DOCSLIB.ORG

Gene Expression by AIRE the Mechanism of Tissue-Restricted

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Gene Expression by AIRE the Mechanism of Tissue-Restricted The Mechanism of Tissue-Restricted Antigen Gene Expression by AIRE Kristina Zumer, Kalle Saksela and B. Matija Peterlin This information is current as J Immunol 2013; 190:2479-2482; ; of September 29, 2021. doi: 10.4049/jimmunol.1203210 http://www.jimmunol.org/content/190/6/2479 Downloaded from References This article cites 58 articles, 20 of which you can access for free at: http://www.jimmunol.org/content/190/6/2479.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on September 29, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Mechanism of Tissue-Restricted Antigen Gene Expression by AIRE Kristina Zumer,*ˇ Kalle Saksela,* and B. Matija Peterlin*,† The autoimmune regulator is a critical transcription sitivity inducing factor (DSIF). The release of RNAPII to factor for generating central tolerance in the thymus. elongation is mediated by the positive transcription elonga- Recent studies have revealed how the autoimmune reg- tion factor b (P-TEFb), composed of a regulatory cyclin sub- ulator targets many otherwise tissue-restricted Ag genes unit (CycT1 or CycT2) and the cyclin-dependent kinase 9 to enable negative selection of autoreactive T cells. The (15). P-TEFb phosphorylates subunits of DSIF and NELF as Journal of Immunology, 2013, 190: 2479–2482. well as serine residues at position 2 (Ser2) in the C-terminal domain (CTD) repeats of the largest RNAPII subunit (RPB1) (16). DSIF is thus changed to an elongation factor, NELF is Downloaded from AIRE he autoimmune regulator ( ) gene was identified released from the nascent RNA, and the phosphorylated by positional cloning of the genetic locus linked to a RNAPII can now elongate (16). The CTD of human RNAPII T rare autoimmune disease, autoimmune-polyendocri- contains 52 heptapeptide repeats (YSPTSPS). The serines, nopathy-candidiasis-ectodermal dystrophy (APECED) (1, 2). threonines, and tyrosines in these repeats are phosphorylated The encoded AIRE protein is expressed primarily in medul- by P-TEFb and other kinases in distinct phases of transcrip- lary thymic epithelial cells (mTECs) (3). AIRE is also ex- tion, giving rise to diverse set of instructions, which are http://www.jimmunol.org/ pressed in peripheral lymphoid tissues (4), where its contri- known as the CTD code (17). The phosphorylated elongating bution to tolerance remains to be investigated. The mouse 2/2 RNAPII directs cotranscriptional processing, that is, splicing model of the human APECED disease, the Aire mouse, and polyadenylation of genes (18). Transcription elongation was instrumental in identifying the cellular role of AIRE, proceeds until termination, upon which RNAPII becomes which is to regulate promiscuous expression of tissue-restricted dephosphorylated, and the cycle begins anew. Recent genome- Ag(TRA)genesinmTECs(5).Thekeyfindingwasthat 2/2 wide analyses revealed an unexpectedly high abundance of mTECs from Aire versus wild-type mice expressed fewer TRAs. Although this promiscuous gene expression in mTECs paused RNAPII at most promoters, including those of inac- by guest on September 29, 2021 had been recognized previously (6), the underlying mecha- tive genes (19–22). nism remained elusive. To date, AIRE is the only identified AIRE is a transcription factor that assembles into oligomers transcription factor that regulates this process. Among others, and forms punctate structures that colocalize with CREB- AIRE activates insulin, interphotoreceptor retinoid-binding binding protein, P-TEFb, and small nuclear ribonucleopro- protein A, and mucin 6 genes, all of which had been linked teins in the nucleus (23–25). The estimated number of AIRE- to autoimmunity in humans or AIRE-deficient mice (7, 8). regulated genes ranges from several hundred to thousands. Expressed TRAs are then processed and presented on the They have diverse promoters and are regulated by distinct surface of mTECs or taken up by dendritic cells (9, 10). Ex- transcription factors in their corresponding tissues. These posure of maturing T cells to these Ags is critical for negative findings raise the conundrum of how AIRE can regulate such selection of T cells in the thymus (11, 12). In the absence of a large repertoire of divergent genes. Recent work from others AIRE, autoreactive T cells mature and escape into the pe- and us has addressed this question and revealed the mecha- riphery, which can lead to autoimmunity (7, 8, 13). nisms of action of this enigmatic protein (26–31). Transcription of protein-coding genes occurs in several The AIRE protein has a predicted molecular mass of 58 phases, all of which are regulated (14). First, transcription kDa (Fig. 1A) (3). It forms large