title: Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes.
abstract: RNA polymerase II (RNAP-II) synthesizes the m(7)G-capped Spliced Leader (SL) RNA and most protein-coding mRNAs in trypanosomes. RNAP-II recruitment to DNA usually requires a set of transcription factors that make sequence-specific contacts near transcriptional start sites within chromosomes. In trypanosomes, the transcription factor TFIIB is necessary for RNAP-II-dependent SL RNA transcription. However, the trypanosomal TFIIB (tTFIIB) lacks the highly basic DNA binding region normally found in the C-terminal region of TFIIB proteins. To assess the precise pattern of tTFIIB binding within the SL RNA gene locus, as well as within several other loci, we performed chromatin immunoprecipitation/microarray analysis using a tiled gene array with a probe spacing of 10 nucleotides. We found that tTFIIB binds non-randomly within the SL RNA gene locus mainly within a 220-nt long region that straddles the transcription start site. tTFIIB does not bind within the small subunit (SSU) rRNA locus, indicating that trypanosomal TFIIB is not a component of an RNAP-I transcriptional complex. Interestingly, discrete binding sites were observed within the putative promoter regions of two loci on different chromosomes. These data suggest that although trypanosomal TFIIB lacks a highly basic DNA binding region, it nevertheless localizes to discrete regions of chromatin that include the SL RNA gene promoter.
authors.affiliation: Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry-New Jersey Medical School, Newark, NJ 07103, USA.
authors.forename: Wenzhe
authors.initials: W
authors.lastname: Liu
authors.forename: Anish
authors.initials: A
authors.lastname: Das
authors.forename: Rachel
authors.initials: R
authors.lastname: Morales
authors.forename: Mahrukh
authors.initials: M
authors.lastname: Banday
authors.forename: Virginie
authors.initials: V
authors.lastname: Aris
authors.forename: David M
authors.initials: DM
authors.lastname: Lukac
authors.forename: Patricia
authors.initials: P
authors.lastname: Soteropoulos
authors.forename: David A
authors.initials: DA
authors.lastname: Wah
authors.forename: Jennifer
authors.initials: J
authors.lastname: Palenchar
authors.forename: Vivian
authors.initials: V
authors.lastname: Bellofatto
mesh_terms: D047369:Chromatin Immunoprecipitation; D002875:Chromosomes / Q000235:genetics* / Q000378:metabolism*; D005786:Gene Expression Regulation; D046228:Microarray Analysis; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D020038:RNA, Spliced Leader; D035581:Transcription Factor TFIIB / Q000378:metabolism*; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000378:metabolism*
chemical_list: D020038:RNA, Spliced Leader; D035581:Transcription Factor TFIIB