Synthetic Histone Code

Total Page:16

File Type:pdf, Size:1020Kb

Synthetic Histone Code Available online at www.sciencedirect.com ScienceDirect Synthetic histone code 1 2 3 Wolfgang Fischle , Henning D Mootz and Dirk Schwarzer Chromatin is the universal template of genetic information in all copies each of the core histones H2A, H2B, H3, and H4 eukaryotic cells. This complex of DNA and histone proteins not and one copy of linker histone H1, Figure 1a) [1]. By only packages and organizes genomes but also regulates gene various levels of folding, the originating primary chroma- expression. A multitude of posttranslational histone tin fiber can be organized into various structural arrange- modifications and their combinations are thought to constitute ments, including highly condensed mitotic chromosomes a code for directing distinct structural and functional states of (Figure 1b). While the basic architecture of nucleosomes chromatin. Methods of protein chemistry, including protein is the same throughout the genome, posttranslational semisynthesis, amber suppression technology, and cysteine modifications (PTMs) of histones are central means of bioconjugation, have enabled the generation of so-called increasing the biochemical divergence that regulates designer chromatin containing histones in defined and chromatin structure and function [2,3]. Histone PTMs homogeneous modification states. Several of these are structurally diverse and include methylation, acetyla- approaches have matured from proof-of-concept studies into tion and ubiquitinylation of lysine, as well as phosphor- efficient tools and technologies for studying the biochemistry of ylation of serine and threonine residues (Figure 1c). More chromatin regulation and for interrogating the histone code. We than 150 histone modification sites have been identified summarize pioneering experiments and recent developments in different experimental systems. Major sites of modifi- in this exciting field of chemical biology. cation cluster within the unstructured regions of the N- Addresses terminal histone tails that vary between 10 and 35 amino 1 Max Planck Institute for Biophysical Chemistry, 37077 Go¨ ttingen, acids in length. These are protruding out from the nucle- Germany osome core (Figure 1a). 2 Institute of Biochemistry, University of Muenster, 48149 Muenster, Germany 3 Research over the past years has focused on defining the Interfaculty Institute of Biochemistry, University of Tu¨ bingen, 72076 Tu¨ bingen, Germany distribution, biochemistry and cellular function of individ- ual and combinations of histone marks. A ‘histone code’ Corresponding authors: Fischle, Wolfgang (wfi[email protected]), Mootz, hypothesis has been put forward that defines chromatin as Henning D ([email protected]) and Schwarzer, Dirk ([email protected]) dynamic programming platform, which integrates internal and external cellular signals [2,3]. Histone modifying enzymes are considered the writers of the histone code. Current Opinion in Chemical Biology 2015, 28:131–140 Chromatin factors possessing PTM-binding domains serve This review comes from a themed issue on Synthetic biomolecules as histone code readers and execute regulatory functions upon recruitment. Finally, dedicated PTM-removing Edited by Christian Hackenberger and Peng Chen enzymes are the erasers of histone PTMs [4–7]. For a complete overview see the Issue and the Editorial Available online 6th August 2015 Deciphering the complex cross-talk between histone http://dx.doi.org/10.1016/j.cbpa.2015.07.005 PTMs, chromatin factors and gene regulation is a major 1367-5931/# 2015 Elsevier Ltd. All rights reserved. research challenge [8]. While the accessibility of ‘designer chromatin’ composed of histones with defined and ho- mogeneous modification states has been a central bottle- neck in chromatin research, novel chemical approaches are providing powerful tools enabling important discov- eries of the rules of the histone code [4–7,9–12]. Chromatin and posttranslational histone modifications Tools for designer chromatin The physiological template of genetic information in all Chromatin research has benefitted strongly from peptide eukaryotic cells is chromatin, the complex of DNA and chemistry. Especially, the availability of building blocks histone proteins. As signaling platform, chromatin inte- of modified amino acids has enabled the synthesis of grates a variety of internal and external cellular inputs. histone peptides with defined modification patterns. These direct distinct local and global structural and Such histone-derived peptides have been instrumental functional states of chromatin, thereby controlling gene for many key discoveries on the readers, writers and expression [1]. eraser of histone PTMs. However, histone-peptides can only recapitulate a minor fraction of the complex In the repeating unit of chromatin, the nucleosome, DNA chromatin structure (Figure 1). Consequently, major is wrapped around an octamer of histone proteins (two efforts have been untertaken to site-specifically introduce www.sciencedirect.com Current Opinion in Chemical Biology 2015, 28:131–140 132 Synthetic biomolecules Figure 1 (a) (c) nucleosome CH3 O H3C O NH 1-3 ⊕ NH NH 0-2 N N N H H H O O O acetyl-lysine methyl-lysine ubiquitin-lysine (Kac) (Kme) (Kub) histone tail O O O P O O P O O O CH3 N N H H O O phospho-serine phospho-threonine (Sph) (Tph) (b) condensation into higher order DNA nucleosomes chromatin structures Current Opinion in Chemical Biology Histones, nucleosomes and chromatin. (a) Structure of the nucleosome core particle. Histones are color-coded as follows: H2A: yellow, H2B: red, H3: blue, H4: green. The illustration was generated from pdb file: 1KX5. (b) Packaging of DNA into nucleosomes and chromosomes. Intermediate packaging stages are not illustrated. (c) Selected posttranslational modifications of histones including acetylation, methylation and ubiquitination of lysine as well as phosphorylation of serine and threonine residues. modification marks into full-length histones, nucleo- 2-chloro-ethyl-methylammonium or bromo-ethyl- somes, arrays of nucleosomes and even into chromatin methylammonium compounds (1) the respective meth- of living cells. These approaches draw from the techno- yl-thialysine (2) residues were generated in high yields logical repertoire of modern protein chemistry [4–7]. (Figure 2a). Downstream experiments showed that these so-called methyl-lysine analogs (MLAs) mim- Selective modification of cysteine residues icked properties of methylated lysine in peptide and The most widely used strategy for generating modified nucleosomal context by recruiting chromatin readers. histones is the selective conversion of cysteine residues into mimics of modified amino acids. The chemical In a similar fashion methyl-arginine analogs (4) were properties of the cysteine thiol group are unique among generated [14]. In this case a,b-unsaturated amidines the proteinogenic amino acids. Selective alkylation of (3) served as alkylation agents. Extending this approach this soft nucleophile has been used in traditional bio- to acetyl-thialysine (6) turned out much more challenging chemistry and this approach has recently experienced a [15]. The treatment of cysteine with 2-bromoethyl-acet- renaissance for site-specific introduction of mimics of ylamine (5) or with more reactive N-acetyl-aziridine, were PTMs. Since natural cysteine residues are absent in core either poor yielding or led to undesired side-products. histones with exception of a single residue in H3, this Alkylation with methylthiocarbonyl-aziridine (7) con- method is particularly attractive for chromatin chemis- verted cysteine residues into methylthiocarbonyl-thialy- try. In a pioneering report site-directed mutagenesis sine (8), which mimicked some aspects of acetylated was used to introduce cysteine at sites of methylated lysine [15]. Efficient formation of acetyl-thiaLys (6) lysine residues in otherwise Cys-free mutant histone was finally achieved with N-vinyl-acetamidine (9), how- H3 as well as histone H4 [13]. Upon treatment with ever not by direct conjugation but via the radical thiol-ene Current Opinion in Chemical Biology 2015, 28:131–140 www.sciencedirect.com Synthetic histone code Fischle, Mootz and Schwarzer 133 Figure 2 (a) O H N N HN (7) SMe HN O X CH3 S + CH3 (1) S N 1-3 N SMe O (2) 1-3 –HX (8) H0-2 O H O NH X = Cl, Br CH 3 HS N CH3 + (3) N H NH2 H (9) O HN CH HN S 3 ν S N N h* , initiator N CH (4) H H (6) 3 O H O O H N CH X 3 (5) cysteine residue O HS R O engineered into (11) HN HN HN S S recombinant histone R –“H2S” N CH3 O O (6) H O (10) (b) – O O O O N + NH N H 3 H recombinant expression recombinant histone Nε-acetyl-lysine with Kac-RS/tRNA containing acetyl-lysine (c) – O – O P O O – – O O O – – O P O O P O H N O HS 2 S SH O O O H H H H N N N H N N 2 S–R H N 2 + 2 H2N N –R–SH H O O O synthetic modified recombinant truncated N-terminal tail peptide histone with N-terminal thiol-thioester semisynthetic histone thioester cysteine residue exchange with modified N-terminal tail (d) ligation 12 + Ub-thioester (NCL) site cleavage of auxiliary O SH HN H HN O N HN N NH2 O (12) H O (13) N NO2 SH O H ligation 13 + Ub-thioester (NCL) photo-cleavable RO site thiol auxiliary OR’ desulfurization Current Opinion in Chemical Biology Chemical approaches for the generation of histones possessing defined modification patterns. (a) Modification of cysteine residues engineered into recombinant histones can be modified into mimics of amino acids carrying posttranslational modifications. (b) Recombinant modified histones are accessible by amber suppression technology. (c) Protein semisynthesis, here: native chemical ligation, affords homogenously modified histones by ligation of synthetic peptide-thioesters and globular folds of histones that possess an N-terminal cysteine residue. (d) Approaches for site-specific ubiquitination of lysine residues by NCL using thiol auxiliaries and d-mercaptolysine. Both approaches can be traceless when the auxiliary is removed by UV irradiation or when the thiol is desulfurized. www.sciencedirect.com Current Opinion in Chemical Biology 2015, 28:131–140 134 Synthetic biomolecules reaction [16].
Recommended publications
  • The Histone Methyltransferase DOT1L Prevents Antigen-Independent
    bioRxiv preprint doi: https://doi.org/10.1101/826255; this version posted November 18, 2019. 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-ND 4.0 International license. The histone methyltransferase DOT1L prevents antigen-independent differentiation and safeguards epigenetic identity of CD8+ T cells Eliza Mari Kwesi-Maliepaard1*, Muhammad Assad Aslam2,3*, Mir Farshid Alemdehy2*, Teun van den Brand4, Chelsea McLean1, Hanneke Vlaming1, Tibor van Welsem1, Tessy Korthout1, Cesare Lancini1, Sjoerd Hendriks1, Tomasz Ahrends5, Dieke van Dinther6, Joke M.M. den Haan6, Jannie Borst5, Elzo de Wit4, Fred van Leeuwen1,7,#, and Heinz Jacobs2,# 1Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands 2Division of Tumor Biology & Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands 3Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, 60800 Multan, Pakistan 4Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, and Oncode Institute, The Netherlands 5Division of Tumor Biology & Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, and Oncode Institute, The Netherlands 6Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Location VUmc, 1081HV Amsterdam, The Netherlands 7Department of Medical Biology, Amsterdam UMC, location AMC, UvA, 1105 AZ Amsterdam, The Netherlands * These authors contributed equally to this work. # Equal contribution and corresponding authors [email protected]; [email protected] Lead contact: Fred van Leeuwen 1 bioRxiv preprint doi: https://doi.org/10.1101/826255; this version posted November 18, 2019. 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.
