SUMMARY Exhausted CD8+ T cells (TEX) in chronic infections and cancer have limited effector function, high inhibitory receptor co-expression and extensive transcriptional changes compared to effector (TEFF) or memory (TMEM) CD8+ T cells. TEX are important clinical targets of checkpoint blockade and other immunotherapies. Epigenetically, TEX are a distinct immune subset, with a unique chromatin landscape compared to TEFF and TMEM. However, the mechanisms governing the transcriptional and epigenetic development of TEX remain unknown. Here, we identify the HMG-box transcription factor TOX as a central regulator of TEX. TOX is largely dispensable for TEFF and TMEM formation, but is critical for exhaustion and without TOX TEX do not form. TOX is induced by calcineurin and NFAT2 and operates in a feed-forward loop to become calcineurin independent and sustained in TEX. Thus, robust TOX expression results in commitment to TEX by translating persistent stimulation into a distinct TEX transcriptional and epigenetic developmental program.

SUMMARY The ectopic expression of transcription factors can reprogram cell fate, yet it is unknown how the initial binding of factors to the genome relates functionally to the binding seen in the minority of cells that become reprogrammed. We report a map of Oct4, Sox2, Klf4, and c-Myc (O, S, K, and M) on the human genome during the first 48 hours of reprogramming fibroblasts to pluripotency. Three striking aspects of the initial chromatin binding events include: An unexpected role for c-Myc in facilitating OSK chromatin engagement, the primacy of O, S, and K as pioneer factors at enhancers of genes that promote reprogramming, and megabase-scale chromatin domains spanned by H3K9me3, including many genes required for pluripotency, that prevent initial OSKM binding and impede the efficiency of reprogramming. We find diverse aspects of initial factor binding that must be overcome in the minority of cells that become reprogrammed.

Macroautophagy (hereafter referred to as autophagy) is a catabolic membrane trafficking process that degrades a variety of cellular constituents, and is associated with human diseases1–3. While extensive studies have focused on autophagic turnover of cytoplasmic materials, little is known regarding the role of autophagy in degrading nuclear components. Here we report that the autophagy machinery mediates degradation of nuclear lamina components in mammals. The autophagy protein LC3/Atg8, which is involved in autophagy membrane trafficking and substrate delivery4–6, is present in the nucleus and directly interacts with the nuclear lamina protein Lamin B1, and binds to lamin-associated domains (LADs) on chromatin. This LC3-Lamin B1 interaction does not downregulate Lamin B1 during starvation, but mediates its degradation upon oncogenic insults, such as by activated Ras. Lamin B1 degradation is achieved by nucleus-to-cytoplasm transport that delivers Lamin B1 to the lysosome. Inhibiting autophagy or the LC3-Lamin B1 interaction prevents activated Ras-induced Lamin B1 loss and attenuates oncogene-induced senescence in primary human cells. Our study suggests this new function of autophagy as a guarding mechanism protecting cells from tumorigenesis.

The organized societies of ants include short-lived worker castes displaying specialized behavior and morphology, and long-lived queens dedicated to reproduction. We sequenced and compared the genomes of two socially divergent ant species: Camponotus floridanus and Harpegnathos saltator. Both genomes contained high amounts of CpG, despite the presence of DNA methylation, which in non-Hymenoptera correlates with CpG depletion. Comparison of gene expression in different castes identified upregulation of telomerase and sirtuin deacetylases in longer-lived H. saltator reproductives, caste-specific expression of miRNAs and SMYD histone methyltransferases, and differential regulation of genes implicated in neuronal function and chemical communication. Our findings provide clues on the molecular differences between castes in these two ants, and establish a new experimental model to study epigenetics in aging and behavior.As eusocial insects, ants live in populous colonies, in which up to millions of individuals delegate the reproductive role to one or few queens, while non-reproductive workers carry out all tasks required for colony maintenance (1). These mutually exclusive morphologies and behaviors arise from a single genome, and are typically not dictated by genetic differences, but by environmental factors (2). The first fertilized (diploid) eggs laid by a founder queen develop into workers, but as the colony enlarges, some diploid embryos take a different developmental path to become virgin queens, leave the nest, mate, and establish new colonies. As colonies mature, queens transition from a broad behavioral repertoire that †

