Project description:We evaluated how HrrA binding (found by ChAP-Seq) impacts the expression of individual target genes, by analyzing the transcriptome of the C. glutamicum wild type strain (ATCC 13032) as well as a ∆hrrA mutant. RNA-Seq analysis was performed prior to the addition of heme (T0) and 0.5 and 4 h after the heme pulse (in medium containing no other iron source).

2019-01-31 | GSE120924 | GEO

ChAP-seq analysis to identify GoxR binding sites

Project description:ChAP-seq analysis to identify GoxR binding sites

| PRJNA670347 | ENA

ChAP-seq analysis to identify GoxR binding sites

Project description:Gene expression in the obligatory aerobic acetic acid bacterium Gluconobacter oxydans was shown to respond to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed the function of a transcriptional regulator named GoxR, which belongs to the FNR family. Here, we applied ChAP-seq analysis with a strep-tagged GoxR version to identify binding sites of this regulator in the genome of G. oxydans.

2021-03-11 | GSE159734 | GEO

ChAP-Seq analysis of HrrA in C. glutamicum

Project description:We evaluated how HrrA binding in response to 4 µM heme as initial stimulus. Analysis was performed prior to the addition of heme (T0) and 0.5, 2, 4, 9, and 24 h after the heme pulse (in medium containing no other iron source).

2019-01-31 | GSE121962 | GEO

Transcriptome analysis for cellobise-adpative C. glutamicum strains

Project description:To understrand the altered gene expressions of cellobiose-positive C. glutamicum over cellobiose-negative C. glutamicum

2016-01-24 | GSE65076 | GEO

Chip-chip of Sir3 and of Sir2, and ChAP-chip of AAR from budding yeast cells

Project description:O-acetyl-ADP-ribose (AAR) is a small metabolic molecule that is generated during NAD-dependent deacetylation by Sir2. Sir2 regulates gene expression, DNA repair, and genome stability. chromatin affinity-precipitation (ChAP) method was used to detect the chromatin fragments at which small molecules interact with binding partners. Chromatin immunoprecipitation of Sir3 and of Sir2, respectively, applied with tilling array chip (ChIP on chip of Sir3 and of Sir2, respectively) and Chromatin affinity-precipitation of AAR applied with tilling array chip (ChAP on chip of AAR ) analysis demonstrated that an extended spreading of Sir3 and of AAR, but not Sir2 in Saccharomyces cerevisiae Ysa1 deleted cells compared with those in wild type cells

2015-12-31 | GSE65672 | GEO

Genome-wide analysis of ADP-ribosylation by ADPr-ChAP reveals its association with chromatin after oxidative stress

Project description:Chromatin ADP-ribosylation regulates important cellular processes. However, the exact location and magnitude of chromatin ADP-ribosylation are largely unknown. A robust and versatile method for assessing chromatin ADP-ribosylation is therefore crucial for further understanding its function. Here, we present a chromatin affinity precipitation method based on the high specificity and avidity of two well-characterized ADP-ribose binding domains to map chromatin ADP-ribosylation at the genome-wide scale and at specific loci. Our ADPr-ChAP method revealed that in cells exposed to oxidative stress, ADP-ribosylation of chromatin scaled with histone density, with highest levels at heterochromatic sites and depletion at active promoters. Furthermore, in growth factor-induced adipocyte differentiation, increased chromatin ADP-ribosylation was observed at PPARγ target genes, whose expression is ADP-ribosylation-dependent. In combination with deep-sequencing and conventional ChIP, the established ADPr-ChAP provides a valuable resource for the bioinformatic comparison of ADP-ribosylation with other chromatin modifications and for addressing its role in other biologically important processes.

2016-02-04 | GSE69885 | GEO

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