1
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Kieft R, Yan H, Schmitz RJ, Sabatini R. Mono-allelic epigenetic regulation of bi-directional polycistronic transcription initiation by RNA Polymerase II in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600114. [PMID: 38948844 PMCID: PMC11213002 DOI: 10.1101/2024.06.21.600114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Unique for a eukaryote, protein-coding genes in trypanosomes are arranged in polycistronic units (PTUs). This genome arrangement has led to a model where Pol II transcription of PTUs is unregulated. The initial step in trypanosome lytic factor (TLF) mediated lysis of Trypanosoma brucei requires high affinity haptoglobin/hemoglobin receptor (HpHbR) binding. Here we demonstrate that by in vitro selection with TLF, resistance is obtained in a stepwise process correlating with loss of HpHbR expression at an allelic level. RNA-seq, Pol II ChIP and run-on analysis indicate HpHbR silencing is at the transcriptional level, where loss of Pol II binding at the promoter region specifically shuts down transcription of the HpHbR containing gene cluster and the adjacent opposing gene cluster. Reversible transcriptional silencing of the divergent PTUs correlates with DNA base J modification of the shared promoter region. Therefore, epigenetic mechanisms exist to regulate gene expression via Pol II transcription initiation of gene clusters in a mono-allelic fashion. These findings suggest epigenetic chromatin-based regulation of gene expression is deeply conserved among eukaryotes, including primitive eukaryotes that rely on polycistronic transcription.
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2
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Sun M, Yan H, Zhang A, Jin Y, Lin C, Luo L, Wu B, Fan Y, Tian S, Cao X, Wang Z, Luo J, Yang Y, Jia J, Zhou P, Tang Q, Jones CS, Varshney RK, Srivastava RK, He M, Xie Z, Wang X, Feng G, Nie G, Huang D, Zhang X, Zhu F, Huang L. Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2348-2357. [PMID: 37530223 PMCID: PMC10579705 DOI: 10.1111/pbi.14136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.
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Affiliation(s)
- Min Sun
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haidong Yan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Aling Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yarong Jin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chuang Lin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Lin Luo
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Bingchao Wu
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuhang Fan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Shilin Tian
- Novogene Bioinformatics InstituteBeijingChina
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life SciencesWuhan UniversityWuhanChina
| | | | - Zan Wang
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Jinchan Luo
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuchen Yang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiyuan Jia
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Puding Zhou
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qianzi Tang
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chris Stephen Jones
- Feed and Forage DevelopmentInternational Livestock Research InstituteNairobiKenya
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- Murdoch's Centre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rakesh K. Srivastava
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
| | - Zheni Xie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- College of Agro‐Grassland ScienceNanjing Agricultural UniversityNanjingChina
| | - Xiaoshan Wang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Guangyan Feng
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Gang Nie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Dejun Huang
- Herbivorous Livestock Research InstituteChongqing Academy of Animal SciencesChongqingChina
| | - Xinquan Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Fangjie Zhu
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Linkai Huang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
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3
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Cordon-Obras C, Gomez-Liñan C, Torres-Rusillo S, Vidal-Cobo I, Lopez-Farfan D, Barroso-Del Jesus A, Rojas-Barros D, Carrington M, Navarro M. Identification of sequence-specific promoters driving polycistronic transcription initiation by RNA polymerase II in trypanosomes. Cell Rep 2022; 38:110221. [PMID: 35021094 DOI: 10.1016/j.celrep.2021.110221] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 11/20/2022] Open
Abstract
Protein-coding genes in trypanosomes occur in polycistronic transcription units (PTUs). How RNA polymerase II (Pol II) initiates transcription of PTUs has not been resolved; the current model favors chromatin modifications inducing transcription rather than sequence-specific promoters. Here, we uncover core promoters by functional characterization of Pol II peaks identified by chromatin immunoprecipitation sequencing (ChIP-seq). Two distinct promoters are located between divergent PTUs, each driving unidirectional transcription. Detailed analysis identifies a 75-bp promoter that is necessary and sufficient to drive full reporter expression and contains functional motifs. Analysis of further promoters suggests transcription initiation is regulated and promoters are either focused or dispersed. In contrast to the previous model of unregulated and promoter-independent transcription initiation, we find that sequence-specific promoters determine the initiation of Pol II transcription of protein-coding genes PTUs. These findings in Trypanosoma brucei suggest that in addition of chromatin modifications, promoter motifs-based regulation of gene expression is deeply conserved among eukaryotes.
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Affiliation(s)
- Carlos Cordon-Obras
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Claudia Gomez-Liñan
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Sara Torres-Rusillo
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Isabel Vidal-Cobo
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Diana Lopez-Farfan
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Alicia Barroso-Del Jesus
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Domingo Rojas-Barros
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain.
