cancer Center, College of Medicine, University of Florida. Gainesville, Florida, United States of America
| | - Lei Zhou
- Graduate Program in Genetics and Genomics, University of Florida Genetics Institute; Department of Molecular Genetics and Microbiology & University of Florida Shands Cancer Center, College of Medicine, University of Florida. Gainesville, Florida, United States of America
- * E-mail:
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89
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Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS. Genome-wide analysis of functional sirtuin chromatin targets in yeast. Genome Biol 2013; 14:R48. [PMID: 23710766 PMCID: PMC4053722 DOI: 10.1186/gb-2013-14-5-r48] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 05/14/2013] [Accepted: 05/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The sirtuins are a conserved family of NAD⁺-dependent histone/protein deacetylases that regulate numerous cellular processes, including heterochromatin formation and transcription. Multiple sirtuins are encoded by each eukaryotic genome, raising the possibility of cooperativity or functional overlap. The scope and variety of chromatin binding sites of the sirtuins in any specific organism remain unclear. RESULTS Here we utilize the ChIP-seq technique to identify and functionally characterize the genome-wide targets of the sirtuins, Sir2, Hst1 to Hst4, and the DNA binding partner of Hst1, Sum 1, in Saccharomyces cerevisiae. Unexpectedly, Sir2, Hst1 and Sum1, but not the other sirtuins, exhibit co-enrichment at several classes of chromatin targets. These include telomeric repeat clusters, tRNA genes, and surprisingly, the open reading frames (ORFs) of multiple highly expressed RNA polymerase II-transcribed genes that function in processes such as fermentation, glycolysis, and translation. Repression of these target genes during the diauxic shift is specifically dependent on Sir2/Hst1/Sum1 binding to the ORF and sufficiently high intracellular NAD⁺ concentrations. Sir2 recruitment to the ORFs is independent of the canonical SIR complex and surprisingly requires Sum1. The shared Sir2/Hst1/Sum1 targets also significantly overlap with condensin and cohesin binding sites, where Sir2, Hst1, and Sum1 were found to be important for condensin and cohesin deposition, suggesting a possible mechanistic link between metabolism and chromatin architecture during the diauxic shift. CONCLUSIONS This study demonstrates the existence of overlap in sirtuin function, and advances our understanding of conserved sirtuin-regulated functions, including the regulation of glycolytic gene expression and condensin loading.
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Affiliation(s)
- Mingguang Li
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
| | - Veena Valsakumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
| | - Kunal Poorey
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA
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90
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Lee NCO, Kononenko AV, Lee HS, Tolkunova EN, Liskovykh MA, Masumoto H, Earnshaw WC, Tomilin AN, Larionov V, Kouprina N. Protecting a transgene expression from the HAC-based vector by different chromatin insulators. Cell Mol Life Sci 2013; 70:3723-37. [PMID: 23677492 PMCID: PMC3771377 DOI: 10.1007/s00018-013-1362-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/25/2013] [Accepted: 04/30/2013] [Indexed: 01/07/2023]
Abstract
Human artificial chromosomes (HACs) are vectors that offer advantages of capacity and stability for gene delivery and expression. Several studies have even demonstrated their use for gene complementation in gene-deficient recipient cell lines and animal transgenesis. Recently, we constructed an advance HAC-based vector, alphoidtetO-HAC, with a conditional centromere. In this HAC, a gene-loading site was inserted into a centrochromatin domain critical for kinetochore assembly and maintenance. While by definition this domain is permissive for transcription, there have been no long-term studies on transgene expression within centrochromatin. In this study, we compared the effects of three chromatin insulators, cHS4, gamma-satellite DNA, and tDNA, on the expression of an EGFP transgene inserted into the alphoidtetO-HAC vector. Insulator function was essential for stable expression of the transgene in centrochromatin. In two analyzed host cell lines, a tDNA insulator composed of two functional copies of tRNA genes showed the highest barrier activity. We infer that proximity to centrochromatin does not protect genes lacking chromatin insulators from epigenetic silencing. Barrier elements that prevent gene silencing in centrochromatin would thus help to optimize transgenesis using HAC vectors.
