To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here, we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. These loops demarcate topological domains and form intricate internal structures within them. Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains. Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes. Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programmes within them.Chromosomal compartmentalization has been recognized as important for genome function. High-resolution techniques such as Hi-C, ChIP- and 4C-seq offer novel insights into cohesin's dynamic role in shaping the nuclear architecture.

The majority of neural stem cells (NSCs) in the adult brain are quiescent, and this fraction increases with aging. Although signaling pathways that promote NSC quiescence have been identified, the transcriptional mechanisms involved are mostly unknown, largely due to lack of a cell culture model. In this study, we first demonstrate that NSC cultures (NS cells) exposed to BMP4 acquire cellular and transcriptional characteristics of quiescent cells. We then use epigenomic profiling to identify enhancers associated with the quiescent NS cell state. Motif enrichment analysis of these enhancers predicts a major role for the nuclear factor one (NFI) family in the gene regulatory network controlling NS cell quiescence. Interestingly, we found that the family member NFIX is robustly induced when NS cells enter quiescence. Using genome-wide location analysis and overexpression and silencing experiments, we demonstrate that NFIX has a major role in the induction of quiescence in cultured NSCs. Transcript profiling of NS cells overexpressing or silenced for Nfix and the phenotypic analysis of the hippocampus of Nfix mutant mice suggest that NFIX controls the quiescent state by regulating the interactions of NSCs with their microenvironment.

IntroductionDLL4 plays a fundamental role in vascular development and angiogenesis. 1,2 DLL4 haploinsufficiency results in extensive arterial defects and embryonic lethality, 3 indicating that the developing vasculature is sensitive to minor alterations in DLL4 dosage. DLL4 expression is mainly restricted to the endothelium of nascent vessels, particularly the tip cells, where it maintains stalk cell identity in neighboring cells, thereby regulating vessel sprouting and branching in response to angiogenic stimuli. 4 The importance of optimal DLL4 expression in physiologic angiogenesis is illustrated through its regulation of intersegmental vessel (ISV) development in zebrafish. Morpholino (MO) knockdown of dll4 in zebrafish results in an increased number of endothelial cells within the ISVs and ectopic ISV branching from the dorsal aorta (DA) because of overactivation of Vegfa signaling. 5,6 DLL4 is relevant in pathologic angiogenesis and is overexpressed in human tumors, often in association with markers of inflammation, hypoxia and angiogenesis. [7][8][9] Inhibition of DLL4 suppresses experimental tumor growth by inducing nonproductive, deregulated angiogenesis. 10,11 We and others have shown that DLL4 expression is up-regulated in lymphatic endothelial cells (LECs) after infection by Kaposi sarcoma herpesvirus (KSHV), 12,13 an oncogenic ␥-herpesvirus that is the etiologic agent of Kaposi sarcoma (KS). KS is an angioproliferative neoplasm composed of cells of endothelial origin. 14 Although accurate regulation of DLL4 levels is a hallmark of angiogenesis, the mechanisms that finely regulate DLL4 expression are not completely defined. Therefore we hypothesized that, in addition to well-known transcriptional mechanisms that affect DLL4 expression, DLL4 is regulated at the posttranscriptional level.MicroRNAs (miRNAs) are small, noncoding RNAs that influence target gene expression through mRNA degradation and translation inhibition. 15 Implicated in key cellular processes, miRNAs play a role in angiogenesis and cancer. 16,17 miR-27b is the only miRNA thus far implicated in DLL4 regulation 18 ; however, this miRNA also regulates sprouty homologue 2 (SPRY2) and semaphorin 6A (SEMA6A), and it is unclear whether its proposed suppression of DLL4 specifically leads to vascular defects. 18,19 We previously described the miRNA signature in KSHV-infected LECs (KLECs). 20 These data indicated significant down-regulation of members of the miR-30 miRNA family postinfection (PI). Encoded by 6 genes and expressed from 4 distinct transcripts across the human genome, the members of the miR-30 family share an identical seed sequence and hence have common predicted targets. 21 Here we show that miR-30b and miR-30c target DLL4 in vitro and in vivo, and that the miR-30 family regulates angiogenesis. Methods Cell cultureLECs were purchased from Promocell and grown in endothelial growth medium MV (Promocell) supplemented with 10 ng/mL VEGF-C (R&D Systems). HUVECs were purchased from Promocell and grown in endothelial growth medium MV2 ...