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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chip-seq to identify HrdB regulated genes in Streptomyces coelicolor

ABSTRACT: Chip-seq to identify the HrdB (SCO5820) binding sites and regulated genes in Streptomyces coelicolor. The HrdB gene was tagged on genome by HA (Human Influenza hemagglutinin derived) epitope (TAC CCG TAC GAT GTG CCG GAT TAC GCG). We have 3 replicates with HrdB tagged by HA and 2 replicates with wild-type strain as controls. Chip-seq experiment was conducted using antibody against HA tag in vegetative growth phase (see protocols).

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Streptomyces coelicolor A3(2)

SUBMITTER: Jiri Vohradsky

PROVIDER: E-MTAB-6926 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor.

Šmídová Klára K Ziková Alice A Pospíšil Jirí J Schwarz Marek M Bobek Jan J Vohradsky Jiri J

Nucleic acids research 20190101 2

HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation o ...[more]

PMID: 30371884

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