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Affiliation(s)
- Nicholas C O Lee
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, MD, 20892, USA
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91
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Razin SV, Gavrilov AA, Ioudinkova ES, Iarovaia OV. Communication of genome regulatory elements in a folded chromosome. FEBS Lett 2013; 587:1840-7. [PMID: 23651551 DOI: 10.1016/j.febslet.2013.04.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
The most popular model of gene activation by remote enhancers postulates that the enhancers interact directly with target promoters via the looping of intervening DNA fragments. This interaction is thought to be necessary for the stabilization of the Pol II pre-initiation complex and/or for the transfer of transcription factors and Pol II, which are initially accumulated at the enhancer, to the promoter. The direct interaction of enhancer(s) and promoter(s) is only possible when these elements are located in close proximity within the nuclear space. Here, we discuss the molecular mechanisms for maintaining the close proximity of the remote regulatory elements of the eukaryotic genome. The models of an active chromatin hub (ACH) and an active nuclear compartment are considered, focusing on the role of chromatin folding in juxtaposing remote DNA sequences. The interconnection between the functionally dependent architecture of the interphase chromosome and nuclear compartmentalization is also discussed.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia.
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92
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Abstract
The architecture of interphase chromosomes is important for the regulation of gene expression and genome maintenance. Chromosomes are linearly segmented into hundreds of domains with different protein compositions. Furthermore, the spatial organization of chromosomes is nonrandom and is characterized by many local and long-range contacts among genes and other sequence elements. A variety of genome-wide mapping techniques have made it possible to chart these properties at high resolution. Combined with microscopy and computational modeling, the results begin to yield a more coherent picture that integrates linear and three-dimensional (3D) views of chromosome organization in relation to gene regulation and other nuclear functions.
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93
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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94
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Van Bortle K, Corces VG. The role of chromatin insulators in nuclear architecture and genome function. Curr Opin Genet Dev 2013; 23:212-8. [PMID: 23298659 DOI: 10.1016/j.gde.2012.11.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/08/2012] [Indexed: 10/27/2022]
Abstract
Eukaryotic genomes are intricately arranged into highly organized yet dynamic structures that underlie patterns of gene expression and cellular identity. The recent adaptation of novel genomic strategies for assaying nuclear architecture has significantly extended and accelerated our ability to query the nature of genome organization and the players involved. In particular, recent explorations of physical arrangements and chromatin landscapes in higher eukaryotes have demonstrated that chromatin insulators, which mediate functional interactions between regulatory elements, appear to play an important role in these processes. Here we reflect on current findings and our rapidly expanding understanding of insulators and their role in nuclear architecture and genome function.
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Affiliation(s)
- Kevin Van Bortle
- Department of Biology, Emory University, Atlanta, GA 30322, United States
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95
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Palstra RJ, Grosveld F. Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux. Front Genet 2012; 3:195. [PMID: 23060900 PMCID: PMC3460357 DOI: 10.3389/fgene.2012.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/12/2012] [Indexed: 12/26/2022] Open
Abstract
The mammalian genome is packed tightly in the nucleus of the cell. This packing is primarily facilitated by histone proteins and results in an ordered organization of the genome in chromosome territories that can be roughly divided in heterochromatic and euchromatic domains. On top of this organization several distinct gene regulatory elements on the same chromosome or other chromosomes are thought to dynamically communicate via chromatin looping. Advances in genome-wide technologies have revealed the existence of a plethora of these regulatory elements in various eukaryotic genomes. These regulatory elements are defined by particular in vitro assays as promoters, enhancers, insulators, and boundary elements. However, recent studies indicate that the in vivo distinction between these elements is often less strict. Regulatory elements are bound by a mixture of common and lineage-specific transcription factors which mediate the long-range interactions between these elements. Inappropriate modulation of the binding of these transcription factors can alter the interactions between regulatory elements, which in turn leads to aberrant gene expression with disease as an ultimate consequence. Here we discuss the bi-modal behavior of regulatory elements that act in cis (with a focus on enhancers), how their activity is modulated by transcription factor binding and the effect this has on gene regulation.
