title: Global 'bootprinting' reveals the elastic architecture of the yeast TFIIIB-TFIIIC transcription complex in vivo.
abstract: TFIIIB and TFIIIC are multi-subunit factors required for transcription by RNA polymerase III. We present a genome-wide high-resolution footprint map of TFIIIB-TFIIIC complexes in Saccharomyces cerevisiae, obtained by paired-end sequencing of micrococcal nuclease-resistant DNA. On tRNA genes, TFIIIB and TFIIIC form stable complexes with the same distinctive occupancy pattern but in mirror image, termed 'bootprints'. Global analysis reveals that the TFIIIB-TFIIIC transcription complex exhibits remarkable structural elasticity: tRNA genes vary significantly in length but remain protected by TFIIIC. Introns, when present, are markedly less protected. The RNA polymerase III transcription terminator is flexibly accommodated within the transcription complex and, unexpectedly, plays a major structural role by delimiting its 3'-boundary. The ETC sites, where TFIIIC binds without TFIIIB, exhibit different bootprints, suggesting that TFIIIC forms complexes involving other factors. We confirm six ETC sites and report a new site (ETC10). Surprisingly, TFIIIC, but not TFIIIB, interacts with some centromeric nucleosomes, suggesting that interactions between TFIIIC and the centromere may be important in the 3D organization of the nucleus.
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
authors.forename: V
authors.initials: V
authors.lastname: Nagarajavel
authors.forename: James R
authors.initials: JR
authors.lastname: Iben
authors.forename: Bruce H
authors.initials: BH
authors.lastname: Howard
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Maraia
authors.forename: David J
authors.initials: DJ
authors.lastname: Clark
mesh_terms: D001665:Binding Sites; D002503:Centromere / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry; D018983:DNA Footprinting / Q000379:methods; D009707:Nucleosomes / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics*; D013728:Terminator Regions, Genetic; D035361:Transcription Factor TFIIIB / Q000378:metabolism*; D019474:Transcription Factors, TFIII / Q000378:metabolism*; D000098832:Transcription Factor TFIIIC
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D035361:Transcription Factor TFIIIB; D019474:Transcription Factors, TFIII; D000098832:Transcription Factor TFIIIC; D012343:RNA, Transfer