    [Show full text]
  • Recognition of Cancer Mutations in Histone H3K36 by Epigenetic Writers and Readers Brianna J
    EPIGENETICS https://doi.org/10.1080/15592294.2018.1503491 REVIEW Recognition of cancer mutations in histone H3K36 by epigenetic writers and readers Brianna J. Kleina, Krzysztof Krajewski b, Susana Restrepoa, Peter W. Lewis c, Brian D. Strahlb, and Tatiana G. Kutateladzea aDepartment of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA; bDepartment of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, USA; cWisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA ABSTRACT ARTICLE HISTORY Histone posttranslational modifications control the organization and function of chromatin. In Received 30 May 2018 particular, methylation of lysine 36 in histone H3 (H3K36me) has been shown to mediate gene Revised 1 July 2018 transcription, DNA repair, cell cycle regulation, and pre-mRNA splicing. Notably, mutations at or Accepted 12 July 2018 near this residue have been causally linked to the development of several human cancers. These KEYWORDS observations have helped to illuminate the role of histones themselves in disease and to clarify Histone; H3K36M; cancer; the mechanisms by which they acquire oncogenic properties. This perspective focuses on recent PTM; methylation advances in discovery and characterization of histone H3 mutations that impact H3K36 methyla- tion. We also highlight findings that the common cancer-related substitution of H3K36 to methionine (H3K36M) disturbs functions of not only H3K36me-writing enzymes but also H3K36me-specific readers. The latter case suggests that the oncogenic effects could also be linked to the inability of readers to engage H3K36M. Introduction from yeast to humans and has been shown to have a variety of functions that range from the control Histone proteins are main components of the of gene transcription and DNA repair, to cell cycle nucleosome, the fundamental building block of regulation and nutrient stress response [8].
    [Show full text]
  • Screening for Genes That Accelerate the Epigenetic Aging Clock in Humans Reveals a Role for the H3K36 Methyltransferase NSD1 Daniel E
    Martin-Herranz et al. Genome Biology (2019) 20:146 https://doi.org/10.1186/s13059-019-1753-9 RESEARCH Open Access Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1 Daniel E. Martin-Herranz1,2* , Erfan Aref-Eshghi3,4, Marc Jan Bonder1,5, Thomas M. Stubbs2, Sanaa Choufani6, Rosanna Weksberg6, Oliver Stegle1,5,7, Bekim Sadikovic3,4, Wolf Reik8,9,10*† and Janet M. Thornton1*† Abstract Background: Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data and have emerged in the last few years as the most accurate biomarkers of the aging process. However, little is known about the molecular mechanisms that control the rate of such clocks. Here, we have examined the human epigenetic clock in patients with a variety of developmental disorders, harboring mutations in proteins of the epigenetic machinery. Results: Using the Horvath epigenetic clock, we perform an unbiased screen for epigenetic age acceleration in the blood of these patients. We demonstrate that loss-of-function mutations in the H3K36 histone methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic aging. Furthermore, we show that the normal aging process and Sotos syndrome share methylation changes and the genomic context in which they occur. Finally, we found that the Horvath clock CpG sites are characterized by a higher Shannon methylation entropy when compared with the rest of the genome, which is dramatically decreased in Sotos syndrome patients. Conclusions: These results suggest that the H3K36 methylation machinery is a key component of the epigenetic maintenance system in humans, which controls the rate of epigenetic aging, and this role seems to be conserved in model organisms.
    [Show full text]
  • Histone H3 Lysine 36 Methylation Affects Temperature-Induced Alternative Splicing and Flowering in Plants A
    Pajoro et al. Genome Biology (2017) 18:102 DOI 10.1186/s13059-017-1235-x RESEARCH Open Access Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants A. Pajoro1,2, E. Severing3,4, G. C. Angenent1,2 and R. G. H. Immink1,2* Abstract Background: Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses in plants, yet its regulation is poorly understood. An increase in temperature promotes changes in plant morphology as well as the transition from the vegetative to the reproductive phase in Arabidopsis thaliana via changes in splicing of key regulatory genes. Here we investigate whether a particular histone modification affects ambient temperature-induced alternative splicing and flowering time. Results: We use a genome-wide approach and perform RNA-sequencing (RNA-seq) analyses and histone H3 lysine 36 tri-methylation (H3K36me3) chromatin immunoprecipitation sequencing (ChIP-seq) in plants exposed to different ambient temperatures. Analysis and comparison of these datasets reveal that temperature-induced differentially spliced genes are enriched in H3K36me3. Moreover, we find that reduction of H3K36me3 deposition causes alteration in temperature-induced alternative splicing. We also show that plants with mutations in H3K36me3 writers, eraser, or readers have altered high ambient temperature-induced flowering. Conclusions: Our results show a key role for the histone mark H3K36me3 in splicing regulation and plant plasticity to fluctuating ambient temperature. Our findings open new perspectives for the breeding of crops that can better cope with environmental changes due to climate change.
