Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional profiling of a slyA mutant and a slyA-overexpression strain of Escherichia coli MG1655 in order to elucidate the SlyA regulon

ABSTRACT: A microarray study was performed to identify the Escherichia coli SlyA regulon. The wild-type (parental) Escherichia coli MG1655 strain was compared to an isogenic slyA deletion mutant, whilst a slyA-overexpression strain (in pET28a) was compared to an empty (pET28a) vector control. Continuous chemostat cultures were obtained (Evans medium pH 6.9, 0.2 h-1 dilution rate, 1 culture volume per hour air input, 400 rpm). Samples were eluted directly into RNAprotect, RNA purified and then hybridised in a reference-style format to micorarrays.

INSTRUMENT(S): Labfors 2 chemostat (Infors AG, Bottmingen, Switzerland)

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Jeff Green

PROVIDER: E-MTAB-5220 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Chromatin immunoprecipitation microarray (ChIP-chip) study using 3 human cell lines (K562, U937, CD14+); of 19 histone modifications across 1% of the human genome used in the pilot phase of the ENCODE project.<br>paper abstract: It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), linking chromatin structure and function to co- transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.

Dataset Information

Transcriptional profiling of a slyA mutant and a slyA-overexpression strain of Escherichia coli MG1655 in order to elucidate the SlyA regulon

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