Massive parallel cDNA sequencing (RNA-seq) has revolutionized global transcriptomic analysis and revealed an unexpected complexity of the prokaryotic transcriptome landscape.  Apart from mRNAs, ribosomal RNAs, and tRNAs, prokaryotes express a heterogeneous group of non-coding RNA species which can be broadly assigned to two major populations (i) trans-encoded sRNAs, expressed from independent transcription units located in intergenic regions, and (ii) cis-encoded sRNAs, transcribed in sense or antisense to mRNAs. Small non-coding RNAs (sRNAs), may have relevant housekeeping functions, but most often exert post-transcriptional regulation of gene expression, thereby contributing to the adjustment of bacterial physiology to changing environments.

Different experimental RNA-seq set-ups allow for identification of transcription start sites, operon structures and novel transcribed regions including protein-coding and non-coding RNA genes. Since transcription is the first committed and highly regulated step of gene expression in prokaryotes deriving promoter sequences and operon structures from RNA-seq data provides insights into the organization of transcriptional units and largely contributes to a better understanding of gene regulation.

In this project we investigate the transcriptome landscape of Sinorhizobium and related alpha-proteobacteria. Combining experimental and bioinformatics approaches, we aim at the functional analysis of trans-encoded sRNAs and antisense RNAs.

 

Collaborators

Robert Giegerich (Bielefeld University, Germany), Elena Evguenieva-Hackenberg (University of Giessen, Germany) Wolfgang Hess (University of Freiburg, Germany), Sharon R. Long (Stanford University, U.S.A.), Claudio Valverde (Universidad Nacional de Quilmes, Argentina), and José I. Jiménez-Zurdo (CSIC, Granada, Spain)

Funding

Priority Program SPP 1258 (German Research Foundation)

Alexander von Humboldt-Foundation

German Academic Exchange Service, 2010-2011

SYNMIKRO Young Researchers Groups

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