The condensation of nucleosome arrays into higher-order secondary and tertiary chromatin structures likely involves long-range internucleosomal interactions mediated by the core histone tail domains. We have characterized interarray interactions mediated by the H4 tail domain, known to play a predominant role in the formation of such structures. We find that the N-terminal end of the H4 tail mediates interarray contacts with DNA during self-association of oligonucleosome arrays similar to that found previously for the H3 tail domain. However, a site near the histone fold domain of H4 participates in a distinct set of interactions, contacting both DNA and H2A in condensed structures. Moreover, we also find that H4-H2A interactions occur via an intraas well as an internucleosomal fashion, supporting an additional intranucleosomal function for the tail. Interestingly, acetylation of the H4 tail has little effect on interarray interactions by itself but overrides the strong stimulation of interarray interactions induced by linker histones. Our results indicate that the H4 tail facilitates secondary and tertiary chromatin structure formation via a complex array of potentially exclusive interactions that are distinct from those of the H3 tail domain.Eukaryotic DNA is packaged with core histones and other nonhistone chromosomal proteins through multiple levels of increasingly condensed chromatin structures. Arrays of nucleosomes, which form the primary repeating structure of chromatin, fold into secondary chromatin structures such as the 30-nm-diameter chromatin fiber (21, 37, 45). Chromatin fibers and other secondary structures are further condensed into higher-order tertiary chromatin structures such as the 100-to 130-nm-diameter chromonema observed by Belmont and Bruce (7). While models (solenoid, twisted-ribbon, and crossed-linker) have been proposed for the 30-nm-diameter chromatin fiber, to date no definitive model has been broadly accepted (38). Moreover, only very limited structural information is available with regard to tertiary and higher-order chromatin structures (see references 21, 30, and 45 and see below).Although the molecular mechanisms behind the formation of secondary and tertiary chromatin structures remain unclear, work employing model systems has shown that in vitro reconstituted nucleosome arrays containing only DNA and core histone proteins undergo the same initial salt-dependent condensations as native chromatin (17, 21). In solutions containing physiological concentrations of mono-and divalent cations, nucleosome arrays spontaneously fold into structures with the same hydrodynamic shape as the 30-nm-diameter chromatin fiber and reversibly self-associate into larger assemblies with characteristics of native tertiary chromatin structures (21, 45).

The core histone tail domains play a central role in chromatin structure and epigenetic processes controlling gene expression. Although little is known regarding the molecular details of tail interactions, it is likely that they participate in both short-range and long-range interactions between nucleosomes. Previously, we demonstrated that the H3 tail domain participates in internucleosome interactions during MgCl 2 -dependent condensation of model nucleosome arrays. However, these studies did not distinguish whether these internucleosome interactions represented short-range intra-array or longer-range interarray interactions. To better understand the complex interactions of the H3 tail domain during chromatin condensation, we have developed a new site-directed cross-linking method to identify and quantify interarray interactions mediated by histone tail domains. Interarray cross-linking was undetectable under salt conditions that induced only local folding, but was detected concomitant with salt-dependent interarray oligomerization at higher MgCl 2 concentrations. Interestingly, lysine-to-glutamine mutations in the H3 tail domain to mimic acetylation resulted in little or no reduction in interarray cross-linking. In contrast, binding of a linker histone caused a much greater enhancement of interarray interactions for unmodified H3 tails compared to "acetylated" H3 tails. Collectively these results indicate that H3 tail domain performs multiple functions during chromatin condensation via distinct molecular interactions that can be differentially regulated by acetylation or binding of linker histones.

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<p>Analysis of JARID1A-D mRNA levels showed that JARID1D knockdown had insignificant or weak effects on expression levels of JARID1A-C (S1); Gene ontology analysis for genes down-regulated in JARID1D-depleted cells (S2); Heatmap for H3K4me3 ChIP-Seq signals of all the gene-regulatory regions spanning − 2kb to +2kb suggested that many H3K4me3 signals were slightly increased by JARID1D knockdown. (S3); Of JARID1A-1D, only JARID1D mRNA levels were downregulated in metastasis tumors compared to primary tumors (S4); JARID1D mRNA levels were not correlated with MMP2 (S5).</p>

<div>Abstract<p>Entire or partial deletions of the male-specific Y chromosome are associated with tumorigenesis, but whether any male-specific genes located on this chromosome play a tumor-suppressive role is unknown. Here, we report that the histone H3 lysine 4 (H3K4) demethylase JARID1D (also called KDM5D and SMCY), a male-specific protein, represses gene expression programs associated with cell invasiveness and suppresses the invasion of prostate cancer cells <i>in vitro</i> and <i>in vivo</i>. We found that JARID1D specifically repressed the invasion-associated genes <i>MMP1</i>, <i>MMP2</i>, <i>MMP3</i>, <i>MMP7</i>, and Slug by demethylating trimethyl H3K4, a gene-activating mark, at their promoters. Our additional results demonstrated that JARID1D levels were highly downregulated in metastatic prostate tumors compared with normal prostate tissues and primary prostate tumors. Furthermore, the <i>JARID1D</i> gene was frequently deleted in metastatic prostate tumors, and low JARID1D levels were associated with poor prognosis in prostate cancer patients. Taken together, these findings provide the first evidence that an epigenetic modifier expressed on the Y chromosome functions as an anti-invasion factor to suppress the progression of prostate cancer. Our results also highlight a preclinical rationale for using JARID1D as a prognostic marker in advanced prostate cancer. <i>Cancer Res; 76(4); 831–43. ©2016 AACR</i>.</p></div>