DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers ...and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell ...and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has ...systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution 'footprints'. Using genomic DNaseI footprinting across 41 diverse ...cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell- selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Browning induction or transplantation of brown adipose tissue (BAT) or brown/beige adipocytes derived from progenitor or induced pluripotent stem cells (iPSCs) can represent a powerful strategy to ...treat metabolic diseases. However, our poor understanding of the mechanisms that govern the differentiation and activation of brown adipocytes limits the development of such therapy. Various genetic factors controlling the differentiation of brown adipocytes have been identified, although most studies have been performed using in vitro cultured pre-adipocytes. We investigate here the differentiation of brown adipocytes from adipose progenitors in the mouse embryo. We demonstrate that the formation of multiple lipid droplets (LDs) is initiated within clusters of glycogen, which is degraded through glycophagy to provide the metabolic substrates essential for de novo lipogenesis and LD formation. Therefore, this study uncovers the role of glycogen in the generation of LDs.
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•Brown adipocytes are functionally differentiated at E17.5 in the mouse embryo•Lipid droplets are formed within glycogen clusters•Glycogen production is crucial for lipid droplet biogenesis during BAT differentiation•Glycophagy-mediated glycogen degradation drives lipid droplet formation
Lipid droplet formation is a major feature of brown adipocyte differentiation. Mayeuf-Louchart et al. characterize the different steps of brown adipocyte differentiation in the mouse embryo and report the essential role of glycogen production and degradation by glycophagy for lipid droplet biogenesis.
The reduction in infant birth weight and increased frequency of preeclampsia (PE) in high-altitude residents have been attributed to greater placental hypoxia, smaller uterine artery (UA) diameter, ...and lower UA blood flow (Q(UA)). This cross-sectional case-control study determined UA, common iliac (CI), and external iliac (EI) arterial blood flow in Andeans residing at 3,600-4,100 m, who were either nonpregnant (NP, n = 23), or experiencing normotensive pregnancies (NORM; n = 155), preeclampsia (PE, n = 20), or gestational hypertension (GH, n = 12). Pregnancy enlarged UA diameter to ~0.62 cm in all groups, but indices of end-arteriolar vascular resistance were higher in PE or GH than in NORM. Q(UA) was lower in early-onset (≤34 wk) PE or GH than in NORM, but was normal in late-onset (>34 wk) illness. Left Q(UA) was consistently greater than right in NORM, but the pattern reversed in PE. Although Q(CI) and Q(EI) were higher in PE and GH than NORM, the fraction of Q(CI) distributed to the UA was reduced 2- to 3-fold. Women with early-onset PE delivered preterm, and 43% had stillborn small for gestational age (SGA) babies. Those with GH and late-onset PE delivered at term but had higher frequencies of SGA babies (GH=50%, PE=46% vs. NORM=15%, both P < 0.01). Birth weight was strongly associated with reduced Q(UA) (R(2) = 0.80, P < 0.01), as were disease severity and adverse fetal outcomes. We concluded that high end-arteriolar resistance, not smaller UA diameter, limited Q(UA) and restricted fetal growth in PE and GH. These are, to our knowledge, the first quantitative measurements of Q(UA) and pelvic blood flow in early- vs. late-onset PE in high-altitude residents.
The pathophysiology of AMS remains unexplained. In high altitude cerebral edema, considered a late‐form of AMS, there is marked vasogenic cerebral edema. However, whether the brain swells in AMS has ...not been thoroughly explored.
Methods: To explore the role of brain swelling in AMS we exposed 25 healthy volunteers to simulated high altitude in a hypobaric chamber (Pb=430 mmHg) for 10 hrs in a placebo‐controlled, cross‐over, single blind trial. 15 of the 25 developed AMS (headache plus nausea, dizziness or lightheadedness) with a Lake Louise AMS score > 2. Volunteers completed high‐resolution 3‐T, T1‐SPGR MRI scans before and after hypobaric exposure. Volumetric analyses were completed using FSL SIENA.
Results: Brain volume was greater in AMS+ (p<0.01). 15 AMS+ subjects were invited back for the 2nd arm of the trial in which they received 4mg dexamethasone (DEX) PO q 8h, starting the day before hypobaric exposure. One investigator was aware of the assigned medication (VB), but was not involved in symptom assessment, MRI imaging or data analysis. 10 subjects completed DEX prophylaxis. DEX completely blocked brain swelling and AMS symptoms. The mechanisms by which DEX blocks brain swelling in acute hypobaric hypoxia are unknown. Possibilities include prevention of blood‐brain barrier breakdown. We conclude that AMS may be initiated by brain swelling.