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Kraus AJ, Vanselow JT, Lamer S, Brink BG, Schlosser A, Siegel TN. Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes. Nat Commun 2020; 11:1498. [PMID: 32198348 PMCID: PMC7083915 DOI: 10.1038/s41467-020-15274-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/01/2020] [Indexed: 12/29/2022] Open
Abstract
Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histones or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in Trypanosoma brucei, we identified 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we found TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription. Histone modification and deposition are key regulators of transcription. Here, Kraus et al. provide a quantitative histone acetylome for Trypanosoma brucei, identify histone modifications enriched at transcription start sites, and show how H4 and H2A.Z acetylation affect histone deposition and transcription in trypanosomes.
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Affiliation(s)
- Amelie J Kraus
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany.,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.,Research Center for Infectious Diseases, University of Würzburg, 97080, Würzburg, Germany.,Institute for Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany.,German Federal Institute for Risk Assessment, Unit Safety of Chemicals, Department Chemicals and Product Safety, Berlin, Germany
| | - Stephanie Lamer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Benedikt G Brink
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany.,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - T Nicolai Siegel
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany. .,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany. .,Research Center for Infectious Diseases, University of Würzburg, 97080, Würzburg, Germany.
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5
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Efficient and specific oligo-based depletion of rRNA. Sci Rep 2019; 9:12281. [PMID: 31439880 PMCID: PMC6706579 DOI: 10.1038/s41598-019-48692-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/06/2019] [Indexed: 01/09/2023] Open
Abstract
In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.
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6
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Müller LSM, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba AE, Sebra RP, Siegel TN. Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature 2018; 563:121-125. [PMID: 30333624 PMCID: PMC6784898 DOI: 10.1038/s41586-018-0619-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/03/2018] [Indexed: 01/15/2023]
Abstract
Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host1. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility2,3. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding4. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses-Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing-that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
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Affiliation(s)
- Laura S M Müller
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Raúl O Cosentino
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- ZB MED - Information Centre for Life Sciences, Cologne, Germany
- TH Köln, Faculty of Information Science and Communication Studies, Cologne, Germany
- Core Unit Systems Medicine, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Julien Guizetti
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolin Wedel
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Noam Kaplan
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Panagiota Arampatzi
- Core Unit Systems Medicine, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | | | - Thomas D Otto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Robert P Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T Nicolai Siegel
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, Munich, Germany.
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany.
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7
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Vasquez JJ, Wedel C, Cosentino RO, Siegel TN. Exploiting CRISPR-Cas9 technology to investigate individual histone modifications. Nucleic Acids Res 2018; 46:e106. [PMID: 29912461 PMCID: PMC6182134 DOI: 10.1093/nar/gky517] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/13/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Despite their importance for most DNA-templated processes, the function of individual histone modifications has remained largely unknown because in vivo mutational analyses are lacking. The reason for this is that histone genes are encoded by multigene families and that tools to simultaneously edit multiple genomic loci with high efficiency are only now becoming available. To overcome these challenges, we have taken advantage of the power of CRISPR-Cas9 for precise genome editing and of the fact that most DNA repair in the protozoan parasite Trypanosoma brucei occurs via homologous recombination. By establishing an episome-based CRISPR-Cas9 system for T. brucei, we have edited wild type cells without inserting selectable markers, inserted a GFP tag between an ORF and its 3'UTR, deleted both alleles of a gene in a single transfection, and performed precise editing of genes that exist in multicopy arrays, replacing histone H4K4 with H4R4 in the absence of detectable off-target effects. The newly established genome editing toolbox allows for the generation of precise mutants without needing to change other regions of the genome, opening up opportunities to study the role of individual histone modifications, catalytic sites of enzymes or the regulatory potential of UTRs in their endogenous environments.
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Affiliation(s)
- Juan-José Vasquez
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
| | - Carolin Wedel
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
| | - Raul O Cosentino
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752 Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752 Munich, Germany
- Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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8
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Wedel C, Förstner KU, Derr R, Siegel TN. GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes. EMBO J 2017; 36:2581-2594. [PMID: 28701485 PMCID: PMC5579346 DOI: 10.15252/embj.201695323] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/25/2023] Open
Abstract
Genome‐wide transcription studies are revealing an increasing number of “dispersed promoters” that, unlike “focused promoters”, lack well‐conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well‐defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation. Using a combination of site‐specific and genome‐wide assays, we identified GT‐rich promoters that can drive transcription and promote the targeted deposition of the histone variant H2A.Z in a genomic context‐dependent manner. In addition, upon mapping nucleosome occupancy at high resolution, we find nucleosome positioning to correlate with RNA pol II enrichment and gene expression, pointing to a role in RNA maturation. Nucleosome positioning may thus represent a previously unrecognized layer of gene regulation in trypanosomes. Our findings show that even highly dispersed, unregulated promoters contain specific DNA elements that are able to induce transcription and changes in chromatin structure.
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Affiliation(s)
- Carolin Wedel
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany
| | | | - Ramona Derr
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany .,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, München, Germany.,Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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