4C-Seq identifies the chromatin interaction landscape of the miR-146a promoter region
Ontology highlight
ABSTRACT:
INSTRUMENT(S): HiSeq X Ten
ORGANISM(S): Homo sapiens
SUBMITTER: Guojun Hou
PROVIDER: E-MTAB-13082 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To test the genomic region containing rs2431697 whether forms a cognate enhancer-promoter loop with the miR-146a promoter and modulates the expression of miR-146a, we perfomed 4C-seq in U-937 cell line based on miR-146a promoter view point (First digestion enzyme MboI, second digestion enzyme NlaIII) and rs2431697 view point (First digestion enzyme CSP6I, second digestion enzyme NlaIII).
2020-11-05 | E-MTAB-9581 | biostudies-arrayexpress
Project description:To test the genomic region containing rs2431697 whether forms a cognate enhancer-promoter loop with the miR-146a promoter and modulates the expression of miR-146a, we perfomed 4C-seq in U-937 cell line based on the rs2431697 view point and miR-146a promoter view point.
2020-11-05 | E-MTAB-8974 | biostudies-arrayexpress
Project description:To test if there is a physical interaction between the IRF8 promoter and the rs2280381-containing region, we conducted circular chromatin conformation capture assay in the U937 cell. For the IRF8 viewpoint group, we used CSP6I as the first digested enzyme and NlaIII as the second enzyme. For the rs2280381-containing region, we used MboI as the first digested enzyme and NlaIII as the second enzyme. We use 4C-PCR primer to construct IRF8 point view and rs2280381-containing region 4C library.
2021-07-01 | E-MTAB-10120 | biostudies-arrayexpress
Project description:Drosophila MSL complex binds the single male X chromosome to upregulate gene expression to equal that from the two female X chromosomes. However, it has been puzzling that ~25% of transcribed genes on the X do not stably recruit MSL complex. Here, we find that almost all active genes on the X are associated with robust H4 Lys16 acetylation (H4K16ac), the histone modification catalyzed by MSL complex. The distribution of H4K16ac is much broader than that of MSL complex, and our results favor the idea that chromosome-wide H4K16ac reflects transient association of MSL complex, occurring through spreading or chromosomal looping. Our results parallel those of localized Polycomb repressive complex and its more broadly distributed H3K27me3 chromatin mark, suggesting a common principle for the establishment of active and silenced chromatin domains For ChIP-on-chip experiments in larvae, 1000 third instar larvae were collected and chromatin was prepared as described previously. Five IPs were performed for each of the two biological replicates. For SL2 cells and male larvae, one ChIP-on-chip experiment was performed using anti-H4K16ac from Serotec (AHP417) (1-2 ul/IP). However, this antibody was discontinued, and an additional experiment for each was performed using anti-H4K16ac from Upstate/Millipore (07-329) (3 ul/IP). Both replicates for Kc cells and female larvae were also performed using anti-H4K16ac from Upstate/Millipore. Replicate experiments were highly reproducible.
2009-06-10 | E-GEOD-14884 | biostudies-arrayexpress
Project description:Active genes on the X chromosome of Drosophila males are upregulated by the Male-specific lethal (MSL) complex containing five MSL proteins and two non-coding roX RNAs. To probe the targeting mechanism, we have solved the structure of the MSL3 chromodomain, designed point mutations in key residues that disrupt putative methyl-lysine recognition, and tested their effect on full length MSL3 function. Transgenic males expressing these site-directed point mutants or MSL3short, a naturally occurring MSL3 form lacking the chromodomain, are unhealthy and developmentally delayed. Genomewide analyses of the binding patterns of these mutants support a two-step model: the first step is chromodomain-independent association with “chromatin entry sites” carrying GA-rich MSL recognition elements (MREs). The second step involves spreading from entry sites to the majority of active genes on the X. Either deleting or introducing point mutations in the MSL3 chromodomain disrupts this second step. In vitro studies demonstrate that chromodomain mutants have diminished interaction with recombinant nucleosomes methylated at H3K36. We propose that MSL spreading depends, to a large extent, on the integrity of the MSL3 chromodomain to interact with lysine-methylated nucleosomes. Chromatin immunoprecipitation using TAP-tag was performed as described previously (Alekseyenko et al., 2006). The immunoprecipitated material was eluted from the beads by adding 10 ?L (100 U) of AcTEV protease into 450 ?L of TEV buffer followed by incubation at 25°C for 1 h. To reverse the cross-links, samples were brought to 0.3M NaCl and 1% SDS and incubated at 65°C for 12 h. The samples were then extracted with phenol/chloroform/isoamyl alcohol followed by chloroform, and precipitated by ethanol in the presence of glycogen. The resulting precipitated DNA and the input DNA were amplified using a DNA linker as described (Strutt et al., 1997). LM-PCR (25 cycles) was performed using Platinum Pfu (Invitrogen). The resulting DNA was labeled and hybridized to arrays by NimbleGen Systems, Inc. Two-channel tiling arrays containing 388,000 probes were designed based on FlyBase 3.2. Chromosomes X and 19.6Mb of 2L were covered. The ChIP sample of interest was hybridized on one channel and genomic DNA was used as the reference on the other channel. Each ChIP-chip experiment was performed in duplicate.
