title: Spatio-temporal dynamics of replication and transcription sites in the mammalian cell nucleus.
abstract: To study when and where active genes replicated in early S phase are transcribed, a series of pulse-chase experiments are performed to label replicating chromatin domains (RS) in early S phase and subsequently transcription sites (TS) after chase periods of 0 to 24 h. Surprisingly, transcription activity throughout these chase periods did not show significant colocalization with early RS chromatin domains. Application of novel image segmentation and proximity algorithms, however, revealed close proximity of TS with the labeled chromatin domains independent of chase time. In addition, RNA polymerase II was highly proximal and showed significant colocalization with both TS and the chromatin domains. Based on these findings, we propose that chromatin activated for transcription dynamically unfolds or "loops out" of early RS chromatin domains where it can interact with RNA polymerase II and other components of the transcriptional machinery. Our results further suggest that the early RS chromatin domains are transcribing genes throughout the cell cycle and that multiple chromatin domains are organized around the same transcription factory.
authors.affiliation: Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
authors.forename: Kishore S
authors.initials: KS
authors.lastname: Malyavantham
authors.forename: Sambit
authors.initials: S
authors.lastname: Bhattacharya
authors.forename: William D
authors.initials: WD
authors.lastname: Alonso
authors.forename: Raj
authors.initials: R
authors.lastname: Acharya
authors.forename: Ronald
authors.initials: R
authors.lastname: Berezney
mesh_terms: D002467:Cell Nucleus / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism; D045584:Chromosome Positioning; D004261:DNA Replication; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted; D012319:RNA Polymerase II / Q000378:metabolism; D016196:S Phase; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D012319:RNA Polymerase II