oligomers, which are detected factors and RNA polymerase II (RNAPII) are recruited to in a .670-kDa fraction by gel filtration (32). The N terminus promoters. Although RNAPII initiates transcription, it then of AIRE contains the homogeneously staining region (HSR) pauses because of the action of negative elongation factor and the Sp100, AIRE-1, NucP41/75, and DEAF-1 (SAND) (NELF) and 6-dichloro-1-a-D-ribofuranosylbenzimidazole sen- domain (Fig. 1A). Mutations in HSR from APECED patients *Department of Virology, Haartman Institute, Helsinki University Central Hospital, PK, DNA-dependent protein kinase; DSIF, 6-dichloro-1-a-D-ribofuranosylbenzimidazole University of Helsinki, FIN-00014 Helsinki, Finland; and †Department of Medicine, sensitivity inducing factor; H3K4, histone H3 unmodified at Lys4; HSR, homogeneously The Rosalind Russell Medical Research Center, University of California at San Fran- staining region; NELF, negative elongation factor; PHD, plant homology domain; P- cisco, San Francisco, CA 94143 TEFb, positive transcription elongation factor b; RNAPII, RNA polymerase II; SAND, Sp100, AIRE-1, NucP41/75, and DEAF-1; TAD, transcriptional activation domain; Received for publication November 21, 2012. Accepted for publication January 8, 2013. TRA, tissue-restricted Ag. Address correspondence and reprint requests to Dr. B. Matija Peterlin, University of California at San Francisco, 533 Parnassus Avenue, Box 0703, Room U-432, San Copyright Ó 2013 by The American Association of Immunologists, Inc. 0022-1767/13/$16.00 Francisco, CA 94143-0703. E-mail address: [email protected] Abbreviations used in this article: AIRE, autoimmune regulator; APECED, autoimmune- polyendocrinopathy-candidiasis-ectodermal dystrophy; CTD, C-terminal domain; DNA- www.jimmunol.org/cgi/doi/10.4049/jimmunol.1203210 2480 BRIEF REVIEWS: MECHANISM OF AIRE FUNCTION Downloaded from http://www.jimmunol.org/ FIGURE 1. AIRE protein domains, key interacting partners, and mechanism of TRA gene expression. (A) AIRE contains several domains that are related to those in other transcription factors. From the N terminus they are: HSR (green), which is important for the oligomerization of AIRE and may function as a caspase recruitment domain (58); SAND (green); PHD1 and PHD2 (violet); proline-rich region (PRR; orange); and the TAD (red). Protein residues cor- responding to human AIRE are labeled above, and the position of the four LXXLL motifs is marked below the diagram. The location of the nuclear localization signal is also indicated (KRK). Mutations discussed in this review are marked with an asterisk below the diagram with accompanying labels. Arrows depict interactions between DNA-PK, H3K4, P-TEFb, and AIRE. (B) Schematic diagram depicting the molecular mechanism of AIRE-regulated TRA gene expression. by guest on September 29, 2021 Combinatorial interactions between AIRE, unmodified H3K4 (yellow), DNA-PK (red), and RNAPII (blue) recruit AIRE to a TRA promoter. AIRE brings P- TEFb (red) to phosphorylate the RNAPII CTD, and this results in transcription elongation, mRNA processing, and TRA gene expression. Histone H2AX with phosphorylated Ser139 (gH2AX), which marks DNA double-strand breaks, is depicted in yellow. (C) The Venn diagram marks sets of genes that contain un- modified H3K4, engaged RNAPII, and DNA-PK at their promoters. AIRE is targeted to and can regulate expression of genes at the intersection of these sets. disrupt multimerization, which is essential for AIRE function in proteins involved in ubiquitylation (40). PHDs are pro- (32, 33). The AIRE SAND domain is also involved in this tein–protein interaction modules, which can mediate binding oligomer formation. It lacks the canonical KDWK motif, to nucleosomes (41, 42). Such PHDs bind to N-terminal tails which is required for DNA binding of other SAND domains of histone H3, discriminating between those methylated (34). Although DNA binding of the AIRE SAND domain (H3K4me3) or unmodified (H3K4) at Lys4. AIRE PHD1 is had been reported in vitro (35, 36), it appears to be non- most closely related to the BHC80 PHD that interacts
Load more

Recommended publications
  • DNA Methylation Regulates Discrimination of Enhancers From
