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ChIP-seq analysis of SRT1 and H3K9ac in MH63 and srt1 RNAi.

ABSTRACT: We report the high-throughput profiling of H3K9ac and SRT1 in MH63 and SRT1 RNAi. By obtaining about 8 million pair-end reads from H3K9ac and 6 million pair-end reads from SRT1, we find that about 45% of rice genes are marked by H3K9ac in 11 day-old seedlings. There are 1824 genes may be bound directly by OsSRT1. OsSRT1 is a site-specific deacetylase involved in deacetylation of H3K9 over specific genes. Overlapping between increased H3K9ac peaks in the RNAi plants and that of OsSRT1-binding was found over 37 genes, suggesting that OsSRT1 directly targeted to these genes for H3K9 deacetylation. The observations that H3K9ac was enriched at the 5’ end of genes larger than 1.5 kb and OsSRT1 RNAi enhanced the enrichment at that position. However, the OsSRT1-binding was found to be enriched over gene bodies. While the meaning of this binding profile is not yet clear, it is speculated that OsSRT1 may contribute to maintain the low level of H3K9ac in the gene body. In addition, this work revealed that OsSRT1 is enriched over retrotransposons.

ORGANISM(S): Oryza sativa

PROVIDER: GSE40054 | GEO | 2013/02/10

SECONDARY ACCESSION(S): PRJNA172844

REPOSITORIES: GEO

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ChIP-seq analysis of SRT1 and H3K9ac in MH63 and srt1 RNAi.

Project description:We report the high-throughput profiling of H3K9ac and SRT1 in MH63 and SRT1 RNAi. By obtaining about 8 million pair-end reads from H3K9ac and 6 million pair-end reads from SRT1, we find that about 45% of rice genes are marked by H3K9ac in 11 day-old seedlings. There are 1824 genes may be bound directly by OsSRT1. OsSRT1 is a site-specific deacetylase involved in deacetylation of H3K9 over specific genes. Overlapping between increased H3K9ac peaks in the RNAi plants and that of OsSRT1-binding was found over 37 genes, suggesting that OsSRT1 directly targeted to these genes for H3K9 deacetylation. The observations that H3K9ac was enriched at the 5M-bM-^@M-^Y end of genes larger than 1.5 kb and OsSRT1 RNAi enhanced the enrichment at that position. However, the OsSRT1-binding was found to be enriched over gene bodies. While the meaning of this binding profile is not yet clear, it is speculated that OsSRT1 may contribute to maintain the low level of H3K9ac in the gene body. In addition, this work revealed that OsSRT1 is enriched over retrotransposons. Examination of H3K9ac in MH63(WT) and SRT1-RNAi, OsSRT1 in MH63.

2013-02-10 | E-GEOD-40054 | biostudies-arrayexpress

ChIP-Seq of H3K9 acetylation for wildtype and ada2Δ cells in Cryptococcus neoformans

Project description:SAGA member Ada2 is required for the majority of H3K9 acetylation in C. neoformans. To identify specific genomic loci that exhibit Ada2-dependent H3K9 acetylation, we performed ChIP-Seq against H3K9ac in wildtype and ada2Δ cells. ChIP-Seq was performed using antibodies for H3K9ac in KN99 wildtype cells and ada2Δ cells. Input and IPed DNA was collected in triplicate from each strain and sequenced on an Illumnina HiSeq 2000 flow cell producing 84 million reads. Due to the lack of quality scores, raw reads are omitted from the submission.

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RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Project description:In eukaryotes, the Suv39 family of proteins tri-methylate lysine 9 of histone H3 (H3K9me) to form constitutive heterochromatin. However, how Suv39 proteins are nucleated at heterochromatin is not fully described. In the fission yeast, current models posit that Argonaute1-associated small RNAs (sRNAs) nucleate the sole H3K9 methyltransferase, Clr4/SUV39H, to centromeres. Here, we show that in the absence of all sRNAs and H3K9me, the Mtl1 and Red1 core (MTREC)/PAXT complex nucleates Clr4/SUV39H at a heterochromatic long noncoding RNA (lncRNA) at which the two H3K9 deacetylases, Sir2 and Clr3, also accumulate by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4/SUV39H from the nucleation center in an sRNA-independent manner, generating a basal H3K9me state. This is acted upon by the RNAi machinery to augment and amplify the Clr4/H3K9me signal at centromeres to establish heterochromatin. Overall, our data reveal that lncRNAs and RNA quality control factors can nucleate heterochromatin and function as epigenetic silencers in eukaryotes.

