Genome-Wide uH2A Localization Analysis Highlights Bmi1-Dependent Deposition of the Mark at Repressed Genes
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{"title"=>"Genome-wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes", "type"=>"journal", "authors"=>[{"first_name"=>"Eric M.", "last_name"=>"Kallin", "scopus_author_id"=>"14071622700"}, {"first_name"=>"Ru", "last_name"=>"Cao", "scopus_author_id"=>"7103341393"}, {"first_name"=>"Raja", "last_name"=>"Jothi", "scopus_author_id"=>"6602359586"}, {"first_name"=>"Kai", "last_name"=>"Xia", "scopus_author_id"=>"15123470900"}, {"first_name"=>"Kairong", "last_name"=>"Cui", "scopus_author_id"=>"8785222500"}, {"first_name"=>"Keji", "last_name"=>"Zhao", "scopus_author_id"=>"7202071783"}, {"first_name"=>"Yi", "last_name"=>"Zhang", "scopus_author_id"=>"35365765300"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"67651022266", "doi"=>"10.1371/journal.pgen.1000506", "isbn"=>"1553-7404 (Electronic)", "pmid"=>"19503595", "issn"=>"15537390", "scopus"=>"2-s2.0-67651022266", "pui"=>"354995753"}, "id"=>"8758fa0e-eaf3-3fe0-ad4b-f60a06b3d93b", "abstract"=>"Polycomb group (PcG) proteins control organism development by regulating the expression of developmental genes. Transcriptional regulation by PcG proteins is achieved, at least partly, through the PRC2-mediated methylation on lysine 27 of histone H3 (H3K27) and PRC1-mediated ubiquitylation on lysine 119 of histone H2A (uH2A). As an integral component of PRC1, Bmi1 has been demonstrated to be critical for H2A ubiquitylation. Although recent studies have revealed the genome-wide binding patterns of some of the PRC1 and PRC2 components, as well as the H3K27me3 mark, there have been no reports describing genome-wide localization of uH2A. Using the recently developed ChIP-Seq technology, here, we report genome-wide localization of the Bmi1-dependent uH2A mark in MEF cells. Gene promoter averaging analysis indicates a peak of uH2A just inside the transcription start site (TSS) of well-annotated genes. This peak is enriched at promoters containing the H3K27me3 mark and represents the least expressed genes in WT MEF cells. In addition, peak finding reveals regions of local uH2A enrichment throughout the mouse genome, including almost 700 gene promoters. Genes with promoter peaks of uH2A exhibit lower-level expression when compared to genes that do not contain promoter peaks of uH2A. Moreover, we demonstrate that genes with uH2A peaks have increased expression upon Bmi1 knockout. Importantly, local enrichment of uH2A is not limited to regions containing the H3K27me3 mark. We describe the enrichment of H2A ubiquitylation at high-density CpG promoters and provide evidence to suggest that DNA methylation may be linked to uH2A at these regions. Thus, our work not only reveals Bmi1-dependent H2A ubiquitylation, but also suggests that uH2A targeting in differentiated cells may employ a different mechanism from that in ES cells.", "link"=>"http://www.mendeley.com/research/genomewide-uh2a-localization-analysis-highlights-bmi1dependent-deposition-mark-repressed-genes", "reader_count"=>90, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>10, "Researcher"=>32, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>3, "Student > Master"=>8, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>10, "Researcher"=>32, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>3, "Student > Master"=>8, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>73, "Medicine and Dentistry"=>2, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>73}, "Computer Science"=>{"Computer Science"=>4}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"South Korea"=>1, "Sweden"=>1, "United States"=>5, "Denmark"=>1, "France"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>8}