    Sharifi-Zarchi et al. BMC Genomics (2017) 18:964 DOI 10.1186/s12864-017-4353-7 RESEARCHARTICLE Open Access DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism Ali Sharifi-Zarchi1,2,3,4†, Daniela Gerovska5†, Kenjiro Adachi6, Mehdi Totonchi3, Hamid Pezeshk7,8, Ryan J. Taft9, Hans R. Schöler6,10, Hamidreza Chitsaz2, Mehdi Sadeghi8,11, Hossein Baharvand3,12* and Marcos J. Araúzo-Bravo5,13,14* Abstract Background: DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. Results: We investigated the relationship between DNA methylation and active chromatin marks through genome- wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci. We hypothesized “seesaw” dynamics between H3K4me1 and H3K4me3 in the low and intermediate DNA methylation range, in which DNA methylation discriminates between enhancers and promoters, marked by H3K4me1 and H3K4me3, respectively. Low methylated regions are H3K4me3 enriched, while those with intermediate DNA methylation levels are progressively H3K4me1 enriched. Additionally, the enrichment of H3K27ac, distinguishing active from primed enhancers, follows a plateau in the lower range of the intermediate DNA methylation level, corresponding to active enhancers, and decreases linearly in the higher range of the intermediate DNA methylation. Thus, the decrease of the DNA methylation switches smoothly the state of the enhancers from a primed to an active state.
    [Show full text]
  • Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin
    cells Review Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin Agnieszka Bochy ´nska,Juliane Lüscher-Firzlaff and Bernhard Lüscher * ID Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany; [email protected] (A.B.); jluescher-fi[email protected] (J.L.-F.) * Correspondence: [email protected]; Tel.: +49-241-8088850; Fax: +49-241-8082427 Received: 18 January 2018; Accepted: 27 February 2018; Published: 2 March 2018 Abstract: Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex.
    [Show full text]
  • Modeling of Histone Modifications Reveals Formation Mechanism and Function of Bivalent Chromatin
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.03.429504; this version posted February 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Modeling of histone modifications reveals formation mechanism and function of bivalent chromatin Wei Zhao1,2, Lingxia Qiao1, Shiyu Yan2, Qing Nie3,*, Lei Zhang1,2,* 1 Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China 2 Center for Quantitative Biology, Peking University, Beijing 100871, China 3 Department of Mathematics and Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA. *Corresponding authors: Qing Nie, email: [email protected]; Lei Zhang, email: [email protected] Abstract Bivalent chromatin is characterized by occupation of both activating histone modifications and repressive histone modifications. While bivalent chromatin is known to link with many biological processes, the mechanisms responsible for its multiple functions remain unclear. Here, we develop a mathematical model that involves antagonistic histone modifications H3K4me3 and H3K27me3 to capture the key features of bivalent chromatin. Three necessary conditions for the emergence of bivalent chromatin are identified, including advantageous methylating activity over demethylating activity, frequent noise conversions of modifications, and sufficient nonlinearity. The first condition is further confirmed by analyzing the
    [Show full text]
  • Epigenetic Regulation of Promiscuous Gene Expression in Thymic Medullary Epithelial Cells
    Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells Lars-Oliver Tykocinskia,1,2, Anna Sinemusa,1, Esmail Rezavandya, Yanina Weilandb, David Baddeleyb, Christoph Cremerb, Stephan Sonntagc, Klaus Willeckec, Jens Derbinskia, and Bruno Kyewskia,3 aDivision of Developmental Immunology, Tumor Immunology Program, German Cancer Research Center, D-69120 Heidelberg, Germany; bKirchhoff Institute for Physics, University of Heidelberg, D-69120 Heidelberg, Germany; and cInstitute for Genetics, University of Bonn, D-53117 Bonn, Germany Edited* by Philippa Marrack, National Jewish Health, Denver, CO, and approved September 28, 2010 (received for review July 2, 2010) Thymic central tolerance comprehensively imprints the T-cell re- ing of delimited regions allowing access of general and specific ceptor repertoire before T cells seed the periphery. Medullary transcriptional factors to act on gene-specific control elements thymic epithelial cells (mTECs) play a pivotal role in this process by (8). This scenario is clearly different from the intricate regulation virtue of promiscuous expression of tissue-restricted autoantigens. of functionally related gene families like the Hox gene locus or β The molecular regulation of this unusual gene expression, in the -globin gene locus (9). A similar phenomenon as observed in Drosophila particular the involvement of epigenetic mechanisms is only poorly has been reported for housekeeping genes but not for understood. By studying promiscuous expression of the mouse TRAs in vertebrates (10). casein locus, we report that transcription of this locus proceeds Here we analyzed the interrelationship between emerging gene expression patterns at the single cell level, promoter-associated from a delimited region (“entry site”) to increasingly complex pat- epigenetic marks, and the differentiation of mTECs in the murine terns along with mTEC maturation.
