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Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.

Metastases are the main cause of cancer deaths, but the mechanisms underlying metastatic progression remain poorly understood. We isolated pure populations of cancer cells from primary tumors and metastases from a genetically engineered mouse model of human small cell lung cancer (SCLC) to investigate the mechanisms that drive the metastatic spread of this lethal cancer. Genome-wide characterization of chromatin accessibility revealed the opening of large numbers of distal regulatory elements across the genome during metastatic progression. These changes correlate with copy number amplification of the Nfib locus, and differentially accessible sites were highly enriched for Nfib transcription factor binding sites. Nfib is necessary and sufficient to increase chromatin accessibility at a large subset of the intergenic regions. Nfib promotes pro-metastatic neuronal gene expression programs and drives the metastatic ability of SCLC cells. The identification of widespread chromatin changes during SCLC progression reveals an unexpected global reprogramming during metastatic progression.

Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the yeast metabolic cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here, we demonstrate that the INO80 chromatin-remodeling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC1-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin to restrict proliferation to metabolically optimal states. [ABSTRACT FROM AUTHOR]

Telomeres are regions of repeated DNA sequence that cap the ends of eukaryotic chromosomes. They act as disposable safeguards to prevent the loss of important genetic information during DNA replication due to the inability of DNA polymerase to replicate DNA to the ends of linear chromosomes. The synthesis of new telomeric repeats using an RNA molecule as a template is catalyzed by the enzyme telomerase. In embryonic stem cells, the gene encoding the catalytic protein subunit of the telomerase complex (telomere reverse transcriptase [ TERT]) is transcriptionally active and critical for telomere elongation, allowing for continued cellular differentiation during development. The TERT gene is down-regulated as embryogenesis progresses to limit the proliferative capacity of cells. As a result, in normal human adult somatic cells the TERT gene is silenced. However, in over 90% of cancers, the TERT gene is reactivated, allowing cells to bypass senescence and become immortalized. In this study, we explore the molecular mechanisms that regulate transcriptional expression of the TERT gene. Bioinformatic analysis of the noncoding genomic regions around the human TERT gene identified a TERT ultra-conserved (TUC) module located 5 kb upstream of the transcription start site. This 308 bp region is over 75% conserved between distantly related mammalian species and over 91% conserved among primate species. The cis-regulatory potential of the TUC region was tested in cell-based reporter gene assays. Transient transfections into HeLa and lung fibroblast cells demonstrated that the TUC module has transcriptional enhancer activity. Further bioinformatic analysis revealed that the TUC region is highly enriched in putative transcription factor binding sites for proteins involved during hematopoiesis, indicating that the TUC module may be an enhancer for the TERT gene in specific cell lineages. [ABSTRACT FROM AUTHOR]