The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation.

TitleThe genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation.
Publication TypeJournal Article
Year of Publication2013
AuthorsNguyen-Duc, T., L. van Oeffelen, N. Song, G. Hassanzadeh-Ghassabeh, S. Muyldermans, D. Charlier, and E. Peeters
JournalBMC Genomics
Volume14
Pagination828
Date Published2013
ISSN1471-2164
KeywordsArchaeal Proteins, Binding Sites, Chromatin Immunoprecipitation, Clustered Regularly Interspaced Short Palindromic Repeats, Gene Expression Regulation, Archaeal, High-Throughput Nucleotide Sequencing, Nucleotide Motifs, Promoter Regions, Genetic, Protein Binding, RNA, Messenger, Sulfolobus solfataricus, Transcription Factors, Transcription, Genetic
Abstract

BACKGROUND: Gene regulatory processes are largely resulting from binding of transcription factors to specific genomic targets. Leucine-responsive Regulatory Protein (Lrp) is a prevalent transcription factor family in prokaryotes, however, little information is available on biological functions of these proteins in archaea. Here, we study genome-wide binding of the Lrp-like transcription factor Ss-LrpB from Sulfolobus solfataricus.RESULTS: Chromatin immunoprecipitation in combination with DNA microarray analysis (ChIP-chip) has revealed that Ss-LrpB interacts with 36 additional loci besides the four previously identified local targets. Only a subset of the newly identified binding targets, concentrated in a highly variable IS-dense genomic region, is also bound in vitro by pure Ss-LrpB. There is no clear relationship between the in vitro measured DNA-binding specificity of Ss-LrpB and the in vivo association suggesting a limited permissivity of the crenarchaeal chromatin for transcription factor binding. Of 37 identified binding regions, 29 are co-bound by LysM, another Lrp-like transcription factor in S. solfataricus. Comparative gene expression analysis in an Ss-lrpB mutant strain shows no significant Ss-LrpB-mediated regulation for most targeted genes, with exception of the CRISPR B cluster, which is activated by Ss-LrpB through binding to a specific motif in the leader region.CONCLUSIONS: The genome-wide binding profile presented here implies that Ss-LrpB is associated at additional genomic binding sites besides the local gene targets, but acts as a specific transcription regulator in the tested growth conditions. Moreover, we have provided evidence that two Lrp-like transcription factors in S. solfataricus, Ss-LrpB and LysM, interact in vivo.

DOI10.1186/1471-2164-14-828
Alternate JournalBMC Genomics
PubMed ID24274039
PubMed Central IDPMC4046817
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