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Genome-wide analysis of intracellular notch1(ICN1) targets in gamma delta T cells (gd T cells).

ABSTRACT: We performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) for ICN1 in thymic gd T cells from neonates of C57BL/6 mice. Sequence reads for ICN1 and Input were aligned with the mouse reference genome (mm10) by bowtie program (v1.0.0), and peak detection and identification of ICN1 binding sites were obtained with MACS program (v1.4.2). ChIP-seq data revealed that 12%, 6% and 47% of ICN1 binding sites were within -10kb upstream of transcription start site, +10kb downstream of 3'end and the bodies of genes, respectively. The other of ICN1 binding sites was intergenic. We also found that ICN1 directly bound -5.4kb upstream of transcript start site of IL-7 receptor alpha (IL-7Ra) locus, which were estimated as a new promoter region of IL-7Ra. Some of ICN1 binding sites (e.g. TCF1 promoter) were consistent with previous reports, but others (e.g. Nr4a1 promoter) were novel. These suggests that ICN1 was associated with a lot of transcriptional regulation in gd T cells. Examination of ICN1 binding sites in gd T cells

ORGANISM(S): Mus musculus

SUBMITTER: Masataka Nakamura

PROVIDER: E-GEOD-56756 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of intracellular notch1(ICN1) targets in gamma delta T cells (gd T cells).

Project description:We performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) for ICN1 in thymic gd T cells from neonates of C57BL/6 mice. Sequence reads for ICN1 and Input were aligned with the mouse reference genome (mm10) by bowtie program (v1.0.0), and peak detection and identification of ICN1 binding sites were obtained with MACS program (v1.4.2). ChIP-seq data revealed that 12%, 6% and 47% of ICN1 binding sites were within -10kb upstream of transcription start site, +10kb downstream of 3'end and the bodies of genes, respectively. The other of ICN1 binding sites was intergenic. We also found that ICN1 directly bound -5.4kb upstream of transcript start site of IL-7 receptor alpha (IL-7Ra) locus, which were estimated as a new promoter region of IL-7Ra. Some of ICN1 binding sites (e.g. TCF1 promoter) were consistent with previous reports, but others (e.g. Nr4a1 promoter) were novel. These suggests that ICN1 was associated with a lot of transcriptional regulation in gd T cells.

2014-11-14 | GSE56756 | GEO

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

Project description:Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. We find that upstream antisense RNAs are cleaved and polyadenylated at poly(A) sites (PASs) shortly after initiation. De novo motif analysis shows PAS signals and U1 small nuclear ribonucleoprotein (snRNP) recognition sites to be the most depleted and enriched sequences, respectively, in the sense direction relative to the upstream antisense direction. These U1 snRNP sites and PAS sites are progressively gained and lost, respectively, at the 5' end of coding genes during vertebrate evolution. Functional disruption of U1 snRNP activity results in a dramatic increase in promoter-proximal cleavage events in the sense direction with slight increases in the antisense direction. These data suggest that a U1-PAS axis characterized by low U1 snRNP recognition and a high density of PASs in the upstream antisense region reinforces promoter directionality by promoting early termination in upstream antisense regions, whereas proximal sense PAS signals are suppressed by U1 snRNP. We propose that the U1-PAS axis limits pervasive transcription throughout the genome. 3' end sequencing of poly (A) + RNAs in mouse ES cells with and without U1 snRNP inhibition using antisense morpholino oligonucleotides (AMO). Each with two biological replicates.

2013-06-28 | E-GEOD-46433 | biostudies-arrayexpress

UTX Chromatin Immunoprecipitation on human HG18 Nimblegen 2 array promoter set

Project description:UTX binding sites were located genome wide in primary human fibroblasts (foot and lung) Tiled promoters with a probe per 100bp of refseq known genes 3kb upstream and 700 bp downstream of transcriptional start 8 samples (2 cell types (foot and lung primary human fibroblasts) x 2 set promoter arrays x 2 channels (channel 1 = ChIP = Cy5, channel 2 = input (10% of total genomic DNA hybed) = Cy3)

2010-06-24 | E-GEOD-16221 | biostudies-arrayexpress

Differentially methylated genes in human IL-7Ra high and low EM CD8+ T cells

Project description:Genome wide DNA methylation profiling of IL-7Ra high and low EM CD8+ T cells. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,578 CpGs. Samples included 2 IL-7Ra high EM CD8+ T cells and 2 IL-7Ra high EM CD8+ T cells.