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  • {"files"=>["https://ndownloader.figshare.com/files/443439", "https://ndownloader.figshare.com/files/443608", "https://ndownloader.figshare.com/files/443648", "https://ndownloader.figshare.com/files/443678", "https://ndownloader.figshare.com/files/443696", "https://ndownloader.figshare.com/files/443756"], "description"=>"<div><p>Polycomb group (PcG) proteins control organism development by regulating the expression of developmental genes. Transcriptional regulation by PcG proteins is achieved, at least partly, through the PRC2-mediated methylation on lysine 27 of histone H3 (H3K27) and PRC1-mediated ubiquitylation on lysine 119 of histone H2A (uH2A). As an integral component of PRC1, Bmi1 has been demonstrated to be critical for H2A ubiquitylation. Although recent studies have revealed the genome-wide binding patterns of some of the PRC1 and PRC2 components, as well as the H3K27me3 mark, there have been no reports describing genome-wide localization of uH2A. Using the recently developed ChIP-Seq technology, here, we report genome-wide localization of the Bmi1-dependent uH2A mark in MEF cells. Gene promoter averaging analysis indicates a peak of uH2A just inside the transcription start site (TSS) of well-annotated genes. This peak is enriched at promoters containing the H3K27me3 mark and represents the least expressed genes in WT MEF cells. In addition, peak finding reveals regions of local uH2A enrichment throughout the mouse genome, including almost 700 gene promoters. Genes with promoter peaks of uH2A exhibit lower-level expression when compared to genes that do not contain promoter peaks of uH2A. Moreover, we demonstrate that genes with uH2A peaks have increased expression upon Bmi1 knockout. Importantly, local enrichment of uH2A is not limited to regions containing the H3K27me3 mark. We describe the enrichment of H2A ubiquitylation at high-density CpG promoters and provide evidence to suggest that DNA methylation may be linked to uH2A at these regions. Thus, our work not only reveals Bmi1-dependent H2A ubiquitylation, but also suggests that uH2A targeting in differentiated cells may employ a different mechanism from that in ES cells.</p></div>", "links"=>[], "tags"=>["genome-wide", "uh2a", "localization", "highlights", "bmi1-dependent", "deposition", "repressed", "genes"], "article_id"=>147407, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Eric M. Kallin", "Ru Cao", "Raja Jothi", "Kai Xia", "Kairong Cui", "Keji Zhao", "Yi Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000506.s001", "https://dx.doi.org/10.1371/journal.pgen.1000506.s002", "https://dx.doi.org/10.1371/journal.pgen.1000506.s003", "https://dx.doi.org/10.1371/journal.pgen.1000506.s004", "https://dx.doi.org/10.1371/journal.pgen.1000506.s005", "https://dx.doi.org/10.1371/journal.pgen.1000506.s006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_uH2A_Localization_Analysis_Highlights_Bmi1_Dependent_Deposition_of_the_Mark_at_Repressed_Genes/147407", "title"=>"Genome-Wide uH2A Localization Analysis Highlights Bmi1-Dependent Deposition of the Mark at Repressed Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-06-05 02:03:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/895263"], "description"=>"<p>(A) Profiles of per base pair Bmi1-dependent uH2A enrichment across the TSS of well annotated genes. Error bars represent s.e.m. of per base pair average for all genes analyzed (<i>n</i> = 15867). (B) Well-annotated genes were grouped by epigenetic modification state and the average normalized uH2A tag density was determined for each group. No K4/No K27 (<i>n</i> = 4690), purple; both H3K4me3 and H3K27me3 (Bivalent) (<i>n</i> = 1377), green; H3K27me3 only (<i>n</i> = 888), blue; H3K4me3 only (<i>n</i> = 8912), red; all genes (<i>n</i> = 15867), grey.</p>", "links"=>[], "tags"=>["promoter", "uh2a", "enrichment", "correlates", "h3k27me3"], "article_id"=>565712, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Eric M. Kallin", "Ru Cao", "Raja Jothi", "Kai Xia", "Kairong Cui", "Keji Zhao", "Yi Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000506.