A crucial feature of differentiated cells is the rapid activation of enhancer-driven transcriptional programs in response to signals. The potential contributions of physicochemical properties of

We report that a neuron-specific isoform of LSD1, LSD1n, resulting from an alternative splicing event, acquires a novel substrate specificity targeting histone H4 K20 methylation, both in vitro and in vivo. Selective genetic ablation of LSD1n leads to deficits in spatial learning and memory, revealing the functional importance of LSD1n in the regulation of neuronal activity-regulated transcription in a fashion indispensable for long-term memory formation. LSD1n occupies neuronal gene enhancers, promoters and transcribed coding regions, and is required for transcription initiation and elongation steps in response to neuronal activity, indicating the crucial role of H4K20 methylation in coordinating gene transcription with neuronal function. This study reveals that the alternative splicing of LSD1 in neurons, associated with altered substrate specificity, serves as an underlying mechanism acquired by neurons to achieve more precise control of gene expression in the complex processes underlying learning and memory.

SUMMARY Pancreatic beta-cell mass for appropriate blood glucose control is established during early postnatal life. Beta-cell proliferative capacity declines postnatally but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of beta-cell transcriptome dynamics after birth, we generated single-cell RNA-seq data of beta-cells from multiple postnatal time points and ordered cells based on transcriptional similarity using a new analytical tool. This analysis captured signatures of immature, proliferative beta-cells and established high expression of amino acid metabolic, mitochondrial, and Srf/Jun/Fos transcription factor genes as their hallmark feature. Experimental validation revealed high metabolic activity in immature beta-cells and a role for reactive oxygen species and Srf/Jun/Fos transcription factors in driving postnatal beta-cell proliferation and mass expansion. Our work provides the first high-resolution molecular characterization of state changes in postnatal beta-cells and paves the way for the identification of novel therapeutic targets to stimulate beta-cell regeneration.

Background: Small noncoding RNAs (ncRNAs), including short interfering RNAs (siRNAs) and microRNAs (miRNAs), can silence genes at the transcriptional, post-transcriptional or translational level [1,2].

SUMMARY The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress from eRNA synthesis. Using dihydrotestosterone (DHT)-induced binding of androgen receptor (AR) to prostate cancer cell enhancers as a model, we show rapid recruitment, within minutes, of DNA topoisomerase I (TOP1) to a large cohort of AR-regulated enhancers. Furthermore, we show that the DNA nicking activity of TOP1 is a prerequisite for robust eRNA synthesis and enhancer activation, and is kinetically accompanied by the recruitment of ATR and the MRN complex, followed by additional components of DNA damage repair machinery to the AR-regulated enhancers. Together, our studies reveal a linkage between eRNA synthesis and ligand-dependent TOP1-mediated nicking a strategy exerting quantitative effects on eRNA expression in regulating AR-bound enhancer-dependent transcriptional programs.

Post-translational histone modifications play critical roles in regulating transcription, the cell cycle, DNA replication and DNA damage repair1. The identification of new histone modifications critical for transcriptional regulation at initiation, elongation, or termination is of particular interest. Here, we report a new layer of regulation in transcriptional elongation that is conserved from yeast to mammals, based on a phosphorylation of a highly-conserved tyrosine residue, Y57, in histone H2A that is mediated by an unsuspected tyrosine kinase activity of casein kinase 2 (CK2). Mutation of H2A-Y57 in yeast or inhibition of CK2 activity impairs transcriptional elongation in yeast as well as in mammalian cells. Genome-wide binding analysis reveals that CK2α, the catalytic subunit of CK2, binds across RNA polymerase II-transcribed coding genes and active enhancers. Mutation of Y57 causes a loss of H2B mono-ubiquitylation as well as H3K4me3 and H3K79me3, histone marks associated with active transcription. Mechanistically, both CK2 inhibition and H2A-Y57F mutation enhance the H2B deubiquitylation activity of the SAGA complex, suggesting a critical role of this phosphorylation in coordinating the activity of the SAGA during transcription. Together, these results identify a new component of regulation in transcriptional elongation based on CK2-dependent tyrosine phosphorylation of the globular domain of H2A.

The presence of acetylated histone H3K56 (H3K56ac) in human ES cells (ESCs) correlates positively with the binding of Nanog, Sox2, and Oct4 (NSO) transcription factors at their target gene promoters. However, the function of H3K56ac there has been unclear. We now report that Oct4 interacts with H3K56ac in mouse ESC nuclear extracts and that perturbing H3K56 acetylation decreases Oct4-H3 binding. This interaction is likely to be direct because it can be recapitulated in vitro in an H3K56ac-dependent manner and is functionally important because H3K56ac combines with NSO factors in chromatin immunoprecipitation sequencing to mark the regions associated with pluripotency better than NSO alone. Moreover, reducing H3K56ac by short hairpin Asf1a decreases expression of pluripotency-related markers and increases expression of differentiation-related ones. Therefore, our data suggest that H3K56ac plays a central role in binding to Oct4 to promote the pluripotency of ESCs.

Summary The molecular mechanisms underlying the opposing functions of glucocorticoid receptors (GR) and estrogen receptor α (ERα) in breast cancer development remain poorly understood. Here, we report that in breast cancer cells liganded GR represses a large ERα-activated transcriptional program by binding, in trans, to ERα-occupied enhancers. This abolishes effective activation of these enhancers and their cognate target genes, and leads to inhibition of ERα-dependent binding of components of the MegaTrans complex. Consistent with the effects of SUMOylation on other classes of nuclear receptors, dexamethasone (Dex)-induced trans-repression of the estrogen (E2) program appears to depend on GR SUMOylation, which leads to stable trans-recruitment of the GR-NCoR/SMRT-HDAC3 co-repressor complex on these enhancers. Together, these results uncover a mechanism by which competitive recruitment of DNA-binding nuclear receptors/transcription factors in trans to “hot spot” enhancers serves as an effective biological strategy for trans-repression with clear implications for breast cancer and other diseases.