2015)

2015). and is further dynamically modulated in response to steroid hormones. HCRs function as platforms that integrate different signals, resulting in some cases in reverse transcriptional responses to estrogens or progestins. Altogether, these results suggest that steroid hormone receptors take action not only as hormone-regulated sequence-specific transcription factors but also as local and global genome organizers. The folding of the eukaryotic chromatin fiber within the cell nucleus, together with nucleosome occupancy, linker histones, and post-translational modifications of histones tails, plays an important role in modulating the function of the genetic information. It is now well exhibited that this genome is usually nonrandomly organized in a hierarchy of structures, with chromosomes occupying territories that are partitioned into segregated active and inactive chromatin compartments Rabbit Polyclonal to TAF15 (Cavalli and Misteli 2013; Gibcus and Dekker 2013; Fraser et al. 2015). Furthermore, chromosomes are segmented into contiguous topologically associating domains (TADs), within which chromatin interactions are more frequent than with the neighboring regions (Dixon et al. 2012; Nora et al. 2012; Sexton et al. 2012). Such business has been shown to participate in DNA replication and transcription (Cavalli and Misteli 2013; Pope et al. 2014; Lupianez et al. 2015). Boundaries between TADs are conserved among cell types and are enriched for cohesins and CTCF binding sites, as well as for highly expressed genes. However, how boundaries are established and maintained is not yet fully comprehended (Hou et al. 2012; Jin et al. 2013; Dixon et al. 2015). TADs are further organized in subdomains and loops that also depend on CTCF and other factors linked to transcription regulation (Phillips-Cremins et SID 26681509 al. 2013; Dowen et al. 2014; Rao et al. 2014). The sub-TAD business is more divergent between cell types, and it dynamically reorganizes during the process of differentiation (Phillips-Cremins et al. 2013; Ji et al. 2016). In terminally differentiated cells, it remains unclear whether TADs are relatively stable preorganized structures or whether they are dynamically remodeled in response to transient external cues (Jin et al. 2013; Seitan et al. 2013; Le Dily et al. 2014; Kuznetsova et al. 2015). Nevertheless, it is now accepted that TADs facilitate contacts between gene promoters and their regulatory elements located far away around the linear genome (Sanyal et al. 2012; Dowen et al. 2014; Zhan et al. 2017). However, it is not clear to what extent cell-specific transcription factors modulating the activity of those regulatory sites are also involved in organizing this particular level of chromatin folding. Steroid receptors are stimuli-induced transcription factors that regulate the expression of thousands of genes in hormone responsive cells (Cicatiello et al. 2004; Bain et al. 2007; Ballare et al. 2013). Notably, the estrogen and progesterone receptors (ESRs and PGRs, respectively) are known to bind either directly to the promoter of their target genes or to enhancer elements where they orchestrate the recruitment of chromatin remodeling complexes and general transcription factors (Carroll et al. 2005; Hsu et al. 2010; Ballare et al. 2013; Li et al. SID 26681509 2013). Several studies have analyzed the effects of steroids around the 3D business of chromatin at limited resolution, leading to apparently contradictory results. For example, we previously showed that TADs can respond as models to the hormone signals with dynamic reorganization of the entire TAD (Le Dily et al. 2014). In contrast, other studies suggested that enhancers and promoters contacts precede receptor activation (Hakim et al. 2009; Jin et al. 2013). These scenarios are not mutually unique, and it is possible that different regulatory mechanisms are required depending on the general chromatin context (Kuznetsova et al. SID 26681509 2015). Results The TAD encompassing the gene is usually organized around an HCR In a previous study with T47D breast malignancy cells, we observed that TADs can behave as models of response to steroid hormones (Le Dily et al. 2014). One of these steroid-responsive TADs contains the gene (encoding the ESR1 protein) and five other protein-coding genes, which are coordinately up-regulated by estradiol (E2) and down-regulated by progestins (Pg) (Supplemental Fig. S1A; Le Dily et al. 2014). To study at high resolution the organization of this domain (hereafter referred to as gene promoter (Fig. 1B; Supplemental Fig. S1B). Similarly, virtual 4C profile tacking as bait the whole 90-kb intergenic region confirmed that it engaged interactions with virtually all upstream and downstream promoters of protein coding genes as well as with other nonannotated sites marked by H3K4me3 and RNA-Polymerase II (RNA Pol II) within the boundaries of correspond to the normalized count figures per million of genome-wide valid pairs. (correspond to the normalized counts number per million of genome-wide valid pairs. (correspond to Genome Browser songs of ChIP-seq reads per million (rpm) profiles obtained for the different factors.