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.



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)


Priority Program SPP 1258 (German Research Foundation)

Alexander von Humboldt-Foundation

German Academic Exchange Service, 2010-2011

SYNMIKRO Young Researchers Groups

Almost all scientific members of SYNMIKRO are actively involved in DFG’s Collaborative Research Centers (Sonderforschungsbereiche), Research Training Groups (Graduiertenkollegs), or other Cooperative Research projects. Alongside performing adventurous experiments, and reporting excellent science, SYNMIKRO substantially promotes potential Young Research Group Leaders by constantly keeping its doors open to welcome and support Young Researchers planning to set up an Independent Research Group.
Our Young Research Groups