    [Show full text]
  • H3k4me3 Is Neither Instructive For, Nor Informed By, Transcription
    bioRxiv preprint first posted online Jul. 19, 2019; doi: http://dx.doi.org/10.1101/709014. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. H3K4me3 is neither instructive for, nor informed by, transcription. Struan C Murray1, Philipp Lorenz1, Françoise S Howe1, Meredith Wouters1, Thomas Brown1, Shidong Xi1, Harry Fischl1, Walaa Khushaim1, Joseph Regish Rayappu1, Andrew Angel1 & Jane Mellor1* 1Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. *Corresponding author. Tel: +44 1865 613241; E-mail: [email protected] Key words histone modification; gene regulation; H3K4me3; chromatin; RNA polymerase Abstract H3K4me3 is a near-universal histone modification found predominantly at the 5’ region of genes, with a well-documented association with gene activity. H3K4me3 has been ascribed roles as both an instructor of gene expression and also a downstream consequence of expression, yet neither has been convincingly proven on a genome-wide scale. Here we test these relationships using a combination of bioinformatics, modelling and experimental data from budding yeast in which the levels of H3K4me3 have been massively ablated. We find that loss of H3K4me3 has no effect on the levels of nascent transcription or transcript in the population. Moreover, we observe no change in the rates of transcription initiation, elongation, mRNA export or turnover, or in protein levels, or cell-to-cell variation of mRNA. Loss of H3K4me3 also has no effect on the large changes in gene expression patterns that follow galactose induction.
    [Show full text]
  • Dual Recognition of H3k4me3 and H3k27me3 by a Plant Histone Reader SHL
    ARTICLE DOI: 10.1038/s41467-018-04836-y OPEN Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL Shuiming Qian1,2, Xinchen Lv3,4, Ray N. Scheid1,2,LiLu1,2, Zhenlin Yang3,4, Wei Chen3, Rui Liu3, Melissa D. Boersma2, John M. Denu2,5,6, Xuehua Zhong 1,2 & Jiamu Du 3 The ability of a cell to dynamically switch its chromatin between different functional states constitutes a key mechanism regulating gene expression. Histone mark “readers” display 1234567890():,; distinct binding specificity to different histone modifications and play critical roles in reg- ulating chromatin states. Here, we show a plant-specific histone reader SHORT LIFE (SHL) capable of recognizing both H3K27me3 and H3K4me3 via its bromo-adjacent homology (BAH) and plant homeodomain (PHD) domains, respectively. Detailed biochemical and structural studies suggest a binding mechanism that is mutually exclusive for either H3K4me3 or H3K27me3. Furthermore, we show a genome-wide co-localization of SHL with H3K27me3 and H3K4me3, and that BAH-H3K27me3 and PHD-H3K4me3 interactions are important for SHL-mediated floral repression. Together, our study establishes BAH-PHD cassette as a dual histone methyl-lysine binding module that is distinct from others in recognizing both active and repressive histone marks. 1 Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA. 2 Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA. 3 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
    [Show full text]
  • Chromatin Dynamics During DNA Replication Raz Bar-Ziv*, Yoav Voichek* and Naama Barkai†
    Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Chromatin Dynamics during DNA Replication Raz Bar-Ziv*, Yoav Voichek* and Naama Barkai† Affiliations: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel. *these authors contributed equally to the manuscript †Correspondence to: [email protected] Keywords: Chromatin; Replication; Summary: Chromatin is composed of DNA and histones, which provide a unified platform for regulating DNA-related processes, mostly through their post translational modification. During DNA replication, histone arrangement is perturbed, to first allow progression of DNA polymerase and then during repackaging of the replicated DNA. To study how DNA replication influences the pattern of histone modification, we followed the cell-cycle dynamics of ten histone marks in budding yeast. We find that histones deposited on newly replicated DNA are modified at different rates; while some marks appear immediately upon replication (e.g. H4K16ac, H3K4me1), others increase with transcription-dependent delays (e.g. H3K4me3, H3K36me3). Notably, H3K9ac was deposited as a wave preceding the replication fork by ~5-6 kb. This replication-guided H3K9ac was fully dependent on the acetyltransferase Rtt109, while expression-guided H3K9ac was deposited by Gcn5. Further, topoisomerase depletion intensified H3K9ac in front of the replication fork, and in sites where RNA polymerase II was trapped, suggesting supercoiling stresses trigger H3K9 acetylation. Our results assign complementary roles for DNA replication and gene expression in defining the pattern of histone modification. Introduction: In eukaryotic cells, DNA is wrapped around histone octamers to form nucleosomes, the basic building blocks of the chromatin structure.