    [Show full text]
  • The Diverse Functions of Dot1 and H3K79 Methylation
    Downloaded from genesdev.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW The diverse functions of Dot1 and H3K79 methylation Anh Tram Nguyen1,2 and Yi Zhang1,2,3 1Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA; 2Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA DOT1 (disruptor of telomeric silencing; also called ute to transcriptional regulation is to serve as a platform Kmt4) was initially discovered in budding yeast in a genetic for the recruitment of effector proteins. The well-studied screen for genes whose deletion confers defects in telo- lysine methylation residues include K4, K9, K27, K36, meric silencing. Since the discovery ~10 years ago that and K79 of histone H3, and K20 of histone H4. In general, Dot1 and its mammalian homolog, DOT1L (DOT1-Like), methylation at H3K9, H3K27, and H4K20 correlates with possess histone methyltransferase activity toward histone transcriptional repression, while methylation at H3K4, H3 Lys 79, great progress has been made in characterizing H3K36, and H3K79 correlates with gene transcription their enzymatic activities and the role of Dot1/DOT1L- (Kouzarides 2002; Peterson and Laniel 2004; Martin and mediated H3K79 methylation in transcriptional regula- Zhang 2005). In addition to its role in transcriptional tion, cell cycle regulation, and the DNA damage response. regulation, methylation has also been linked to X inacti- In addition, gene disruption in mice has revealed that vation, cell fate determination, terminal differentiation, mouse DOT1L plays an essential role in embryonic de- and the spatiotemporal patterning of Hox genes (Cavalli velopment, hematopoiesis, cardiac function, and the de- 2006; Minard et al.
    [Show full text]
  • Dynamics of Transcription-Dependent H3k36me3 Marking by the SETD2:IWS1:SPT6 Ternary Complex
    bioRxiv preprint doi: https://doi.org/10.1101/636084; this version posted May 14, 2019. 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. Dynamics of transcription-dependent H3K36me3 marking by the SETD2:IWS1:SPT6 ternary complex Katerina Cermakova1, Eric A. Smith1, Vaclav Veverka2, H. Courtney Hodges1,3,4,* 1 Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA 2 Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic 3 Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA 4 Department of Bioengineering, Rice University, Houston, TX, 77005, USA * Lead contact; Correspondence to: [email protected] Abstract The genome-wide distribution of H3K36me3 is maintained SETD2 contributes to gene expression by marking gene through various mechanisms. In human cells, H3K36 is bodies with H3K36me3, which is thought to assist in the mono- and di-methylated by eight distinct histone concentration of transcription machinery at the small portion methyltransferases; however, the predominant writer of the of the coding genome. Despite extensive genome-wide data trimethyl mark on H3K36 is SETD21,11,12. Interestingly, revealing the precise localization of H3K36me3 over gene SETD2 is a major tumor suppressor in clear cell renal cell bodies, the physical basis for the accumulation, carcinoma13, breast cancer14, bladder cancer15, and acute maintenance, and sharp borders of H3K36me3 over these lymphoblastic leukemias16–18. In these settings, mutations sites remains rudimentary.
