RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin throughout Mitosis, Suggesting a Role in Mitotic Bookmarking

Abstract

Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity, and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation. Here, we show that the major transcriptional effector of Notch signaling, RBPJ, is retained on mitotic chromatin, and that this mitotic chromatin association is mediated through the direct association of RBPJ with DNA. We further demonstrate that RBPJ binds directly to nucleosomal DNA in vitro, with a preference for sites close to the entry/exit position of the nucleosomal DNA. Genome-wide analysis in the murine embryonal-carcinoma cell line F9 revealed that roughly 60% of the sites occupied by RBPJ in asynchronous cells were also occupied in mitotic cells. Among them, we found that a fraction of RBPJ occupancy sites shifted between interphase and mitosis, suggesting that RBPJ can be retained on mitotic chromatin by sliding on DNA rather than disengaging from chromatin during mitotic chromatin condensation. We propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon mitotic exit. Strikingly, we found that sites of RBPJ occupancy were enriched for CTCF-binding motifs in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates transcription and bridges long-range chromatin interactions, our results raise the intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that could be propagated through cell division to maintain gene expression programs.

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

“…In addition to the technical reasons invoked above, this might be due to mostly nonspecific DNA binding of SOX2 and/or DNAindependent binding of SOX2 to mitotic chromosomes. In contrast to GATA1 (Kadauke et al 2012), RBPJ (Lake et al 2014), or MLL (Blobel et al 2009) but similar to FOXA1 (Caravaca et al 2013), we did not find enrichment of a particular class of genes bound by SOX2 during mitosis. The functional relevance of the sites specifically bound on mitotic chromosomes remains unclear, and there appears to be no quantitative difference in early G1 transcriptional activity of genes bound by FOXA1 or GATA1 in mitosis compared with genes bound in interphase only (Caravaca et al 2013;Hsiung et al 2016).…”

Cycling through developmental decisions: how cell cycle dynamics control pluripotency, differentiation and reprogramming

“…3). In addition to chromatin modifiers, a select group of transcription factors such as FOXA1, GATA1, RUNX2, ESRRB and RBPJ also bind and 'bookmark' mitotic chromatin (Caravaca et al, 2013;Festuccia et al, 2016;Kadauke et al, 2012;Lake et al, 2014;Young et al, 2007). Interestingly, however, these factors maintain mitotic chromatin binding at only a subset of the specific sites bound during interphase (Caravaca et al, 2013;Kadauke et al, 2012).…”

A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

“…Studies have described such alterations for the recruitment of transcriptional regulators (Raff et al 1994;Martínez-Balbás et al 1995;Dey et al 2000;Christova and Oelgeschläger 2001;Kruhlak et al 2001;Zaidi et al 2003;Young et al 2007;Yang et al 2008Yang et al , 2013Blobel et al 2009;Kadauke et al 2012;Caravaca et al 2013;Poleshko et al 2013;Lake et al 2014;Lodhi et al 2014), deposition of histone variants and modifications (Kruhlak et al 2001;Kelly et al 2010;Varier et al 2010;Wang and Higgins 2012), chromatin structure (Kuo et al 1982;Michelotti et al 1997;Kelly et al 2010;Kadauke et al 2012;Hsiung et al 2014), long-range genome folding (Naumova et al 2013;Dileep et al 2015), lamina-associated genomic domains (Kind et al 2013), and chromosome territories (Walter 2003). Details related to the kinetics, order, and fidelity with which such structures and processes are re-established during the mitosis-G1 transition are largely unknown, except a few examples for factor localization (Prasanth et al 2003;Poleshko et al 2013), lamina-associated domains (Kind et al 2013), and long-range chromosome interactions (Dileep et al 2015).…”