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bmi1_dependent_promoter_uH2A_enrichment_correlates_with_promoter_H3K27me3_enrichment_/565712", "title"=>"Bmi1-dependent promoter uH2A enrichment correlates with promoter H3K27me3 enrichment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:35:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/895346"], "description"=>"<p>(A) Bmi1-dependent tag density at selected gene promoters that contain peaks defined by the TIROE algorithm. Red arrow indicates the start and direction of transcription. (B) ChIP-qPCR validation of uH2A peaks (blue bars) and Bmi1 enrichment (red bars) was carried out in WT and Bmi1 null MEF cells. Enrichment was normalized to input control and data is presented as log<sub>2</sub> value of WT versus Bmi1 null.</p>", "links"=>[], "tags"=>["promoter", "uh2a", "enrichment", "sub-set"], "article_id"=>565792, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Eric M. Kallin", "Ru Cao", "Raja Jothi", "Kai Xia", "Kairong Cui", "Keji Zhao", "Yi Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000506.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bmi1_dependent_promoter_uH2A_enrichment_at_a_sub_set_of_gene_promoters_/565792", "title"=>"Bmi1-dependent promoter uH2A enrichment at a sub-set of gene promoters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:36:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/895443"], "description"=>"<p>(A) Proportion of promoter uH2A peaks (<i>n</i> = 671) (left bar) and non-promoter uH2A peaks (<i>n</i> = 15735)(right bar) which overlap with H3K4/H3K27 methylation peaks. No K4/No K27, purple; both H3K4me3 and H3K27me3 (Bivalent), green; H3K27me3 only, blue; H3K4me3 only, red. (B) Box plot representation of peak tag density distribution for promoter and non-promoter uH2A peaks. Red lines indicate median values. <i>P</i> value derived from Wilcoxon signed-rank test. (C) Box plot representation of peak tag density distribution for promoter (+) and non-promoter (−) uH2A peaks further sub-divided by H3K4me3/H3K27me3 co-localization. No K4/No K27, purple; both H3K4me3 and H3K27me3 (Bivalent), green; H3K27me3 only, blue; H3K4me3 only, red. White lines indicate median values. <i>P</i> value derived from Wilcoxon signed-rank test.</p>", "links"=>[], "tags"=>["non-promoter", "peaks", "bmi1-dependent", "uh2a"], "article_id"=>565886, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Eric M. Kallin", "Ru Cao", "Raja Jothi", "Kai Xia", "Kairong Cui", "Keji Zhao", "Yi Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000506.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Promoter_and_non_promoter_peaks_of_Bmi1_dependent_uH2A_are_distinct_/565886", "title"=>"Promoter and non-promoter peaks of Bmi1-dependent uH2A are distinct.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:38:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/895520"], "description"=>"<p>(A) Bmi1-dependent per base pair uH2A tag density was determined for genes defined as high CpG dinucleotide promoter content (HCP, blue) (<i>n</i> = 10,310), intermediate CpG dinucleotide promoter content (ICP, red) (<i>n</i> = 2889), low CpG dinucleotide promoter content (LCP, green) (<i>n</i> = 2668). (B) HCP class genes with available DNA methylation data were grouped based on the presence (+) (<i>n</i> = 266) or absence (−) (<i>n</i> = 8230) of a promoter bound peak of Bmi1-dependent uH2A and the distribution of DNA methylation values for each group was visualized using a standard box plot. Red lines indicate median values. <i>P</i> value derived from Wilcoxon signed-rank test. (C) Western blotting of uH2A was carried out using cell lysate prepared from wild-type and Dnmt1 null MEFs. H3 was used as a loading control. (D) Cytosine extension analysis was carried out using wild-type and Bmi1 null MEFs as well as Dnmt1 null and control cells. Biotin labeled restriction digests were spotted in triplicate onto a Nylon membrane and visualized using alkaline phosphatase. The procedure was repeated three independent times and data for one representative experiment is shown. (E) Data presented in panel D were quantified and presented as the ratio between methylation sensitive <i>HpaII</i> incorporation versus methylation insensitive <i>MspI</i> incorporation. Error bars represent s.e.m. (<i>n</i> = 3).