RT Journal
A1 Baudement, Marie-Odile
A1 Cournac, Axel
A1 Court, Franck
A1 Seveno, Marie
A1 Parrinello, Hugues
A1 Reynes, Christelle
A1 Sabatier, Robert
A1 Bouschet, Tristan
A1 Yi, Zhou
A1 Sallis, Sephora
A1 Tancelin, Mathilde
A1 Rebouissou, Cosette
A1 Cathala, Guy
A1 Lesne, Annick
A1 Mozziconacci, Julien
A1 Journot, Laurent
A1 Forné, Thierry
T1 High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
JF Genome Research 
JO Genome Research 
YR 2018 
FD November 01 
VO 28 
IS 11 
SP 1733 
OP 1746 
DO 10.1101/gr.237073.118 
UL http://genome.cshlp.org/content/28/11/1733.abstract 
AB The mammalian cell nucleus contains numerous discrete suborganelles named nuclear bodies. While recruitment of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the high-salt–recovered sequences-sequencing (HRS-seq) method, a straightforward genome-wide approach whereby we isolated and sequenced genomic regions associated with large high-salt insoluble RNP complexes. By using mouse embryonic stem cells (ESCs), we showed that these regions essentially correspond to the most highly expressed genes, and to cis-regulatory sequences like super-enhancers, that belong to the active A chromosomal compartment. They include both cell-type–specific genes, such as pluripotency genes in ESCs, and housekeeping genes associated with nuclear bodies, such as histone and snRNA genes that are central components of Histone Locus Bodies and Cajal bodies. We conclude that HRSs are associated with the active chromosomal compartment and with large RNP complexes including nuclear bodies. Association of such chromosomal regions with nuclear bodies is in agreement with the recently proposed phase separation model for transcription control and might thus play a central role in organizing the active chromosomal compartment in mammals.