Cells differentiate when transcription factors (TFs) bind accessible cis-regulatory elements to establish specific gene expression programs. In differentiating embryonic stem (ES) cells, chromatin at lineage-restricted genes becomes sequentially accessible1-4, probably by virtue of “pioneer” TF activity5, but tissues may utilize other strategies in vivo. Lateral inhibition is a pervasive process in which one cell forces a different identity on its neighbors6, and it is unclear how chromatin in equipotent progenitors undergoing lateral inhibition quickly enables distinct, transiently reversible cell fates. Here we report the chromatin and transcriptional underpinnings of differentiation in mouse small intestine crypts, where Notch signaling mediates lateral inhibition to assign progenitor cells into absorptive or secretory lineages7-9. Transcript profiles in isolated LGR5+ intestinal stem cells (ISC)10 and secretory and absorptive progenitors indicated that each cell population was distinct and the progenitors specified. Nevertheless, secretory and absorptive progenitors showed comparable levels of H3K4me2 and H3K27ac histone marks and DNaseI hypersensitivity - signifying accessible, permissive chromatin - at most of the same cis-elements. Enhancers acting uniquely in progenitors were well-demarcated in LGR5+ ISC, revealing early priming of chromatin for divergent transcriptional programs, and retained active marks well after lineages were specified. On this chromatin background, ATOH1, a secretory-specific TF, controls lateral inhibition through Delta-like Notch ligand genes and also drives numerous secretory lineage genes. Depletion of ATOH1 from specified secretory cells converted them into functional enterocytes, indicating prolonged responsiveness of marked enhancers to presence or absence of a key TF. Thus, lateral inhibition and intestinal crypt lineage plasticity involve interaction of a lineage-restricted TF with broadly permissive chromatin established in multipotent stem cells.

Transcription factors that potently induce cell fate often remain expressed in the induced organ throughout life, but their requirements in adults are uncertain and varied. Mechanistically, it is unclear if they activate only tissue-specific genes or also directly repress heterologous genes. We conditionally inactivated mouse Cdx2, a dominant regulator of intestinal development, and mapped its genome occupancy in adult intestinal villi. Although homeotic transformation, observed in Cdx2-null embryos, was absent in mutant adults, gene expression and cell morphology were vitally compromised. Lethality was significantly accelerated in mice lacking both Cdx2 and its homolog Cdx1, with particular exaggeration of defects in villus enterocyte differentiation. Importantly, Cdx2 occupancy correlated with hundreds of transcripts that fell but not with equal numbers that rose with Cdx loss, indicating a predominantly activating role at intestinal cis-regulatory regions. Integrated consideration of a transcription factor's mutant phenotype and cistrome hence reveals the continued and distinct requirement in adults of a critical developmental regulator that activates tissue-specific genes.

Several epidemiologic studies have reported that cyclooxygenase (COX) inhibitors prevent/delay the onset of Alzheimer's disease (AD). Recent experimental studies suggest that these compounds can also diminish amyloidβ (Aβ) neuropathology in rodent models of AD. To explore the relationship of COX expression to Aβ neuropathology, we crossed mice expressing both mutant amyloid precursor protein [K670N/M671L (APP swe )] and mutant PS1 (A246E) with mice expressing human COX-2 selectively in neurons. We show here that human COX-2 expression in APP swe /PS1/COX-2 mice induces potentiation of brain parenchymal amyloid plaque formation and a greater than twofold increase in prostaglandin E 2 production, at 24 months of age. This increased amyloid plaque formation coincided with a preferential elevation of Aβ 1-40 and Aβ 1-42 with no change in total amyloid precursor protein (APP) expression/content in the brain. Collectively these data suggest that COX-2 influences APP processing and promotes amyloidosis in the brain. COX-2Amyloid Alzheimer's disease Inflammation A large number of epidemiological studies have indi-(14,21) have shown that COX-2 expression is elevated in the AD brain and that this elevation is corre-cated that the use of nonsteroidal anti-inflammatory drugs (NSAIDs) may prevent or delay the clinical fea-lated with the severity of brain amyloid plaque pathology (6). Additionally, a recent study found a tures of Alzheimer's disease (AD) (7,13,18). However, recent therapeutic studies with both cyclooxygenase preferential loss of hippocampal COX-2-immunopositive neurons in the brains of AD patients suffering (COX)-inhibiting NSAIDs and steroids could not confirm this epidemiological evidence (9).severe dementia (22). However, recent evidence indicates that nonselective COX, rather than selective The pharmacological activity of NSAIDs is generally attributed to the inhibition of COX, a rate-limit-COX-2-specific inhibitors, has been found to influence amyloid precursor protein (APP) processing. ing enzyme necessary for the production of prostaglandins (PGs). COX-2 is the inducible form of COX Thus, the characterization of COX activities in the brain and their role in AD amyloidosis is receiving a and is involved in inflammatory responses but also neuronal functions (22). We (5,6,15) and others great deal of attention.