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Affiliation(s)
- Robert-Jan Palstra
- Department of Cell Biology, Erasmus MC University Medical Center Rotterdam, Netherlands
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96
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TFIIIC bound DNA elements in nuclear organization and insulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:418-24. [PMID: 23000638 DOI: 10.1016/j.bbagrm.2012.09.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/14/2012] [Accepted: 09/15/2012] [Indexed: 11/23/2022]
Abstract
tRNA genes (tDNAs) have been known to have barrier insulator function in budding yeast, Saccharomyces cerevisiae, for over a decade. tDNAs also play a role in genome organization by clustering at sites in the nucleus and both of these functions are dependent on the transcription factor TFIIIC. More recently TFIIIC bound sites devoid of pol III, termed Extra-TFIIIC sites (ETC) have been identified in budding yeast and these sites also function as insulators and affect genome organization. Subsequent studies in Schizosaccharomyces pombe showed that TFIIIC bound sites were insulators and also functioned as Chromosome Organization Clamps (COC); tethering the sites to the nuclear periphery. Very recently studies have moved to mammalian systems where pol III genes and their associated factors have been investigated in both mouse and human cells. Short interspersed nuclear elements (SINEs) that bind TFIIIC, function as insulator elements and tDNAs can also function as both enhancer - blocking and barrier insulators in these organisms. It was also recently shown that tDNAs cluster with other tDNAs and with ETCs but not with pol II transcribed genes. Intriguingly, TFIIIC is often found near pol II transcription start sites and it remains unclear what the consequences of TFIIIC based genomic organization are and what influence pol III factors have on pol II transcribed genes and vice versa. In this review we provide a comprehensive overview of the known data on pol III factors in insulation and genome organization and identify the many open questions that require further investigation. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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97
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Abstract
Long-range interactions between transcription regulatory elements play an important role in gene activation, epigenetic silencing, and chromatin organization. Transcriptional activation or repression of developmentally regulated genes is often accomplished through tissue-specific chromatin architecture and dynamic localization between active transcription factories and repressive Polycomb bodies. However, the mechanisms underlying the structural organization of chromatin and the coordination of physical interactions are not fully understood. Insulators and Polycomb group proteins form highly conserved multiprotein complexes that mediate functional long-range interactions and have proposed roles in nuclear organization. In this review, we explore recent findings that have broadened our understanding of the function of these proteins and provide an integrative model for the roles of insulators in nuclear organization.
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Affiliation(s)
- Kevin Van Bortle
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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98
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Van Bortle K, Corces VG. tDNA insulators and the emerging role of TFIIIC in genome organization. Transcription 2012; 3:277-84. [PMID: 22889843 DOI: 10.4161/trns.21579] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent findings provide evidence that tDNAs function as chromatin insulators from yeast to humans. TFIIIC, a transcription factor that interacts with the B-box in tDNAs as well as thousands of ETC sites in the genome, is responsible for insulator function. Though tDNAs are capable of enhancer-blocking and barrier activities for which insulators are defined, new insights into the relationship between insulators and chromatin structure suggest that TFIIIC serves a complex role in genome organization. We review the role of tRNA genes and TFIIIC as chromatin insulators, and highlight recent findings that have broadened our understanding of insulators in genome biology.
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99
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The BEAF insulator regulates genes involved in cell polarity and neoplastic growth. Dev Biol 2012; 369:124-32. [PMID: 22743648 DOI: 10.1016/j.ydbio.2012.06.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/01/2012] [Accepted: 06/20/2012] [Indexed: 01/05/2023]
Abstract
Boundary Element Associated Factor-32 (BEAF-32) is an insulator protein predominantly found near gene promoters and thought to play a role in gene expression. We find that mutations in BEAF-32 are lethal, show loss of epithelial morphology in imaginal discs and cause neoplastic growth defects. To investigate the molecular mechanisms underlying this phenotype, we carried out a genome-wide analysis of BEAF-32 localization in wing imaginal disc cells. Mutation of BEAF-32 results in miss-regulation of 3850 genes by at least 1.5-fold, 794 of which are bound by this protein in wing imaginal cells. Up-regulated genes encode proteins involved in cell polarity, cell proliferation and cell differentiation. Among the down-regulated genes are those encoding components of the wingless pathway, which is required for cell differentiation. Miss-regulation of these genes explains the unregulated cell growth and neoplastic phenotypes observed in imaginal tissues of BEAF-32 mutants.
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100
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Sexton T, Kurukuti S, Mitchell JA, Umlauf D, Nagano T, Fraser P. Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip. Nat Protoc 2012; 7:1335-50. [PMID: 22722369 DOI: 10.1038/nprot.2012.071] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromosome conformation capture (3C) is a powerful technique for analyzing spatial chromatin organization in vivo. Technical variants of the assay ('4C') allow the systematic detection of genome-wide coassociations with bait sequences of interest, enabling the nuclear environments of specific genes to be probed. We describe enhanced 4C (e4C, enhanced chromosome conformation capture on chip), a technique incorporating additional enrichment steps for bait-specific sequences, and thus improving sensitivity in the detection of weaker, distal chromatin coassociations. In brief, e4C entails the fixation, restriction digestion and ligation steps of conventional 3C, with an optional chromatin immunoprecipitation (ChIP) step to select for subsets of chromatin coassociations, followed by bait enrichment by biotinylated primer extension and pull-down, adapter ligation and PCR amplification. Chromatin coassociations with the bait sequence can then be assessed by hybridizing e4C products to microarrays or sequencing. The e4C procedure takes approximately 1 week to go from tissue to DNA ready for microarray hybridization.
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Affiliation(s)
- Tom Sexton
- Laboratory of Chromatin and Cell Biology, Institute of Human Genetics, Montpellier, France
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