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Identification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing

ABSTRACT: Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions.

ORGANISM(S): Agrobacterium tumefaciens

PROVIDER: GSE59123 | GEO | 2014/12/04

SECONDARY ACCESSION(S): PRJNA254473

REPOSITORIES: GEO

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Identification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing

Project description:Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions. 8 cDNA libraries were sequenced. A. tumefaciens hfq3xFlag and hfqWT (control) strains were grown to stationary and exponential growth phase and under non-induced and virulence induced conditions.

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