Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers

Abstract

DNase I hypersensitive sites (DHSs) are a hallmark of chromatin regions containing regulatory DNA such as enhancers and promoters; however, the factors affecting the establishment and maintenance of these sites are not fully understood. We now show that HMGN1 and HMGN2, nucleosome-binding proteins that are ubiquitously expressed in vertebrate cells, maintain the DHS landscape of mouse embryonic fibroblasts (MEFs) synergistically. Loss of one of these HMGN variants led to a compensatory increase of binding of the remaining variant. Genome-wide mapping of the DHSs in Hmgn1 −/− , Hmgn2 −/− , and Hmgn1 −/− n2 −/− MEFs reveals that loss of both, but not a single HMGN variant, leads to significant remodeling of the DHS landscape, especially at enhancer regions marked by H3K4me1 and H3K27ac. Loss of HMGN variants affects the induced expression of stress-responsive genes in MEFs, the transcription profiles of several mouse tissues, and leads to altered phenotypes that are not seen in mice lacking only one variant. We conclude that the compensatory binding of HMGN variants to chromatin maintains the DHS landscape, and the transcription fidelity and is necessary to retain wildtype phenotypes. Our study provides insight into mechanisms that maintain regulatory sites in chromatin and into functional compensation among nucleosome binding architectural proteins. [Supplemental material is available for this article.]Tissue-and developmental-specific gene expression is facilitated by the binding of transcription factors to unique DNA sequences at regulatory sites in chromatin, such as enhancers and promoters. At these sites, the organization of the nucleosomes is altered, rendering the DNA more accessible to regulatory factors and hypersensitive to digestion by various nucleases including DNase I. DNase I hypersensitive sites (DHSs) are a hallmark of chromatin regions containing regulatory DNA and are used to identify regulatory sites in chromatin. The DHSs chromatin landscape is cell-type specific and dynamic, reflecting changes in the cellular transcription profile occurring during development, or as a consequence of genomic changes leading to altered cellular phenotypes (Gross and Garrard 1988;Boyle et al. 2008;Thurman et al. 2012;Calo and Wysocka 2013;Stergachis et al. 2013).The molecular mechanisms that establish and maintain DHSs and their role in gene expression are key questions in chromatin biology. DHSs are established by the combined action of transcription factors that bind dynamically to specific DNA sequences and 12 These authors contributed equally to this work.

Histone H1 and Chromosomal Protein HMGN2 Regulate Prolactin-induced STAT5 Transcription Factor Recruitment and Function in Breast Cancer Cells

“…Likewise, HMGN2 and H1 have also been implicated in enhancer function. Knock-out of Hmgn1 and Hmgn2 in mouse embryo fibroblasts results in the loss of DNase I-hypersensitive sites, particularly at enhancer regions (63). In breast cancer cells, the depletion of certain H1 subtypes, including H1.2, is associated with histone marks indicative of strong enhancers (37).…”

Functional interplay between histone H1 and HMG proteins in chromatin

“…As elaborated below, this octapeptide serves as the anchoring point of HMGNs on the nucleosome [20]. Genome wide, HMGN proteins preferentially bind to DNase I hypersensitive sites, the hallmark of regulatory chromatin sites [21–23]. HMGNs have been shown to modulate the global and local structure of chromatin [24], and the levels of histone modifications [25, 26], factors which may be involved in their ability to affect gene expression [27].…”

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress inC. elegans

“…Results from yeast (Weiner et al 2010;Xi et al 2011;Kubik et al 2015), plants (Vera et al 2014), mouse (Lombraña et al 2013;Deng et al 2015;Iwafuchi-Doi et al 2016;Mieczkowski et al 2016), worm (Ooi et al 2010), and fly (Henikoff et al 2009; have identified highly labile nucleosomes in 5 ′ and 3 ′ "nucleosome-free" regions. In yeast, Xi et al (2011) observed that fragile nucleosomes were associated with H2A.Z-containing promoter nucleosomes, believed to be involved in stress response (Li et al 2005;Zhang et al 2005).…”