Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries.
Chromosomes in all organisms are highly organized and divided into multiple chromosomal interaction domains, or topological domains. Regions of active, high transcription help establish and maintain domain boundaries, but precisely how this occurs remains unclear. Here, using fluorescence microscopy and chromosome conformation capture in conjunction with deep sequencing (Hi-C), we show that in Caulobacter crescentus, both transcription rate and transcript length, independent of concurrent translation, drive the formation of domain boundaries. We find that long, highly expressed genes do not form topological boundaries simply through the inhibition of supercoil diffusion. Instead, our results support a model in which long, active regions of transcription drive local decompaction of the chromosome, with these more open regions of the chromosome forming spatial gaps in vivo that diminish contacts between DNA in neighboring domains. These insights into the molecular forces responsible for domain formation in Caulobacter likely generalize to other bacteria and possibly eukaryotes.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
Tung Bk
0000-0003-4764-8851
TB
Le
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA laub@mit.edu.
Michael T
0000-0002-8288-7607
MT
Laub
D016935:Caulobacter crescentus / Q000235:genetics* / Q000378:metabolism*; D002876:Chromosomes, Bacterial / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D008856:Microscopy, Fluorescence; D009690:Nucleic Acid Conformation; D014158:Transcription, Genetic
Hi‐C; chromosomal domains; chromosome organization; supercoil diffusion; transcription