Genomes are organized into high-level 3-dimensional structures, and DNA elements separated by long genomic distances could functionally interact. Many transcription factors bind to regulatory DNA elements distant from gene promoters. While distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Therefore, we developed Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) for de novo detection of global chromatin interactions, and comprehensively mapped the chromatin interaction network bound by oestrogen receptor α (ERα) in the human genome. We found that most high-confidence remote ERα binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ERα functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.

The NKX3-1 gene is a homeobox gene required for prostate tumor progression, but how it functions is unclear. Here, using chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-seq) we showed that NKX3-1 colocalizes with the androgen receptor (AR) across the prostate cancer genome. We uncovered two distinct mechanisms by which NKX3-1 controls the AR transcriptional network in prostate cancer. First, NKX3-1 and AR directly regulate each other in a feed-forward regulatory loop. Second, NKX3-1 collaborates with AR and FoxA1 to mediate genes in advanced and recurrent prostate carcinoma. NKX3-1-and AR-coregulated genes include those found in the "protein trafficking" process, which integrates oncogenic signaling pathways. Moreover, we demonstrate that NKX3-1, AR, and FoxA1 promote prostate cancer cell survival by directly upregulating RAB3B, a member of the RAB GTPase family. Finally, we show that RAB3B is overexpressed in prostate cancer patients, suggesting that RAB3B together with AR, FoxA1, and NKX3-1 are important regulators of prostate cancer progression. Collectively, our work highlights a novel hierarchical transcriptional regulatory network between NKX3-1, AR, and the RAB GTPase signaling pathway that is critical for the genetic-molecular-phenotypic paradigm in androgen-dependent prostate cancer.

Estrogens, such as 17␤-estradiol (E 2 ), 3 are pleiotropic hormones whose effects are responsible for many physiological processes, including normal growth, development, and the precise and coordinated regulation of gene expression in tissues of the reproductive tract, central nervous system, and bone (1, 2).Estrogens also have important functions in hormone-dependent diseases, such as breast cancer and osteoporosis (1, 2). Selective estrogen receptor modulators, therapeutic agents that act as agonists or antagonists depending on the target tissue, are currently used in the treatment and prevention of these and other hormone-related disorders (1-3). Estrogens and selective estrogen receptor modulators exert their effects through two estrogen receptors (ERs), ER alpha (ER␣/ESR1/NR3A1) and ER beta (ER␤/ESR2/NR3A2), which belong to a large superfamily of nuclear hormone receptor proteins (2, 3). ERs share a conserved structural and functional organization with other members of the nuclear hormone receptor superfamily, including domains responsible for ligand binding, dimerization, DNA binding, and transcriptional activation (2, 3).As their domain structures imply, ERs behave as ligand-inducible, DNA binding transcription factors (2, 3). Their transcriptional activities require the recruitment of a variety of coregulatory proteins by the receptors to estrogen-regulated promoters through either direct or indirect interactions (2, 3). A group of factors, including the p160/steroid receptor co-activator (SRC) family of proteins and the Mediator-like complexes (e.g. TRAP, DRIP, and ARC), have been shown to interact with and stimulate the transcriptional activities of ERs by interacting directly with the ligand binding domain in a ligand and activation function-2-dependent manner (2, 3). Other factors that contain enzymatic activities, such as the histone acetyltransferase p300/CBP and the histone methyltransferase CARM-1, are recruited indirectly by ERs mainly via interactions with the SRC proteins (2, 3). A smaller subset of ER-interacting factors has been shown to bind primarily to the N-terminal A/B region of the receptors, including the RNA-binding protein p68/p72 and SRA (2, 3). Together, these co-regulatory proteins are recruited by ERs in a precise temporal and coordinated manner in response to estrogen to promote local changes in histone modifications, chromatin structure, and the recruitment of RNA polymerase II to the promoters of target genes.Numerous estrogen target genes have been identified through expression microarray studies (reviewed in Ref. 4); however, it is unclear what fraction of these genes are directly regulated by ERs. Direct regulation by estrogen is largely due to the recruitment of ERs to genomic regions containing sequence specific cis-regulatory motifs (2, 3). These sequences mostly

Graphical AbstractHighlights d Decreased hepatic division during regeneration correlates with impaired metabolic homeostasis d Impaired mitochondrial respiration/oxidation results in compromised metabolic homeostasis d Non-dividing hepatocytes increase alanine transaminase flux during tissue repair

The Infinium Human Methylation450 BeadChip Array (Infinium 450K) is a robust and cost-efficient survey of genome-wide DNA methylation patterns. Macaca fascicularis (Cynomolgus macaque) is an important disease model; however, its genome sequence is only recently published, and few tools exist to interrogate the molecular state of Cynomolgus macaque tissues. Although the Infinium 450K is a hybridization array designed to the human genome, the relative conservation between the macaque and human genomes makes its use in macaques feasible. Here, we used the Infinium 450K array to assay DNA methylation in 11 macaque muscle biopsies. We showed that probe hybridization efficiency was related to the degree of sequence identity between the human probes and the macaque genome sequence. Approximately 61% of the Human Infinium 450K probes could be reliably mapped to the Cynomolgus macaque genome and contain a CpG site of interest. We also compared the Infinium 450K data to reduced representation bisulfite sequencing data generated on the same samples and found a high level of concordance between the two independent methodologies, which can be further improved by filtering for probe sequence identity and mismatch location. We conclude that the Infinium 450K array can be used to measure the DNA methylome of Cynomolgus macaque tissues using the provided filters. We also provide a pipeline for validation of the array in other species using a simple BLAST-based sequence identify filter.

Wharton’s jelly-derived Mesenchymal Stem Cells (MSCs) isolated from newborns with intrauterine fetal growth restriction were previously shown to exert anabolic features including insulin hypersensitivity. Here, we extend these observations and demonstrate that MSCs from small for gestational age (SGA) individuals have decreased mitochondrial oxygen consumption rates. Comparing normally grown and SGA MSCs using next generation sequencing studies, we measured global transcriptomic and epigenetic profiles and identified E2F1 as an over-expressed transcription factor regulating oxidative metabolism in the SGA group. We further show that E2F1 regulates the differential transcriptome found in SGA derived MSCs and is associated with the activating histone marks H3K27ac and H3K4me3. One of the key genes regulated by E2F1 was found to be the fatty acid elongase ELOVL2, a gene involved in the endogenous synthesis of docosahexaenoic acid (DHA). Finally, we shed light on how the E2F1-ELOVL2 pathway may alter oxidative respiration in the SGA condition by contributing to the maintenance of cellular metabolic homeostasis.

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