2015-08-06 | GSE67816 | GEO

ChIP-Seq revealed c-Jun promotes the transcriptional activities of the p35 and EBI3 promoters in human HepG2 cells.

Project description:we performed ChIP-Seq to clarify whether c-Jun activated by pCMV-HBx transfection could bind to the promoter of the IL-35 gene. The results showed that the transcriptional activity of c-Jun was significantly enhanced in the 3-kb region upstream and downstream of the IL-35 transcription start site. This finding suggests that the transcription factor c-Jun binds the promoter sequence of IL-35 and activates its transcription.

2022-02-12 | GSE196403 | GEO

Differentially methylated genes in human IL-7Ra high and low EM CD8+ T cells

2015-08-06 | E-GEOD-67816 | biostudies-arrayexpress

The SPARC complex defines RNAPII promoters in Trypanosoma brucei

Project description:Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodomain protein CRD1 are tightly concentrated at RNAPII transcription start regions (TSRs). Here we report that SET27 and CRD1, together with four previously uncharacterized constituents, form the SET27 promoter-associated regulatory complex (SPARC), which is specifically enriched at TSRs. SET27 loss leads to aberrant RNAPII recruitment to promoter sites, accumulation of polyadenylated transcripts upstream of normal transcription start sites, and conversion of some normally unidirectional promoters to bidirectional promoters. Transcriptome analysis in the absence of SET27 revealed upregulated mRNA expression in the vicinity of SPARC peaks within the main body of chromosomes in addition to derepression of genes encoding variant surface glycoproteins (VSGs) located in subtelomeric regions. These analyses uncover a novel chromatin-associated complex required to establish accurate promoter position and directionality.

2023-03-11 | PXD036454 | Pride

IL-6R identifies early differentiated human effector memory CD8+ T cells that potently expand and produce IL-2 and IL-13

Project description:We found a unique subset of effector memory (EM) CD8+ T cells that expressed high levels of IL-6 receptor in human peripheral blood. These cells which also expressed high levels of IL-7Ra (referred to as IL-6R high IL-7Rahigh cells) had the a distinct gene expression profile and cellular characteristics compared to other EM CD8+ T cells. IL-6R high IL-7Ra high cells were early differentiated EM CD8+ T cells with decreased expression of T-bet, KLRG1, perforin and granzyme B. These cells had increased cell proliferation likely secondary to enhanced IL-2 production and high affinity IL-2R expression. IL-6R high IL-7Ra high EM CD8+ T cells exclusively produced high levels of IL-2, IL-5, IL-9 and IL-13 although IFN-r was produced by this cell subset and other EM CD8+ T cells. Of interest, IL-6R high IL-7Ra high EM CD8+ T cells expanded in the peripheral blood of patients with chronic obstructive pulmonary disease (COPD) and asthma where CD8+ T cells, IL-13 and IFN-r are suggested to be involved in the pathogenesis. Being the early-differentiated EM CD8+ T cells with a potent capacity to proliferate, survive and generate multiple cytokines, IL-6R high IL-7Ra high EM CD8+ T cells may serve as a primary reservoir for effector CD8+ T cells which potently expand and produce cytokines upon immune stimulation.

2012-12-31 | GSE34562 | GEO

A library of yeast transcription factor motifs

Project description:The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes. One-third of the binding specificities have not been previously reported. Several binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture. Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially ~100 bp upstream of transcription start sites. Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters. Keywords: Protein binding microarrays, DNA, proteins

2008-12-26 | GSE12349 | GEO

Integration of epigenetic and transcriptional mechanisms governs functional commitment versus plasticity of gd T cell subsets

Project description:gd T cells are major innate sources of interleukin-17 (IL-17) and interferon-g (IFN-g), which are differentially produced by two thymically-derived subsets segregated on CD27 expression. However, the molecular mechanisms that program the functional differentiation of gd cells remain incompletely understood. Here we show that CD27+ gd cells are epigenetically committed to express Ifng but not Il17, whereas CD27- gd cells spontaneously make IL-17 but can be induced to produce IFN-g under specific inflammatory conditions. This “plastic” behavior of CD27- gd cells associates with permissive histone H3 marks at loci encoding Ifng and upstream “type 1” transcription factors. By contrast, Il17 and related “type 17” factors are epigenetically and transcriptionally active in CD27- but silenced in CD27+ gd cells. Hence, stable versus plastic behaviors of gd cell subsets are controlled by integrated epigenetic and transcriptional mechanisms that regulate the expression of “master” transcription factors and effector cytokine genes.

2013-09-01 | GSE42098 | GEO

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