title: The global regulatory architecture of transcription during the Caulobacter cell cycle.
abstract: Each Caulobacter cell cycle involves differentiation and an asymmetric cell division driven by a cyclical regulatory circuit comprised of four transcription factors (TFs) and a DNA methyltransferase. Using a modified global 5' RACE protocol, we globally mapped transcription start sites (TSSs) at base-pair resolution, measured their transcription levels at multiple times in the cell cycle, and identified their transcription factor binding sites. Out of 2726 TSSs, 586 were shown to be cell cycle-regulated and we identified 529 binding sites for the cell cycle master regulators. Twenty-three percent of the cell cycle-regulated promoters were found to be under the combinatorial control of two or more of the global regulators. Previously unknown features of the core cell cycle circuit were identified, including 107 antisense TSSs which exhibit cell cycle-control, and 241 genes with multiple TSSs whose transcription levels often exhibited different cell cycle timing. Cumulatively, this study uncovered novel new layers of transcriptional regulation mediating the bacterial cell cycle.
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhou
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Jared M
authors.initials: JM
authors.lastname: Schrader
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Virginia S
authors.initials: VS
authors.lastname: Kalogeraki
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Abeliuk
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Cong B
authors.initials: CB
authors.lastname: Dinh
authors.affiliation: Department of Computer Science, Stanford University, Stanford, California, United States of America.
authors.forename: James Q
authors.initials: JQ
authors.lastname: Pham
authors.affiliation: Department of Electrical Engineering, Stanford University, Stanford, California, United States of America.
authors.forename: Zhongying Z
authors.initials: ZZ
authors.lastname: Cui
authors.affiliation: Department of Computer Science, Stanford University, Stanford, California, United States of America.
authors.forename: David L
authors.initials: DL
authors.lastname: Dill
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Harley H
authors.initials: HH
authors.lastname: McAdams
authors.affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America.
authors.forename: Lucy
authors.initials: L
authors.lastname: Shapiro
mesh_terms: D001483:Base Sequence; D016935:Caulobacter crescentus / Q000235:genetics* / Q000254:growth & development; D002453:Cell Cycle / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D005809:Genes, Regulator; D008780:Methyltransferases / Q000235:genetics; D059372:Nucleotide Motifs / Q000235:genetics; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D008780:Methyltransferases