title: The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation.
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.
authors.forename: Trong
authors.initials: T
authors.lastname: Nguyen-Duc
authors.forename: Liesbeth
authors.initials: L
authors.lastname: van Oeffelen
authors.forename: Ningning
authors.initials: N
authors.lastname: Song
authors.forename: Gholamreza
authors.initials: G
authors.lastname: Hassanzadeh-Ghassabeh
authors.forename: Serge
authors.initials: S
authors.lastname: Muyldermans
authors.forename: Daniel
authors.initials: D
authors.lastname: Charlier
authors.affiliation: Research group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. espeeter@vub.ac.be.
authors.forename: Eveline
authors.initials: E
authors.lastname: Peeters
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism*; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D019848:Gene Expression Regulation, Archaeal; D059014:High-Throughput Nucleotide Sequencing; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D048229:Sulfolobus solfataricus / Q000235:genetics* / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D019843:Archaeal Proteins; D012333:RNA, Messenger; D014157:Transcription Factors