Eukaryotic cells compact their DNA into a nucleoprotein complex known as chromatin. The most basic repeating unit of chromatin is the nucleosome, consisting of ϳ147 bp of DNA wrapped around an octamer of histone proteins (38). Nucleosomes are one of the most stable protein-DNA complexes known (38) and can effectively inhibit all DNA-dependent processes, including transcription, replication, repair, and recombination, by limiting the access of proteins to DNA (17). As a result, the mechanisms by which chromatin structure and nucleosome positions are specified and maintained in vivo are critical for the regulation of all DNA-dependent processes.Genome-wide maps of nucleosome positions have recently been generated in a number of organisms, including Saccharomyces cerevisiae (1,7,19,30,33,36,37,41,50,56,63,68,69), Drosophila melanogaster (42), Caenorhabditis elegans (31, 60), Oryzias latipes (52), and humans (6, 54). Each of these organisms displays a characteristic chromatin structure spanning gene-coding regions and transcriptional regulatory regions. Gene-coding regions generally have high nucleosome occupancy with arrays of well-phased nucleosomes extending from the 5Ј end of a gene. In contrast, transcriptional regulatory regions, such as promoters, enhancers, and terminators, have low nucleosome occupancy and often contain a nucleosomefree region (NFR). NFRs, also known as nucleosome-depleted regions (NDRs), typically represent regions with an increased accessibility to micrococcal nuclease (MNase) digestion. Thus, the term NFR refers to a deficiency in experimentally determined canonical nucleosomes and does not necessarily imply a complete lack of histones.To date, predominately two major classes of NFRs, 5Ј-NFRs and 3Ј-NFRs, have been characterized. In S. cerevisiae, these NFRs are typically ϳ80 to 300 bp in length and are flanked by two well-positioned nucleosomes that often contain the histone variant Htz1 (1, 50). 5Ј-NFRs, associated with the promoters of many genes, are highly enriched for sequence-specific transcription factor binding sites (7,37,63,68) and demarcate the mRNA transcription start site (TSS) to their downstream edge (1,37,63). 3Ј-NFRs are located at the 3Ј ends of genes and are enriched for transcription termination sites (TTSs) (41).Recent genome-wide expression analyses have demonstrated that the majority of eukaryotic genomes are transcribed (11-13, 16, 26, 43-45, 49, 51, 55, 64, 66), resulting in the identification of numerous noncoding RNA (ncRNA) transcripts. In S. cerevisiae, many of these ncRNA transcripts were found to initiate at the upstream edge of 5Ј-NFRs between tandemly oriented genes or at 3Ј-NFRs (45, 66). However, whether these transcripts are subjected to active regulation is not known. The conserved locations of ncRNA TSSs around NFRs strongly suggest that NFRs are general locations of transcription initiation and that the mechanisms controlling NFR accessibility are critical to transcriptional regulation of ncRNA.Multiple factors, including the physical properties of...

Highlights d MYC overexpression reversibly induces CIN by reprogramming mitotic gene expression d MYC impairs mitotic spindle formation d High TPX2 expression allows cells that overexpress MYC to adapt to spindle stress d TPX2 depletion is synthetic lethal with MYC overexpression

Embryonal carcinoma and embryonic stem cells expressed a novel form of platelet-derived growth factor receptor mRNA which was -1,100 base pairs shorter than the 5.3-kilobase (kb) transcript expressed in fibroblasts and other cell types. The 4.2-kb stem cell transcript was initiated within the genomic region immediately upstream of exon 6 of the 5.3-kb transcript and therefore lacked the first five exons, which encode much of the extracellular domain of the receptor expressed in fibroblasts. In stem cells, the short form was predominant, although both forms were present at low levels. Following differentiation in vitro, expression levels of the long form increased dramatically. These findings suggest that during early embryogenesis, a stem cell-specific promoter is used in a stage-and cell type-specific manner to express a form of the platelet-derived growth factor receptor that lacks much of the extracellular domain and may function independently of ligand.

Few patients with triple negative breast cancer (TNBC) benefit from immune checkpoint inhibitors with complete and durable remissions being quite rare. Oncogenes can regulate tumor immune infiltration, however whether oncogenes dictate diminished response to immunotherapy and whether these effects are reversible remains poorly understood. Here, we report that TNBCs with elevated MYC expression are resistant to immune checkpoint inhibitor therapy. Using mouse models and patient data, we show that MYC signaling is associated with low tumor cell PD-L1, low overall immune cell infiltration, and low tumor cell MHC-I expression. Restoring interferon signaling in the tumor increases MHC-I expression. By combining a TLR9 agonist and an agonistic antibody against OX40 with anti-PD-L1, mice experience tumor regression and are protected from new TNBC tumor outgrowth. Our findings demonstrate that MYC-dependent immune evasion is reversible and druggable, and when strategically targeted, may improve outcomes for patients treated with immune checkpoint inhibitors.