DOCSLIB.ORG

Histone Modifications and Their Role in Epigenetics of Atopy and Allergic Diseases

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Histone Modifications and Their Role in Epigenetics of Atopy and Allergic Diseases Histone modifications and their role in epigenetics of atopy and allergic diseases The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Alaskhar Alhamwe, B., R. Khalaila, J. Wolf, V. von Bülow, H. Harb, F. Alhamdan, C. S. Hii, et al. 2018. “Histone modifications and their role in epigenetics of atopy and allergic diseases.” Allergy, Asthma, and Clinical Immunology : Official Journal of the Canadian Society of Allergy and Clinical Immunology 14 (1): 39. doi:10.1186/ s13223-018-0259-4. http://dx.doi.org/10.1186/s13223-018-0259-4. Published Version doi:10.1186/s13223-018-0259-4 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:37160091 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Alaskhar Alhamwe et al. Allergy Asthma Clin Immunol (2018) 14:39 Allergy, Asthma & Clinical Immunology https://doi.org/10.1186/s13223-018-0259-4 REVIEW Open Access Histone modifcations and their role in epigenetics of atopy and allergic diseases Bilal Alaskhar Alhamwe1,2†, Razi Khalaila1†, Johanna Wolf1†, Verena von Bülow1, Hani Harb1,2,6,8, Fahd Alhamdan1, Charles S. Hii3,4, Susan L. Prescott2,5, Antonio Ferrante2,3,4, Harald Renz1,2,6‡, Holger Garn1,6‡ and Daniel P. Potaczek1,2,6,7*‡ Abstract This review covers basic aspects of histone modifcation and the role of posttranslational histone modifcations in the development of allergic diseases, including the immune mechanisms underlying this development. Together with DNA methylation, histone modifcations (including histone acetylation, methylation, phosphorylation, ubiquitina- tion, etc.) represent the classical epigenetic mechanisms. However, much less attention has been given to histone modifcations than to DNA methylation in the context of allergy. A systematic review of the literature was undertaken to provide an unbiased and comprehensive update on the involvement of histone modifcations in allergy and the mechanisms underlying this development. In addition to covering the growing interest in the contribution of histone modifcations in regulating the development of allergic diseases, this review summarizes some of the evidence sup- porting this contribution. There are at least two levels at which the role of histone modifcations is manifested. One is the regulation of cells that contribute to the allergic infammation (T cells and macrophages) and those that partici- pate in airway remodeling [(myo-) fbroblasts]. The other is the direct association between histone modifcations and allergic phenotypes. Inhibitors of histone-modifying enzymes may potentially be used as anti-allergic drugs. Further- more, epigenetic patterns may provide novel tools in the diagnosis of allergic disorders. Keywords: Allergy, Asthma, Atopy, Epigenetic (-s), Histone acetylation, Histone methylation, Histone modifcation (-s), Histone phosphorylation, Infammation, Immunity Background phenomenon [5–9]. While DNA methylation has been In the last few decades, there has been a substantial extensively studied as the epigenetic mechanism involved increase in the prevalence of allergic diseases in the in the etiopathogenesis of allergic disorders, posttrans- industrialized countries [1–3]. Since this change could lational histone modifcations, another important clas- not be explained by a rather stable population genetic sical epigenetic mechanism, have not been as widely profle [2–4], increased exposure to harmful and reduced investigated and discussed because it is not considered exposure to protective epigenetically-mediated envi- as important as DNA methylation [5–7, 10]. Te review ronmental factors have been considered, at least in frstly describes the (bio-) chemical basics of epigenetic part, as a possible explanation for this epidemiological histone modifcations. Tis is followed by an assessment of recent evidence that supports a role for histone modif- cations in the epigenetic regulation of the pathogenesis of *Correspondence: [email protected]‑marburg.de allergy and related disorders, together with a description †Bilal Alaskhar Alhamwe, Razi Khalaila and Johanna Wolf contributed equally to this work as frst authors of the underlying cellular and molecular mechanisms. ‡Harald Renz, Holger Garn and Daniel P. Potaczek contributed equally to this work as senior authors Main text 1 Institute of Laboratory Medicine and Pathobiochemistry, Molecular Histone modifcations: the basics Diagnostics, Philipps University Marburg, Hans‑Meerwein‑Straße 3, 35043 Marburg, Germany Similarly to DNA methylation, posttranslational histone Full list of author information is available at the end of the article modifcations do not afect DNA nucleotide sequence but © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat​iveco​mmons​.org/licen​ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat​iveco​mmons​.org/ publi​cdoma​in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Alaskhar Alhamwe et al. Allergy Asthma Clin Immunol (2018) 14:39 Page 2 of 16 can modify its availability to the transcriptional machin- summarizes the various forms of histone modifcations ery. Although histone modifcations play also other roles, appearing in this review along with their efects on gene such as histone phosphorylation, best known for its transcriptional activity. contribution to DNA repair in