    [Show full text]
  • Histone H3Q5 Serotonylation Stabilizes H3K4 Methylation and Potentiates Its Readout
    Histone H3Q5 serotonylation stabilizes H3K4 methylation and potentiates its readout Shuai Zhaoa,1, Kelly N. Chuhb,1, Baichao Zhanga,1, Barbara E. Dulb, Robert E. Thompsonb, Lorna A. Farrellyc,d, Xiaohui Liue, Ning Xue, Yi Xuee, Robert G. Roederf, Ian Mazec,d,2, Tom W. Muirb,2, and Haitao Lia,g,2 aMinistry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; bDepartment of Chemistry, Princeton University, Princeton, NJ 08540; cNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029; dDepartment of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029; eNational Protein Science Technology Center, School of Life Sciences, Tsinghua University, Beijing 100084, China; fLaboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065; and gTsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China Edited by Peter Cheung, York University, Toronto, ON, Canada, and accepted by Editorial Board Member Karolin Luger November 12, 2020 (received for review August 7, 2020) Serotonylation of glutamine 5 on histone H3 (H3Q5ser) was recently established that H3K4me3 regulates gene expression through re- identified as a permissive posttranslational modification that coexists cruitment of nuclear factors that contain reader domains specific with adjacent lysine 4 trimethylation (H3K4me3). While the resulting for the mark. These include ATP-dependent chromatin remod- dual modification, H3K4me3Q5ser, is enriched at regions of active eling enzymes, as well as several transcription factors (13).
    [Show full text]
  • Genome-Wide Mapping of Histone H3 Lysine 4
    Hussey et al. BMC Plant Biology (2015) 15:117 DOI 10.1186/s12870-015-0499-0 RESEARCH ARTICLE Open Access Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem Steven G Hussey1, Eshchar Mizrachi1, Andrew Groover2,3, Dave K Berger4 and Alexander A Myburg1* Abstract Background: Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Results: Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq.
    [Show full text]
  • Embryonic Transcription Is Controlled by Maternally Defined Chromatin State
    ARTICLE Received 12 May 2015 | Accepted 10 Nov 2015 | Published 18 Dec 2015 DOI: 10.1038/ncomms10148 OPEN Embryonic transcription is controlled by maternally defined chromatin state Saartje Hontelez1,*, Ila van Kruijsbergen1,*, Georgios Georgiou1,*, Simon J. van Heeringen1, Ozren Bogdanovic2, Ryan Lister2,3 & Gert Jan C. Veenstra1 Histone-modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during embryonic development. Here we generate a comprehensive set of epigenome reference maps, which we use to determine the extent to which maternal factors shape chromatin state in Xenopus embryos. Using a-amanitin to inhibit zygotic transcription, we find that the majority of H3K4me3- and H3K27me3-enriched regions form a maternally defined epigenetic regulatory space with an underlying logic of hypomethylated islands. This maternal regulatory space extends to a substantial proportion of neurula stage-activated promoters. In contrast, p300 recruitment to distal regulatory regions requires embryonic transcription at most loci. The results show that H3K4me3 and H3K27me3 are part of a regulatory space that exerts an extended maternal control well into post-gastrulation development, and highlight the combinatorial action of maternal and zygotic factors through proximal and distal regulatory sequences. 1 Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, PO Box 9101, 6500 HB Nijmegen, The Netherlands. 2 ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia. 3 The Harry Perkins Institute of Medical Research, Perth, Western Australia 6009, Australia. * These authors contributed equally to this work.