2008-11-18 | E-GEOD-11817 | biostudies-arrayexpress
Project description:In Drosophila, X chromosome dosage compensation requires the male-specific lethal (MSL) complex, which associates with actively transcribed genes on the single male X chromosome to upregulate transcription approximately 2-fold. We found that on the male X chromosome, or when MSL complex is ectopically localized to an autosome, histone H3K36 trimethylation (H3K36me3) is a strong predictor of MSL binding. We isolated mutants lacking Set2, the H3K36me3 methyltransferase, and found that Set2 is an essential gene in both sexes of Drosophila. In set2 mutant males, MSL complex maintains X specificity but exhibits reduced binding to target genes. Furthermore, recombinant MSL3 protein preferentially binds nucleosomes marked by H3K36me3 in vitro. Our results support a model in which MSL complex uses high-affinity sites to initially recognize the X chromosome and then associates with many of its targets through sequence-independent features of transcribed genes. Keywords: ChIP-chip ChIP-chip experiments were performed on custom Nimblegen arrays (GPL5636). Each array contained 388,000 oligonucleotide probes covering all of the X and the 2L chromosomes, with a 100 bp resolution (50mer probes with 50 bp gaps). The design was based on FlyBase 3.2. For the superspreading experiments, an additional array was used that contains the entire X chromosome and 3R (GPL5660). MSL complex binding sites on both arrays are the same and signal on the 3R chromosome was at background level.
2007-09-20 | E-GEOD-8557 | biostudies-arrayexpress
Project description:Two biological replicates Hi-C and HPV16-specific Region Capture Hi-C libraries were prepared for each of the W12 cell lines. Capture Hi-C was performed using HPV16-specific RNA baits. Hi-C libraries alone were prepared from normal cervix tissue (Ncx).
2021-06-18 | E-MTAB-10152 | biostudies-arrayexpress
Project description:In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with MboI restriction enzyme having as starting material 1 million (M), 100 thousand (k), 50k, 25k, 10k or 1k cells. As well as, to 2 samples digested with HindIII restriction enzyme that had as starting material 5M or 100k cells. Traditional in situ Hi-C protocols recommend 5-10 million starting cells. The aim of the experiment was to assess the impact of decreasing the cell number on reproducibility, library complexity, chromatin structure visualization in order to adapt the method to the study of rare cell populations. Furthermore, we have characterised the 3D structure of peripheral blood mononuclear cells (PBMCs) obtained from a blood extraction from a healthy donor and from a lymph node biopsy from a DLBCL patient as a proof of concept for the suitability of Low-C for rare cell population analysis.
2018-11-30 | E-MTAB-5875 | biostudies-arrayexpress
Project description:Transcriptional profiling from young, old, healthy, or injured rat iliac arteries. We studied the gene expression profile in a model of mechanical vascular injury in the iliac artery of aging (22 months old) and young rats (4 months old). We investigated aging-related variations in gene expression at 30 min, 3d and 7d post injury.
2011-10-18 | E-GEOD-29255 | biostudies-arrayexpress
Project description:Human SGBS preadipocytes were differentiated into adipocytes, and human iPSCs were differentiated into hypothalamic neurons. Cells were collected for in situ promoter capture Hi-C [PMID: 29988018] at several differentiation stages. The differentiations were performed in one biological replicate, with two technical replicates (different wells of the differentiation that were also processed individually during library preparation). SGBS Day0: Represents the preadipocyte state. SGBS Day2: Represents immature adipocytes. SGBS Day8: Represents early mature adipocytes. SGBS Day16: Represents mature adipocytes. Hypothalamic Day 12: Represents early hypothalamic neurons. Hypothalamic Day 16: Represents mid hypothalamic neurons. Hypothalamic Day 27: Represents mature hypothalamic neurons.
2021-05-29 | E-MTAB-10488 | biostudies-arrayexpress