Supported, in part, by NIH‐HL‐070362.
Cerebral autoregulation (CA) is impaired after prolonged exposure to hypoxia; however, no studies have investigated CA in acute hypoxia. Objective: To assess changes in CA over a 9 hr exposure to ...hypobaric hypoxia (HX: Pbar = 425 mmHg; 16,000 ft).
Methods
26 healthy subjects were studied at baseline (BL: Pbar = 625 mmHg; 5,400 ft) and then following 4 and 9 hrs of HX. Radial artery blood pressure (ABP) and middle cerebral artery blood flow velocity (CBFv) were recorded for 6 min at BL, 4 & 9hr. We assessed ABP to CBFv relationships using cross spectral analysis over 3 regions of physiological interest (B‐waves: 0.008 to 0.05 Hz; M‐waves: 0.05 to 0.15 Hz; R‐waves: 0.15 to 0.50 Hz R‐waves). Increased coherence, gain and/or decreased phase shift are considered indicators of impaired CA.
Results
During BL, CA resembled a high pass filter (highest gain & lowest phase shift across R‐waves, p<0.01), suggesting intact CA. During HX, spectral density of CBFv, coherence & gain were increased across B‐waves after 4 hr (p<0.05). M‐wave spectral densities of ABP and CBFv increased, but gain was dampened at 9hr (p<0.05). R‐wave phase shift was delayed compared to BL at 4 and 9hr (p<0.05).
Conclusions
Acute HX alters the high pass filter properties of intact CA. During HX, CA resembled a low pass filter, where oscillations in ABP were readily transmitted to changes in CBFv across B‐waves (low freq), dampened across M‐waves (middle freq) and delayed across R‐waves (high freq).
Supported by NIH HL070362
CONTEXT Insomnia and generalized anxiety disorder (GAD) are prevalent disorders that may coexist. OBJECTIVE To determine the efficacy of eszopiclone combined with escitalopram oxalate in treating ...insomnia comorbid with GAD. DESIGN Double-blind, randomized, placebo-controlled, parallel-group, add-on therapy 10-week study. SETTING Multicenter outpatient study from July 2005 to April 2006. PATIENTS Adults aged 18 to 64 years meeting DSM-IV-TR criteria for GAD and insomnia. INTERVENTIONS Patients received 10 mg of escitalopram oxolate for 10 weeks and were randomized to also receive either 3 mg of eszopiclone (n = 294) or placebo (n = 301) nightly for 8 weeks. For the last 2 weeks, eszopiclone was replaced with a single-blind placebo. MAIN OUTCOME MEASURES Sleep, daytime functioning, psychiatric measures, and adverse events. RESULTS Compared with treatment with placebo and escitalopram, treatment with eszopiclone and escitalopram resulted in significantly improved sleep and daytime functioning (P < .05), with no evidence of tolerance. Patients taking eszopiclone and escitalopram had greater improvements in total Hamilton Anxiety Scale (HAM-A) scores at each week (P < .05) and at weeks 4 through 10 with the insomnia item removed. Clinical Global Impressions (CGI) of Improvement scores were improved with eszopiclone and escitalopram at every point (P < .02), while CGI of Severity of Illness scores were not significantly different after week 1. The HAM-A response (63% vs 49%, respectively, P = .001) and remission (42% vs 36%, respectively, P = .09) rates at week 8 were higher in patients treated with eszopiclone and escitalopram than those treated with placebo and escitalopram, and median time to onset of anxiolytic response was significantly reduced (P ≤ .05). After eszopiclone discontinuation, there was no evidence of rebound insomnia, and while treatment differences in anxiety measures were maintained, differences in sleep outcomes were not. Overall adverse event rates were 77.6% with cotherapy and 67.9% with monotherapy. The most common adverse events with cotherapy were unpleasant taste, headache, dry mouth, and somnolence. CONCLUSIONS Coadministration of eszopiclone and escitalopram was well tolerated and associated with significantly improved sleep, daytime functioning, anxiety, and mood in patients with insomnia and GAD. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00235508Arch Gen Psychiatry. 2008;65(5):551-562-->
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