response to cell damage, this review deals primarily with general mechanisms of histone modifcations in the context of their role in epi- Histone acetylation genetic modulation of gene expression. Several types of Histone acetylation status is regulated by two groups of histone modifcations are known, amongst which acety- enzymes exerting opposite efects, histone acetyltrans- lation, methylation, phosphorylation, and ubiquitination ferases (HATs) and histone deacetylases (HDACs). HATs are the best studied and most important in terms of the catalyze the transfer of an acetyl group from acetyl-CoA regulation of chromatin structure and (transcriptional) to an amino acid group of the target lysine residues in activity [11–15]. In general, histone modifcations are the histone tails, which leads to the removal of a posi- catalyzed by specifc enzymes that act, predominantly, tive charge on the histones, weakening the interaction but not exclusively (e.g. some types of histone phospho- between histones and (negatively charged phosphate rylation), at the histone N-terminal tails involving amino groups of) DNA. Tis in turn typically makes the chro- acids such as lysine or arginine as well as serine, threo- matin less compact and thus more accessible to the tran- nine, tyrosine, etc. Histone acetylation usually leads to scriptional machinery. HDACs remove acetyl groups higher gene expression. Tis may not always be the case from histone tail lysine residues and thereby work as for histone H4 [16–18]. Histone methylation in turn has repressors of gene expression [5, 14, 21–24]. either transcriptionally permissive or repressive charac- HATs are classifed into fve (or sometimes six) fami- ter, depending on the location of targeted amino acid res- lies. Te GCN5-related N-acetyltransferase (GNAT) idues in the histone tail and/or the number of modifying family comprises KAT2A and KAT2B enzymes. Tey (e.g. methyl) groups added [5, 6, 14, 15, 19, 20]. Table 1 are involved in acetylation of histones and transcription Table 1 List of histone modifcations appearing in this review along with their efects on the transcriptional activity Modifcation and site Abbreviation Efect on transcriptiona Histone acetylation Histone 3 panacetylation H3ac Activating/permissive Histone 4 panacetylation H4ac Activating/permissiveb Histone 3 lysine 4 acetylation H3K4ac Activating/permissive Histone 3 lysine 9 acetylation H3K9ac Activating/permissive Histone 3 lysine 14 acetylation H3K14ac Activating/permissive Histone 3 lysine 18 acetylation H3K18ac Activating/permissive Histone 3 lysine 27 acetylation H3K27ac Activating/permissive Histone 4 lysine 16 acetylation H4K16ac Activating/permissive Histone methylation Histone 3 lysine 4 methylation H3K4me1 Activating/permissive Histone 3 lysine 4 dimethylation H3K4me2 Activating/permissive Histone 3 lysine 4 trimethylation H3K4me3 Activating/permissive Histone 3 lysine 9 dimethylation H3K9me2 Repressive Histone 3 lysine 9 trimethylation H3K9me3 Repressive Histone 3 lysine 27 trimethylation H3K27me3 Repressive Histone 3 lysine 36 trimethylation H3K36me3 Activating/permissive Histone 3 lysine 79 methylation H3K79me1 Activating/permissive Histone phosphorylation Histone 3 serine 10 phosphorylation H3S10ph Activating/permissive Histone ubiquitination Histone 2A ubiquitination H2Aub Repressive Histone 2B ubiquitination H2Bub Activating/permissive a According to the cells signaling technology webpage [100] and/or other sources referenced in the “Main text” and/or Tables 2 and 3 of this review b See also “Histone modifcations: the basics” Alaskhar Alhamwe Table 2 Studies on the role
Load more

Recommended publications
  • Histone H3K4 Demethylation Is Negatively Regulated by Histone H3 Acetylation in Saccharomyces Cerevisiae
    Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae Vicki E. Maltbya, Benjamin J. E. Martina, Julie Brind’Amourb,1, Adam T. Chruscickia,1, Kristina L. McBurneya, Julia M. Schulzec, Ian J. Johnsona, Mark Hillsd, Thomas Hentrichc, Michael S. Koborc, Matthew C. Lorinczb, and LeAnn J. Howea,2 Departments of aBiochemistry and Molecular Biology and bMedical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; cCenter for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4; and dTerry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3 Edited by Kevin Struhl, Harvard Medical School, Boston, MA, and approved September 12, 2012 (received for review February 6, 2012) Histone H3 lysine 4 trimethylation (H3K4me3) is a hallmark of of lysine-specific HDMs have been identified: amine oxidases, transcription initiation, but how H3K4me3 is demethylated during such as LSD1, and the JmjC (Jumonji C) domain–containing gene repression is poorly understood. Jhd2, a JmjC domain protein, demethylases. This latter class of demethylases can be split fur- was recently identified as the major H3K4me3 histone demethylase ther into several subfamilies, including the evolutionarily con- (HDM) in Saccharomyces cerevisiae. Although JHD2 is required for served JARID1 family of demethylases, which is characterized JHD2 removal of methylation upon gene repression, deletion of does not only by a JmjC domain but also by JmjN, AT-rich interactive, not result in increased levels of H3K4me3 in bulk histones, indicating C5HC2 zinc finger, and PHD finger domains (6). In the yeast S. that this HDM is unable to demethylate histones during steady-state cerevisiae, the lone member of the JARID1 family of demethy- conditions.