Senescence is a stable proliferation arrest, associated with an altered secretory pathway, thought to promote tumor suppression and tissue aging. While chromatin regulation and lamin B1 down-regulation have been implicated as senescence effectors, functional interactions between them are poorly understood. We compared genome-wide Lys4 trimethylation on histone H3 (H3K4me3) and H3K27me3 distributions between proliferating and senescent human cells and found dramatic differences in senescence, including large-scale domains of H3K4me3-and H3K27me3-enriched ''mesas'' and H3K27me3-depleted ''canyons.'' Mesas form at lamin B1-associated domains (LADs) in replicative senescence and oncogene-induced senescence and overlap DNA hypomethylation regions in cancer, suggesting that pre-malignant senescent chromatin changes foreshadow epigenetic cancer changes. Hutchinson-Gilford progeria syndrome fibroblasts (mutant lamin A) also show evidence of H3K4me3 mesas, suggesting a link between premature chromatin changes and accelerated cell senescence. Canyons mostly form between LADs and are enriched in genes and enhancers. H3K27me3 loss is correlated with up-regulation of key senescence genes, indicating a link between global chromatin changes and local gene expression regulation. Lamin B1 reduction in proliferating cells triggers senescence and formation of mesas and canyons. Our data illustrate profound chromatin reorganization during senescence and suggest that lamin B1 down-regulation in senescence is a key trigger of global and local chromatin changes that impact gene expression, aging, and cancer.

SUMMARYTP53 is the most frequently mutated gene among all human cancers. Prevalent p53 missense mutations abrogate its tumor suppressive function and lead to “gain-of-function” (GOF) that promotes cancer. Here we show that p53 GOF mutants bind to and upregulate chromatin regulatory genes, including the methyltransferases KMT2A (MLL1) and KMT2D (MLL2), and acetyltransferase KAT6A (MOZ or MYST3), resulting in genome-wide increases of histone methylation and acetylation. Analysis of The Cancer Genome Atlas shows specific upregulation of MLL1, MLL2, and MOZ in p53 GOF patient-derived tumors, but not in p53 wildtype or p53 null tumors. Cancer cell proliferation is dramatically lowered by genetic knockdown of MLL1, or by pharmacological inhibition of the MLL1 methyltransferase complex. Our study reveals a novel chromatin mechanism underlying the progression of tumors with GOF p53, and suggests new possibilities for designing combinatorial chromatin-based therapies for treating individual cancers driven by prevalent GOF p53 mutations.

SUMMARY Metabolic production of acetyl-CoA is linked to histone acetylation and gene regulation, yet the precise mechanisms are largely unknown. Here we show that the metabolic enzyme acetyl-CoA synthetase 2 (ACSS2) is a direct regulator of histone acetylation in neurons and of spatial memory in mammals. In a neuronal cell culture model, ACSS2 increases in nuclei of differentiating neurons and localizes to upregulated neuronal genes near elevated histone acetylation. Reduction of ACSS2 lowers nuclear acetyl-CoA levels, histone acetylation, and responsive expression of the cohort of neuronal genes. In adult mice, attenuation of hippocampal ACSS2 expression impairs long-term spatial memory, a cognitive process reliant on histone acetylation. ACSS2 reduction in hippocampus also leads to defective upregulation of memory-related neuronal genes that are pre-bound by ACSS2. These results reveal a unique connection between cellular metabolism, gene regulation, and neural plasticity, establishing a link between acetyl-CoA generation “on-site” at chromatin for histone acetylation and the transcription of critical neuronal genes.

SUMMARY Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of MNase digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.