</p>", "links"=>[], "tags"=>["deposition", "linked", "dna"], "article_id"=>565969, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Eric M. Kallin", "Ru Cao", "Raja Jothi", "Kai Xia", "Kairong Cui", "Keji Zhao", "Yi Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000506.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_uH2A_deposition_is_linked_to_DNA_methylation_/565969", "title"=>"uH2A deposition is linked to DNA methylation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:39:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/895623"], "description"=>"<p>(A) Bmi1-dependent uH2A tag density surrounding the TSSs of genes was calculated and grouped into 10 bins (<i>n</i>≈1335 for each group) based on <i>de novo</i> gene expression levels in MEF cells. (B) Bmi1-dependent uH2A tag density was calculated for the region indicated in (A) for genes grouped based on <i>de novo</i> expression in MEF cells (<i>n</i> = 4007, <i>n</i> = 2674, <i>n</i> = 2668, <i>n</i> = 4005; highest expressed to lowest expressed). Error bars represent the s.e.m. of the highest expressed and lowest expressed gene groups. (C) WT MEF expression of genes with (+, <i>n</i> = 483) and without (−, <i>n</i> = 12,871) a peak of Bmi1-dependent uH2A was subjected to data distribution analysis by standard box plot. Red lines indicate median values. <i>P</i> value derived from Wilcoxon signed-rank test is indicated. (D) Gene promoters with (+) and without (−) peaks of uH2A were analyzed for the presence of H3K4/H3K27 methylation peaks. No K4/No K27, purple; both H3K4me3 and H3K27me3 (Bivalent), green; H3K27me3 only, blue; H3K4me3 only, red. (E) Box plot of expression data distribution for promoters with (+) and without (−) uH2A peaks in WT MEFs were further sub-divided by H3K4/H3K27 co-localization. No K4/No K27, purple; both H3K4me3 and H3K27me3 (Bivalent), green; H3K27me3 only, blue; H3K4me3 only, red. White lines indicate median values. <i>P</i> value derived from Wilcoxon signed-rank test is shown. (F) Genes containing a peak of Bmi1-dependent uH2A were divided into three groups based on increasing peak tag density (<i>n</i> = 157, 157, and 158, respectively) and the distribution of log<sub>2</sub> expression change (Bmi1 null versus WT MEF cells) was presented by box plot. Red lines indicate median values. <i>P</i> value derived from Wilcoxon signed-rank test is shown.</p>", "links"=>[], "tags"=>["uh2a", "enriched", "repressed"], "article_id"=>566073, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Eric M. Kallin", "Ru Cao", "Raja Jothi", "Kai Xia", "Kairong Cui", "Keji Zhao", "Yi Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000506.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bmi1_dependent_uH2A_is_enriched_at_repressed_genes_/566073", "title"=>"Bmi1-dependent uH2A is enriched at repressed genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:41:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/895731"], "description"=>"*<p>Total base pairs refer to alignable portion of the genome.</p>**<p>Two-sided proportional test of Genome BP coverage as compared to Peak BP coverage.</p>", "links"=>[], "tags"=>["genetics and genomics/epigenetics", "genetics and genomics/gene expression", "molecular biology/dna methylation", "molecular biology/histone modification"], "article_id"=>566181, "categories"=>["Genetics", "Molecular Biology"], "users"=>["Eric M. Kallin", "Ru Cao", "Raja Jothi", "Kai Xia", "Kairong Cui", "Keji Zhao", "Yi Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000506.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bmi1_dependent_peak_distribution_throughout_the_mouse_genome_/566181", "title"=>"Bmi1-dependent peak distribution throughout the mouse genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-05 01:43:01"}

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