    [Show full text]
  • Recognition of Histone Acetylation by the GAS41 YEATS Domain Promotes H2A.Z Deposition in Non-Small Cell Lung Cancer
    Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer Chih-Chao Hsu,1,2,8 Jiejun Shi,3,8 Chao Yuan,1,2,7,8 Dan Zhao,4,5,8 Shiming Jiang,1,2 Jie Lyu,3 Xiaolu Wang,1,2 Haitao Li,4,5 Hong Wen,1,2 Wei Li,3 and Xiaobing Shi1,2,6 1Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 2Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 3Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; 4MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; 5Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; 6Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA Histone acetylation is associated with active transcription in eukaryotic cells. It helps to open up the chromatin by neutralizing the positive charge of histone lysine residues and providing binding platforms for “reader” proteins. The bromodomain (BRD) has long been thought to be the sole protein module that recognizes acetylated histones. Re- cently, we identified the YEATS domain of AF9 (ALL1 fused gene from chromosome 9) as a novel acetyl-lysine- binding module and showed that the ENL (eleven-nineteen leukemia) YEATS domain is an essential acetyl-histone reader in acute myeloid leukemias.
    [Show full text]
  • Deciphering the Histone Code to Build the Genome Structure
    bioRxiv preprint doi: https://doi.org/10.1101/217190; this version posted November 20, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Deciphering the histone code to build the genome structure Kirti Prakasha,b,c,* and David Fournierd,* aPhysico-Chimie Curie, Institut Curie, CNRS UMR 168, 75005 Paris, France; bOxford Nanoimaging Ltd, OX1 1JD, Oxford, UK; cMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK; dFaculty of Biology and Center for Computational Sciences, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; *Correspondence: [email protected], [email protected] Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutrali- sation, molecular specificity, robustness and evolvability. Next, we present evidence for the association among different histone modi- fications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replica- tion and cell division. Finally, we propose a model where the histone code can set critical checkpoints for chromatin to fold reversibly be- tween different orders of the organisation in response to a biological stimulus. DNA | nucleosomes | histone modifications | chromatin domains | chro- mosomes | histone code | chromatin folding | genome structure Introduction The genetic information within chromosomes of eukaryotes is packaged into chromatin, a long and folded polymer of double-stranded DNA, histones and other structural and non- structural proteins.