2024-05-16 | PXD039519 | Pride

Mapping of H3, H3K4me3 and H3K9ac on Ring and Schizont stages of P. falciparum

Project description:Epigenome profiling has led to the paradigm that promoters of active genes are decorated with H3K4me3 and H3K9ac marks. These data on synchronized parasites reveals significant developmental stage specificity of the epigenome. In rings, H3K4me3 and H3K9ac are homogenous across the genes marking active and inactive genes equally, whilst in schizonts they are enriched at the 5’end of active genes.

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Histone Deacetylase 3 is an Epigenomic Brake in Macrophage Alternative Activation (ChIP-Seq)

Project description:We report the genomic regions enriched in Histone Deacetylase 3 (HDAC3) in mouse bone marrow derived macrophages. Furthermore, we also report the genomic acetylation pattern on Histone 3, Lysine 9 (H3K9) in macrophages with and without HDAC3 and/or treated with Th2 cytokine IL-4. HDAC3 enriched genomic regions in mouse bone marrow dervied macrophages and H3K9Ac enriched genomic regions in wild-type macrophages and macrophages treated with IL-4 and/or deficient in HDAC3.

2011-11-10 | E-GEOD-33596 | biostudies-arrayexpress

Mapping of H3, H3K4me3 and H3K9ac on Ring and Schizont stages of P. falciparum

2010-05-19 | E-GEOD-16095 | biostudies-arrayexpress

Effect of Gfi1 36N variant on genome-wide H3K9 Acetylation patterns

Project description:ChIP-Seq Analysis of H3K9Ac in pairs of mouse and human samples carrying either the Gfi136S or the GFi136N variants. The objective of the study was to identify the changes in H3K9 acetylation at gene promoters that occur in samples expressing the 36N variant of the Gfi1 gene. 3 pairs of bone-marrow AML samples were obtained from mice where 1 mouse in each pair was homozygous for Gfi136S and 1 heterozygous for Gfi136N, or homozygous for 36N in one case. 2 pairs of AML samples were obtained from human patients were 1 patient was homozygous for Gfi1 36S and one was heterozygous for Gfi1 36N. H3 and H3K9Ac ChIP-Seq was carried out on each sample.

2016-08-01 | E-GEOD-71254 | biostudies-arrayexpress

RNAseq in whole freshwater planarians, Schmidtea mediterranea, following RNAi of the transcription factors lhx1/5-1 and pitx.

Project description:Freshwater planarians can be used as a model to investigate neuronal function and maintenance in adults in vivo. We knocked down expression for 2 transcription factors, then sequenced resulting animals to examine transcriptional changes that may have occurred. There are 3 triplicated conditions: control(RNAi) using the unc22 gene from C. elegans, lhx1/5-1(RNAi), and pitx(RNAi). Worms were fed RNAi for each gene 5 times over 12 days then were collected 12 days later. Approximately 50 million single-end reads were performed on each sample.

2013-05-31 | E-GEOD-47348 | biostudies-arrayexpress

The effect of diet on H3K9-butyryl and H3K9-acetyl in the heart before and after transverse aortic constriction in C57Bl/6J mice

Project description:Mice (C57Bl/6J) that are fed increasing levels of dietary fat (0, 10, and 60 Kcal%) show a parallel increasing decline in global promoter-H3K9-butyryl (H3K9Bu), but none in promoter-H3K9-acetyl (H3K9ac), in the heart. Additionally, transverse aortic constriction (TAC) induces a further decline in H3K9Bu, compared to an increase in H3K9ac.

2021-05-11 | GSE165279 | GEO

RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Project description:RNA surveillance (MTREC) and degradation (exosome) complexes nucleate Clr4/SUV39H at a heterochromatic long noncoding RNA, at which the two deacetylases, Sir2 and Clr3, also amass by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4 from the nucleation center which with the help from RNAi establish heterochromatin. (this is like the abstract for the paper) To identify nuclear Sir2-interacting proteins, a protocol was adopted by which frozen intact nuclei suitable for biochemical purifications were released by low pressure, semi-automated cryogrinding of frozen yeast pellets after which the nuclei were isolated by differential centrifugation. From these nuclear extracts, FLAG-tagged Sir2 was purified and analyzed by nanoscale micro-capillary tandem mass spectrometry.

2024-02-25 | MSV000094160 | MassIVE

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