Dataset Information

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.

ABSTRACT: Recent studies on targeted gene integrations in bacteria have demonstrated that chromosomal location can substantially affect a gene's expression level. However, these studies have only provided information on a small number of sites. To measure position effects on transcriptional propensity at high resolution across the genome, we built and analyzed a library of over 144,000 genome-integrated, standardized reporters in a single mixed population of Escherichia coli. We observed more than 20-fold variations in transcriptional propensity across the genome when the length of the chromosome was binned into broad 4 kbp regions; greater variability was observed over smaller regions. Our data reveal peaks of high transcriptional propensity centered on ribosomal RNA operons and core metabolic genes, while prophages and mobile genetic elements were enriched in less transcribable regions. In total, our work supports the hypothesis that E. coli has evolved gene-independent mechanisms for regulating expression from specific regions of its genome.

SUBMITTER: Scholz SA

PROVIDER: S-EPMC6508686 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.

Scholz Scott A SA Diao Rucheng R Wolfe Michael B MB Fivenson Elayne M EM Lin Xiaoxia Nina XN Freddolino Peter L PL

Cell systems 20190320 3

Recent studies on targeted gene integrations in bacteria have demonstrated that chromosomal location can substantially affect a gene's expression level. However, these studies have only provided information on a small number of sites. To measure position effects on transcriptional propensity at high resolution across the genome, we built and analyzed a library of over 144,000 genome-integrated, standardized reporters in a single mixed population of Escherichia coli. We observed more than 20-fold ...[more]

PMID: 30904377

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Project description:Genome-wide mapping of nucleosomes has revealed a great deal about the relationships between chromatin structure and control of gene expression, and has led to mechanistic hypotheses regarding the rules by which chromatin structure is established. High-throughput sequencing has recently become the technology of choice for chromatin mapping studies, yet analysis of these experiments is still in its infancy. Here, we introduce a pipeline for analyzing deep sequencing maps of chromatin structure and apply it to data from S. cerevisiae. We analyze digestion series where nucleosomes are isolated from under- and over-digested chromatin. We find that certain classes of nucleosomes are unusually susceptible or resistant to overdigestion, with promoter nucleosomes easily digested and mid-coding region nucleosomes being quite stable. We find evidence for highly sensitive nucleosomes located within “nucleosome-free regions,” suggesting that these regions are not always completely naked but instead are likely associated with easily-digested nucleosomes. Finally, since RNA polymerase is the dominant energy-consuming machine that operates on the chromatin template, we analyze changes in chromatin structure when RNA polymerase is inactivated via a temperature-sensitive mutation. We find evidence that RNA polymerase plays a role in nucleosome eviction at promoters, and is also responsible for retrograde shifts in nucleosomes during transcription. Loss of RNA polymerase results in a relaxation of chromatin structure to more closely match in vitro nucleosome positioning preferences. Together, these results provide analytical tools and experimental guidance for nucleosome mapping experiments, and help disentangle the interlinked processes of transcription and chromatin packaging. Keywords: Genomic Solexa/Illumina sequencing of mononucleosomes. Titration series: gel-purified mononucleosomal DNA from three different titration levels – underdigested, typical digestion, and overdigested. RP021 series: MNase-seq at 0, 20, and 120 minutes after shifting these cells from 25 C to 37 C.

Dataset Information

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.

Publications

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.

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