    [Show full text]
  • Transcription Shapes Genome-Wide Histone Acetylation Patterns
    ARTICLE https://doi.org/10.1038/s41467-020-20543-z OPEN Transcription shapes genome-wide histone acetylation patterns Benjamin J. E. Martin 1, Julie Brind’Amour 2, Anastasia Kuzmin1, Kristoffer N. Jensen2, Zhen Cheng Liu1, ✉ Matthew Lorincz 2 & LeAnn J. Howe 1 Histone acetylation is a ubiquitous hallmark of transcription, but whether the link between histone acetylation and transcription is causal or consequential has not been addressed. 1234567890():,; Using immunoblot and chromatin immunoprecipitation-sequencing in S. cerevisiae, here we show that the majority of histone acetylation is dependent on transcription. This dependency is partially explained by the requirement of RNA polymerase II (RNAPII) for the interaction of H4 histone acetyltransferases (HATs) with gene bodies. Our data also confirms the targeting of HATs by transcription activators, but interestingly, promoter-bound HATs are unable to acetylate histones in the absence of transcription. Indeed, HAT occupancy alone poorly predicts histone acetylation genome-wide, suggesting that HAT activity is regulated post- recruitment. Consistent with this, we show that histone acetylation increases at nucleosomes predicted to stall RNAPII, supporting the hypothesis that this modification is dependent on nucleosome disruption during transcription. Collectively, these data show that histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases. 1 Department of Biochemistry and Molecular Biology, Life Sciences Institute, Molecular
    [Show full text]
  • Histone Modifications During the Life Cycle of the Brown Alga Ectocarpus
    Bourdareau et al. Genome Biology (2021) 22:12 https://doi.org/10.1186/s13059-020-02216-8 RESEARCH Open Access Histone modifications during the life cycle of the brown alga Ectocarpus Simon Bourdareau1, Leila Tirichine2, Bérangère Lombard3, Damarys Loew3, Delphine Scornet1, Yue Wu2, Susana M. Coelho1,4* and J. Mark Cock1* * Correspondence: susana.coelho@ tuebingen.mpg.de; cock@sb-roscoff. Abstract fr 1CNRS, Sorbonne Université, UPMC Background: Brown algae evolved complex multicellularity independently of the University Paris 06, Algal Genetics animal and land plant lineages and are the third most developmentally complex Group, UMR 8227, Integrative phylogenetic group on the planet. An understanding of developmental processes in Biology of Marine Models, Station Biologique de Roscoff, CS 90074, this group is expected to provide important insights into the evolutionary events F-29688 Roscoff, France necessary for the emergence of complex multicellularity. Here, we focus on Full list of author information is mechanisms of epigenetic regulation involving post-translational modifications of available at the end of the article histone proteins. Results: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression.
    [Show full text]
  • Histone Methylation Regulation in Neurodegenerative Disorders
    International Journal of Molecular Sciences Review Histone Methylation Regulation in Neurodegenerative Disorders Balapal S. Basavarajappa 1,2,3,4,* and Shivakumar Subbanna 1 1 Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA; [email protected] 2 New York State Psychiatric Institute, New York, NY 10032, USA 3 Department of Psychiatry, College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA 4 New York University Langone Medical Center, Department of Psychiatry, New York, NY 10016, USA * Correspondence: [email protected]; Tel.: +1-845-398-3234; Fax: +1-845-398-5451 Abstract: Advances achieved with molecular biology and genomics technologies have permitted investigators to discover epigenetic mechanisms, such as DNA methylation and histone posttransla- tional modifications, which are critical for gene expression in almost all tissues and in brain health and disease. These advances have influenced much interest in understanding the dysregulation of epigenetic mechanisms in neurodegenerative disorders. Although these disorders diverge in their fundamental causes and pathophysiology, several involve the dysregulation of histone methylation- mediated gene expression. Interestingly, epigenetic remodeling via histone methylation in specific brain regions has been suggested to play a critical function in the neurobiology of psychiatric disor- ders, including that related to neurodegenerative diseases. Prominently, epigenetic dysregulation currently brings considerable interest as an essential player in neurodegenerative disorders, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), Amyotrophic lateral sclerosis (ALS) and drugs of abuse, including alcohol abuse disorder, where it may facilitate connections between genetic and environmental risk factors or directly influence disease-specific Citation: Basavarajappa, B.S.; Subbanna, S.
    [Show full text]
  • Sense and Antisense Transcription Are Associated with Distinct Chromatin Architectures Across Genes Struan C
    Nucleic Acids Research Advance Access published June 29, 2015 Nucleic Acids Research, 2015 1 doi: 10.1093/nar/gkv666 Sense and antisense transcription are associated with distinct chromatin architectures across genes Struan C. Murray, Simon Haenni, Franc¸oise S. Howe, Harry Fischl, Karolina Chocian, Anitha Nair and Jane Mellor* Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK Received February 25, 2015; Revised June 17, 2015; Accepted June 18, 2015 ABSTRACT degraded (3,4), leading to underestimates in the extent of antisense transcription genome-wide (5), and the pro- Genes from yeast to mammals are frequently sub- posal that they may serve no meaningful biological func- ject to non-coding transcription of their antisense tion (6). Genome-wide measurements of nascent transcrip- strand; however the genome-wide role for antisense tion in yeast (7,8), as opposed to transcript levels, give a very Downloaded from transcription remains elusive. As transcription influ- different view of antisense transcription, both in terms of ences chromatin structure, we took a genome-wide its abundance and its relationship with sense (pre-mRNA) approach to assess which chromatin features are as- transcription (9). Firstly, there is no correlation between lev- sociated with nascent antisense transcription, and els of nascent sense and antisense transcription at individual =− contrast these with features associated with nascent genes (rs 0.06) (9). Secondly, antisense transcription is a http://nar.oxfordjournals.org/ sense transcription. We describe a distinct chro- relatively frequent event. The average ratio of nascent sense matin architecture at the promoter and gene body to antisense transcription across a gene is 5:1 for genes with- out a defined antisense transcript, and 5:2 for those with specifically associated with antisense transcription, a defined transcript (9).