    [Show full text]
  • 16-0368 Technical Data Sheet
    Nucleosome, Recombinant Human, H3K79me2 dNuc, Biotinylated Catalog No. 16-0368 Lot No. 19045001 Pack Size 50 µg Product Description: 1 2 Mononucleosomes assembled from recombinant human histones expressed in E. coli (two each of histones H2A, H2B, H3 and H4; accession numbers: H2A-P04908; H2B- O60814; H3.1-P68431; H4-P62805) wrapped by 147 base pairs of 601 positioning sequence DNA. Histone H3 (created by a proprietary synthetic method) contains dimethyl-lysine at position 79. The nucleosome is the basic subunit of chromatin. The 601 sequence, identified by Lowary and Widom, is a 147-base pair sequece that has high affinity for histone octamers and is useful for nucleosome assembly and contains a 5’ biotin-TEG group. Western Blot Data: Western Analysis of Nucleosome, Recombinant Human, H3K79me2. Top Panel: Unmodified H3 Formulation: (Lane 1) and H3K79me2 containing nucleosomes (Lane 2) were Nucleosome, Recombinant Human, H3K79me2 (27.3 µg probed with an anti-H3K79me2 antibody and analyzed via ECL protein weight, 50 µg total weight) in µl of 10 mM Tris readout. Only the H3K79me2sample produced a detectable signal. HCl, pH 7.5, 25 mM NaCl, 1 mM EDTA, 2 mM DTT, 20% Bottom Panel: Detailfrom Coomassie stained gel showing glycerol. unmodified nucleosomes (Lane 1) and H3K79me2 nucleosomes Molarity = μmolar. MW = Da. (Lane 2). Storage and Stability: Stable for six months at -80°C from date of receipt. For best results, aliquot and avoid multiple freeze/thaws. Application Notes: Nucleosome, Recombinant Human, H3K79me2 dNucs are highly purified and are suitable for use as substrates in enzyme screening assays or for effector protein binding experiments.
    [Show full text]
  • Effects of H3.3G34V Mutation on Genomic H3K36 and H3K27 Methylation Patterns in Isogenic Pediatric Glioma Cells
    Huang et al. acta neuropathol commun (2020) 8:219 https://doi.org/10.1186/s40478-020-01092-4 RESEARCH Open Access Efects of H3.3G34V mutation on genomic H3K36 and H3K27 methylation patterns in isogenic pediatric glioma cells Tina Yi‑Ting Huang1, Andrea Piunti2, Jin Qi1, Marc Morgan2, Elizabeth Bartom2, Ali Shilatifard2 and Amanda M. Saratsis1,2,3* Abstract Histone H3.3 mutation (H3F3A) occurs in 50% of cortical pediatric high‑grade gliomas. This mutation replaces glycine 34 with arginine or valine (G34R/V), impairing SETD2 activity (H3K36‑specifc trimethyltransferase). Consequently, reduced H3K36me3 is observed on H3.3G34V nucleosomes relative to wild‑type, contributing to genomic instabil‑ ity and driving a distinct gene expression signature associated with tumorigenesis. However, it is not known if this diferential H3K36me3 enrichment is due to H3.3G34V mutant protein alone. Therefore, we set to elucidate the efect of H3.3G34V mutant protein in pediatric glioma on H3K36me3, H3K27me3 and H3.3 enrichment in vitro. We found that the doxycycline‑inducible shRNA knockdown of mutant H3F3A encoding the H3.3G34V protein resulted in loss of H3.3G34V enrichment and increased H3K36me3 enrichment throughout the genome. After knockdown, H3.3G34V enrichment was preserved at loci observed to have the greatest H3.3G34V and H3K36me3 enrichment prior to knockdown. Induced expression of mutant H3.3G34V protein in vitro was insufcient to induce genomic H3K36me3 enrichment patterns observed in H3.3G34V mutant glioma cells. We also observed strong co‑enrichment of H3.3G34V and wild‑type H3.3 protein, as well as greater H3K27me3 enrichment, in cells expressing H3.3G34V.