    [Show full text]
  • G9a Selectively Represses a Class of Late-Replicating Genes at the Nuclear Periphery
    G9a selectively represses a class of late-replicating genes at the nuclear periphery Tomoki Yokochia,1, Kristina Poducha, Tyrone Rybaa, Junjie Lua, Ichiro Hiratania, Makoto Tachibanab, Yoichi Shinkaib, and David M. Gilberta,2 aDepartment of Biological Science, Florida State University, Tallahassee, FL 32306; and bExperimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan Edited by Mark T. Groudine, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved September 25, 2009 (received for review June 4, 2009) We have investigated the role of the histone methyltransferase G9a ery and that G9a-null ESCs are selectively depleted of the in the establishment of silent nuclear compartments. Following con- H3K9me2 localized at the periphery (13). Chromatin at the nuclear ditional knockout of the G9a methyltransferase in mouse ESCs, 167 periphery also is replicated late during S-phase, and differentiation genes were significantly up-regulated, and no genes were strongly of ESCs leads to changes in the replication timing of large chro- down-regulated. A partially overlapping set of 119 genes were matin domains, accompanied by the movement of those domains up-regulated after differentiation of G9a-depleted cells to neural toward or away from the nuclear periphery and the respective precursors. Promoters of these G9a-repressed genes were AT rich and silencing or activation of genes within those domains (14). To- H3K9me2 enriched but H3K4me3 depleted and were not highly DNA gether, these results suggested the possibility that G9a may help methylated. Representative genes were found to be close to the establish compartments of facultative heterochromatin at the nu- nuclear periphery, which was significantly enriched for G9a-depen- clear periphery.
    [Show full text]
  • Downloaded DNA Methylation, H3k9me1/ Additional Fle 2: Table S2
    Liu et al. Epigenetics & Chromatin (2019) 12:40 https://doi.org/10.1186/s13072-019-0285-6 Epigenetics & Chromatin RESEARCH Open Access H3K4me2 functions as a repressive epigenetic mark in plants Yuhao Liu1, Kunpeng Liu1, Liufan Yin1, Yu Yu1, Ji Qi2, Wen‑Hui Shen1,3, Jun Zhu4, Yijing Zhang5,6* and Aiwu Dong1* Abstract Background: In animals, H3K4me2 and H3K4me3 are enriched at the transcription start site (TSS) and function as epigenetic marks that regulate gene transcription, but their functions in plants have not been fully characterized. Results: We used chromatin immunoprecipitation sequencing to analyze the rice genome‑wide changes to H3K4me1/H3K4me2/H3K4me3 following the loss of an H3K4‑specifc methyltransferase, SDG701. The knockdown of SDG701 resulted in a global decrease in H3K4me2/H3K4me3 levels throughout the rice genome. An RNA‑sequencing analysis revealed that many genes related to diverse developmental processes were misregulated in the SDG701 knockdown mutant. In rice, H3K4me3 and H3K36me3 are positively correlated with gene transcription; however, surprisingly, the H3K4me2 level was negatively associated with gene transcription levels. Furthermore, the H3K4me3 level at the TSS region decreased signifcantly in the genes that exhibited down‑regulated expression in the SDG701 knockdown mutant. In contrast, the genes with up‑regulated expression in the mutant were associated with a con‑ siderable decrease in H3K4me2 levels over the gene body region. Conclusion: A comparison of the genome‑wide distributions of H3K4me2 in eukaryotes indicated that the H3K4me2 level is not correlated with the gene transcription level in yeast, but is positively and negatively correlated with gene expression in animals and plants, respectively.
    [Show full text]