    [Show full text]
  • H3k14ac Polyclonal Antibody - Classic
    H3K14ac polyclonal antibody - Classic Cat. No. C15410310 Specificity: Human: positive / Other species: not tested Type: Polyclonal ChIP-grade Purity: Affinity purified polyclonal antibody in PBS containing Source: Rabbit 0.05% azide and 0.05% ProClin 300 Lot #: A2283P Storage: Store at -20°C; for long storage, store at -80°C Avoid multiple freeze-thaw cycles Size: 50 µg/56 µl Precautions: This product is for research use only Concentration: 0.9 µg/µl Not for use in diagnostic or therapeutic procedures Description : Polyclonal antibody raised in rabbit against the region of histone H3 containing the acetylated lysine 14 (H3K14ac), using a KLH-conjugated synthetic peptide Applications Suggested dilution/amount Results ChIP* 2 µg/ChIP Fig 1 ELISA 1:1,000 - 1:5,000 Fig 2 Dot blotting 1:10,000 Fig 3 WB 1:1,000 Fig 4 *Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 1-5 µg per IP Target description Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”.
    [Show full text]
  • Recombinant Mononucleosomes H3k14ac (EPL) - Biotin Catalog No: 81001, 81701 Quantity: 20, 1000 Μg Lot No: 17717001 Concentration: 0.45 Μg/Μl Expressed In: E
    Recombinant Mononucleosomes H3K14ac (EPL) - biotin Catalog No: 81001, 81701 Quantity: 20, 1000 µg Lot No: 17717001 Concentration: 0.45 µg/µl Expressed In: E. coli Source: Human Buffer Contents: Recombinant Mononucleosomes H3K14ac (EPL) - biotinylated (20 µg protein + 20 µg DNA) is supplied at a protein concentration of 0.45 µg/µl in 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 2 mM DTT and 20% glycerol. Background: In vivo, histones are wrapped around by DNA in chromatin. Therefore, nucleosomes are more physiologically relevant substrates than histones and histone-derived peptides for in vitro studies. More importantly, some histone methyltransferases are significantly more active, as well as specific, when using nucleosomal substrates in HMT assays, such as DOT1L and NSD family enzymes. Nucleosomes are also widely used in histone methyltransferase screening assays to identify small molecular inhibitors for drug discovery. Protein Details: Recombinant Mononucleosomes H3K14ac (EPL) - biotinylated consist of a 167 bp of 601 DNA with 5’ biotin tag and two molecules each of histones H2A that includes amino acids 1-130 (end) (accession number NP_003503.1), H2B that includes amino acids 1-126 (end) (accession number NP_003509.1), H3.2 that includes amino acids 1-136 (end) (accession number NP_066403.2) with acetylation at lysine 14, and H4 that includes amino acids 1-103 (end) (accession number NP_003539.1). All of these histones were expressed in E. coli cells. The molecular weight of histone octamer is ~108 kDa. The recombinant protein is ≥95% by SDS-PAGE gel. H3K14ac (Histone H3 acetyl Lys14) protein is generated using expressed protein ligation (EPL) technology.