    [Show full text]
  • Le G´Enome En Action
    LEGENOME´ EN ACTION SEQUENC´ ¸ AGE HAUT DEBIT´ ET EPIG´ ENOMIQUE´ Epig´enomique´ ? IFT6299 H2014 ? UdeM ? Mikl´osCs}ur¨os Regulation´ d’expression la transcription d’une region´ de l’ADN necessite´ ? liaisons proteine-ADN´ (facteur de transcription et son site reconnu) ? accessibilite´ de la chromatine REVIEWS Identification of regions that control transcription An initial step in the analysis of any gene is the identifi- cation of larger regions that might harbour regulatory control elements. Several advances have facilitated the prediction of such regions in the absence of knowl- edge about the specific characteristics of individual cis- Chromatin regulatory elements. These tools broadly fall into two categories: promoter (transcription start site; TSS) and enhancer detection. The methods are influenced Distal TFBS by sequence conservation between ORTHOLOGOUS genes (PHYLOGENETIC FOOTPRINTING), nucleotide composition and the assessment of available transcript data. Functional regulatory regions that control transcrip- tion rates tend to be proximal to the initiation site(s) of transcription. Although there is some circularity in the Co-activator complex data-collection process (regulatory sequences are sought near TSSs and are therefore found most often in these regions), the current set of laboratory-annotated regula- tory sequences indicates that sequences near a TSS are Transcription more likely to contain functionally important regulatory initiation complex Transcription controls than those that are more distal. However, specifi- initiation cation of the position of a TSS can be difficult. This is fur- ther complicated by the growing number of genes that CRM Proximal TFBS selectively use alternative start sites in certain contexts. Underlying most algorithms for promoter prediction is a Figure 1 | Components of transcriptional regulation.
    [Show full text]
  • Modeling Circrnas Expression Pattern with Integrated Sequence And
    bioRxiv preprint doi: https://doi.org/10.1101/392019; this version posted August 15, 2018. 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. 1 Modeling circRNAs expression pattern with integrated sequence and 2 epigenetic features identifies H3K79me2 as regulators for circRNAs 3 expression 4 Jia-Bin Chen1#, Shan-Shan Dong1#, Shi Yao1, Yuan-Yuan Duan1, Wei-Xin Hu1, Hao 5 Chen1, Nai-Ning Wang1, Ruo-Han Hao1, Ming-Rui Guo1, Yu-Jie Zhang1, Yu Rong1, Yi- 6 Xiao Chen1, Hlaing Nwe Thynn1, Fu-Ling Zhou2, Yan Guo1*, Tie-Lin Yang1* 7 8 Running title: Exploring circRNAs expression regulatory mechanism 9 10 1Key Laboratory of Biomedical Information Engineering of Ministry of Education, 11 School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. 12 China 13 2Department of Hematopathology, Zhongnan Hospital of Wuhan University, Wuhan 14 430071, P. R. China 15 16 #These authors contribute equally to this work. 17 The authors wish it to be known that, in their opinion, the first 2 authors should be 18 regarded as joint First Authors 19 20 *Corresponding Authors: 21 Tie-Lin Yang, Ph.D. 22 Key Laboratory of Biomedical Information Engineering of Ministry of Education, 23 School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. 24 China 25 Tel: 86-29-82668463 1 bioRxiv preprint doi: https://doi.org/10.1101/392019; this version posted August 15, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • Chromatin Poises Mirna- and Protein-Coding Genes for Expression
    Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Chromatin poises miRNA- and protein-coding genes for expression Artem Barski,1,2 Raja Jothi,1,2,3 Suresh Cuddapah,1,2 Kairong Cui,1 Tae-Young Roh,1,4 Dustin E. Schones,1 and Keji Zhao1,5 1Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA Chromatin modifications have been implicated in the regulation of gene expression. While association of certain mod- ifications with expressed or silent genes has been established, it remains unclear how changes in chromatin environment relate to changes in gene expression. In this article, we used ChIP-seq (chromatin immunoprecipitation with massively parallel sequencing) to analyze the genome-wide changes in chromatin modifications during activation of total human CD4+ T cells by T-cell receptor (TCR) signaling. Surprisingly, we found that the chromatin modification patterns at many induced and silenced genes are relatively stable during the short-term activation of resting T cells. Active chromatin modifications were already in place for a majority of inducible protein-coding genes, even while the genes were silent in resting cells. Similarly, genes that were silenced upon T-cell activation retained positive chromatin modifications even after being silenced. To investigate if these observations are also valid for miRNA-coding genes, we systematically identified promoters for known miRNA genes using epigenetic marks and profiled their expression patterns using deep sequencing. We found that chromatin modifications can poise miRNA-coding genes as well. Our data suggest that miRNA- and protein-coding genes share similar mechanisms of regulation by chromatin modifications, which poise inducible genes for activation in response to environmental stimuli.
    [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]