Brown adipose tissue (BAT) and beige fat function in energy expenditure in part due to their role in thermoregulation, making these tissues attractive targets for treating obesity and metabolic disorders. While prolonged cold exposure promotes de novo recruitment of brown adipocytes, the exact sources of cold-induced thermogenic adipocytes are not completely understood. Here, we identify Trpv1-positive vascular smooth muscle (VSM) cells as previously unidentified brown adipocyte progenitors. Analysis of single-cell RNA sequencing from interscapular brown adipose depots reveals, in addition to the previously-known Pdgfra-expressing mesenchymal progenitors, a previously-unidentified VSM-derived adipocyte progenitor (APC) population, which expresses the temperature-sensitive cation channel, Trpv1. Using flow cytometry and lineage tracing, we demonstrate that the Trpv1-positive VSM-APCs are distinct from the Pdgfra-positive progenitors, and can give rise to thermogenic adipocytes in response to cold. Together, these findings illustrate the landscape of the thermogenic adipose niche at the single cell resolution and identify a new cellular origin for the development of brown and beige adipocytes.

A rapid and comprehensive qualitative method has been developed to characterize the different classes of polyphenols, such as anthocyanins, flavonols, phenolic acids, and flavanols/proanthocyanidins, in grape products. The detection was achieved by two runs with the same LC gradient in different MS ionization modes and mobile phase modifiers (positive ionization mode and 0.4% trifluoroacetic acid for anthocyanins and flavonols; negative ionization mode and 0.1% formic acid for phenolic acids and flavanols). From an analysis of the MS and UV data and in comparison with the authenticated standards, a total of 53 compounds were identified, including 33 anthocyanins, 12 flavonols, 4 phenolic acids, and 4 flavanols/proanthocyanidins. With the method developed, a survey was then conducted to qualitatively assess the composition of polyphenols among 29 different grape products including original grape, grape juice, grape wine, and grape-derived dietary supplements, and their chemical profiles were systematically compared. This method provided a comprehensive qualitative insight into the composition of polyphenols in grape-derived products.

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c Methylation of H3K79 is associated with chromatin at expressed genes, though it is unclear if this histone modification is required for transcription of all genes. Recent studies suggest that Wnt-responsive genes depend particularly on H3K79 methylation, which is catalyzed by the methyltransferase DOT1L. Human leukemias carrying MLL gene rearrangements show DOT1L-mediated H3K79 methylation and aberrant expression of leukemogenic genes. DOT1L inhibitors reverse these effects, but their clinical use is potentially limited by toxicity in Wnt-dependent tissues such as intestinal epithelium. Genome-wide positioning of the H3K79me2 mark in Lgr5 ؉ mouse intestinal stem cells and mature intestinal villus epithelium correlated with expression levels of all transcripts and not with Wnt-responsive genes per se. Selective Dot1l disruption in Lgr5؉ stem cells or in whole intestinal epithelium eliminated H3K79me2 from the respective compartments, allowing genetic evaluation of DOT1L requirements. The absence of methylated H3K79 did not impair health, intestinal homeostasis, or expression of Wnt target genes in crypt epithelium for up to 4 months, despite increased crypt cell apoptosis. Global transcript profiles in Dot1l-null cells were barely altered. Thus, H3K79 methylation is not essential for transcription of Wnt-responsive or other intestinal genes, and intestinal toxicity is not imperative when DOT1L is rendered inactive in vivo.C ovalent histone modifications influence chromatin structure and diverse nuclear functions, including gene regulation (1, 2). Expressed genes are associated with di-or trimethylated H3K4, H3K36, and H3K79 and monomethylated H3K9 and H4K20, whereas repressed genes are enriched for trimethylated H3K9, H3K27, and H4K20 (2-4); various lysine methyltransferases (KMTs) place these marks. H3K79me2 denotes active gene transcription in Saccharomyces cerevisiae, Drosophila, and mammalian cells (5-8). Unlike other modified histone N-terminal "tail" residues, H3K79 is exposed on the nucleosome surface, may be methylated at both heterochromatin and euchromatin (5, 9), and is aberrantly methylated in human leukemias that carry MLL1 gene rearrangements (10, 11).Disruption of Dot1 in yeast or its fly (grappa) and mammalian (Dot1l) homologs eliminates H3K79 methylation, revealing these as the only enzymes capable of H3K79 mono-, di-, and trimethylation (8, 12-15). Dot1 and DOT1L/KMT4 differ from other KMTs in possessing an arginine methyltransferase-like domain instead of a canonical SET domain (12), and H3K79 lacks known demethylases (9). Dot1-dependent H3K79 methylation is associated with telomere silencing and meiotic checkpoint controls (16), DNA repair (17), and modulation of constitutive heterochromatin (15), but its role in transcriptional control has drawn particular attention. Fruit fly grappa mutants dysregulate developmental genes and show embryonic defects (14). Dot1l-null mouse embryos are stunted and die in midgestation of restricted cardiovascular defects (15, 18) that seem incompatible with a ...