    [Show full text]
  • A Novel Proteomics Approach to Epigenetic Profiling of Circulating
    www.nature.com/scientificreports OPEN A novel proteomics approach to epigenetic profling of circulating nucleosomes Priscilla Van den Ackerveken1, Alison Lobbens1, Jean‑Valery Turatsinze1, Victor Solis‑Mezarino2, Moritz Völker‑Albert2, Axel Imhof2 & Marielle Herzog1* Alteration of epigenetic modifcations plays an important role in human cancer. Notably, the dysregulation of histone post‑translational modifcations (PTMs) has been associated with several cancers including colorectal cancer (CRC). However, the signature of histone PTMs on circulating nucleosomes is still not well described. We have developed a fast and robust enrichment method to isolate circulating nucleosomes from plasma for further downstream proteomic analysis. This method enabled us to quantify the global alterations of histone PTMs from 9 CRC patients and 9 healthy donors. Among 54 histone proteoforms identifed and quantifed in plasma samples, 13 histone PTMs were distinctive in CRC. Notably, methylation of histone H3K9 and H3K27, acetylation of histone H3 and citrullination of histone H2A1R3 were upregulated in plasma of CRC patients. A comparative analysis of paired samples identifed 3 common histone PTMs in plasma and tumor tissue including the methylation and acetylation state of lysine 27 of histone H3. Moreover, we highlight for the frst time that histone H2A1R3 citrulline is a modifcation upregulated in CRC patients. This new method presented herein allows the detection and quantifcation of histone variants and histone PTMs from circulating nucleosomes in plasma samples and could be used for biomarker discovery of cancer. Colorectal cancer (CRC) is the 4th most common cancer in the world 1. CRC results from an accumulation of genetic and epigenetic alterations in colonic epithelial cells that transforms them into adenocarcinomas2,3.
    [Show full text]
  • Genes for Embryo Development Are Packaged in Blocks of Multivalent Chromatin in Zebrafish Sperm
    Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Research Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm Shan-Fu Wu, Haiying Zhang, and Bradley R. Cairns1 Howard Hughes Medical Institute, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA In mature human sperm, genes of importance for embryo development (i.e., transcription factors) lack DNA methylation and bear nucleosomes with distinctive histone modifications, suggesting the specialized packaging of these developmental genes in the germline. Here, we explored the tractable zebrafish model and found conceptual conservation as well as several new features. Biochemical and mass spectrometric approaches reveal the zebrafish sperm genome packaged in nucleosomes and histone variants (and not protamine), and we find linker histones high and H4K16ac absent, key factors that may contribute to genome condensation. We examined several activating (H3K4me2/3, H3K14ac, H2AFV) and repressing (H3K27me3, H3K36me3, H3K9me3, hypoacetylation) modifications/compositions genome-wide and find developmental genes packaged in large blocks of chromatin with coincident activating and repressing marks and DNA hypomethylation, revealing complex ‘‘multivalent’’ chromatin. Notably, genes that acquire DNA methylation in the soma (muscle) are enriched in transcription factors for alternative cell fates. Remarkably, whereas H3K36me3 is located in the 39 coding region of heavily transcribed genes in somatic cells, H3K36me3 is present in the promoters of ‘‘silent’’ de- velopmental regulators in sperm, suggesting different rules for H3K36me3 in the germline and soma. We also reveal the chromatin patterns of transposons, rDNA, and tDNAs.
    [Show full text]
  • Peroxisomal Β-Oxidation Regulates Histone Acetylation and DNA Methylation in Arabidopsis
    Peroxisomal β-oxidation regulates histone acetylation and DNA methylation in Arabidopsis Lishuan Wanga,1, Chunlei Wangb,1, Xinye Liuc, Jinkui Chenga, Shaofang Lia, Jian-Kang Zhud,e,2, and Zhizhong Gonga,2 aState Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193 Beijing, China; bCollege of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China; cMinistry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, China; dShanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China; and eDepartment of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 Contributed by Jian-Kang Zhu, April 4, 2019 (sent for review March 12, 2019; reviewed by Bao Liu and Jim Peacock) Epigenetic markers, such as histone acetylation and DNA methylation, DNA methylation is a conserved epigenetic marker important determine chromatin organization. In eukaryotic cells, metabolites in genome organization, gene expression, genomic imprinting, from organelles or the cytosol affect epigenetic modifications. How- paramutation, and X chromosome inactivation in organisms (3, ever, the relationships between metabolites and epigenetic modifica- 11–13). DNA methylation patterns are coordinately determined tions are not well understood in plants. We found that peroxisomal by methylation and demethylation reactions in plants and ani- acyl-CoA oxidase 4 (ACX4), an enzyme in the fatty acid β-oxidation mals (13, 14). The active removal of 5mC in Arabidopsis is car- pathway, is required for suppressing the silencing of some endoge- ried out by a subfamily of bifunctional DNA glycosylases/lyases nous loci, as well as Pro35S:NPTII in the ProRD29A:LUC/C24 transgenic represented by REPRESSOR OF SILENCING 1 (ROS1) and line.
    [Show full text]