Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development

Förvaltning av signalkräfta i sjöar

Fisket efter signalkräfta har fått allt större ekonomisk och social betydelse i Sverige. Trots detta saknas väl underbyggda råd för hur ett hållbart fiske ska bedrivas.  Projektet ”Utveckling av fisket efter signalkräfta – hur ska man optimera fiske och förutsäga risken för populationskollapser?” är ett projekt som delfinansieras av Europeiska fiskerifonden 2009-2013. Som en inledande del i detta projekt gjordes en litteratursammanställning, och baserat på denna har planeringen av det framtida arbetet kunnat konkretiseras.  Målsättningen med litteraturgenomgången var att identifiera vilken information om signalkräftans biologi och ekologi som behövdes för att kunna ta fram bra fiskerimodeller för hur ett hållbart fiske bör bedrivas. Dessutom var det viktigt att förstå varför vissa bestånd av signalkräfta har kollapsat.  Fångsterna av signalkräfta varierar mellan sjöar. Denna variation kan, i sjöar som inte är försurade, till stor del förklaras med hur stor andel av sjöns botten som är täckt med sten. Finns det mycket sten i en sjö finns det också mycket signalkräftor. Det finns några få studier i Sverige på signalkräftan där populationer har följts under en längre tid (minst 15 år). Dessa visar att fångst per mjärde och uttag av konsumtionskräftor varierar mellan olika år inom en sjö. Dessa variationer kan till viss del förklaras med temperaturen under föregående år, men mekanismen bakom detta är inte känd. Studier av andra arter sötvattenskräftor och en del marina skaldjur (t.ex. hummer) tyder på att rekryteringen (reproduktionsframgången) till viss del kan förklara variationerna i fångstnivåer mellan olika år.  Denna litteraturgenomgång visar att det saknas väsentlig information om signalkräftans ekologi och biologi för att kunna ta fram teoretiska modeller som ska ligga till grund för rekommendationer om hur ett hållbart fiske ska bedrivas. De beståndsanalyser som bedömts vara intressanta för signalkräfta kräver vissa dataunderlag för att ge tillförlitliga resultat. De enskilt viktigaste faktorerna är rekryteringsframgång, tillväxt, naturlig dödlighet, och detaljerad fiskeristatistik (ansträngning, selektivitet, fångster etc.). Med anledning av resultaten från denna litteraturgenomgång bedömdes följande insatser som prioriterade:  • undersöka betydelsen av honans storlek för rekryteringsframgång • utveckla tekniken för märkning av kräftor i olika typer av bestånd för att sedan kunna använda återfångstdata för att bestämma individuell tillväxt, naturlig dödlighet och fiskeridödlighet  • uppskatta ytan tillgängligt kräfthabitat för olika kräftbestånd och bedöma i vilken mån det påverkar potentiellt fiskeuttag  • analysera ett flertal sjöar med och utan populationskollapser och undersöka vilka miljöfaktorer som kan förklara uppkomsten av kollapser  • analysera såväl pestfrekvens som infektionsgrad i enskilda kräftor och utvärdera om det finns en koppling mellan populationskollapser och ökade pestangrepp i sjöa

Resolution of hepatic fibrosis after ZFN-mediated gene editing in the PiZ mouse model of human α1-antitrypsin deficiency

BACKGROUND: α1-antitrypsin deficiency is most commonly caused by a mutation in exon-7 of SERPINA1 (SA1-ATZ), resulting in hepatocellular accumulation of a misfolded variant (ATZ). Human SA1-ATZ-transgenic (PiZ) mice exhibit hepatocellular ATZ accumulation and liver fibrosis. We hypothesized that disrupting the SA1-ATZ transgene in PiZ mice by in vivo genome editing would confer a proliferative advantage to the genome-edited hepatocytes, enabling them to repopulate the liver. METHODS: To create a targeted DNA break in exon-7 of the SA1-ATZ transgene, we generated 2 recombinant adeno-associated viruses (rAAV) expressing a zinc-finger nuclease pair (rAAV-ZFN), and another rAAV for gene correction by targeted insertion (rAAV-TI). PiZ mice were injected i.v. with rAAV-TI alone or the rAAV-ZFNs at a low (7.5×1010vg/mouse, LD) or a high dose (1.5×1011vg/mouse, HD), with or without rAAV-TI. Two weeks and 6 months after treatment, livers were harvested for molecular, histological, and biochemical analyses. RESULTS: Two weeks after treatment, deep sequencing of the hepatic SA1-ATZ transgene pool showed 6%±3% or 15%±4% nonhomologous end joining in mice receiving LD or HD rAAV-ZFN, respectively, which increased to 36%±12% and 36%±12%, respectively, 6 months after treatment. Two weeks postinjection of rAAV-TI with LD or HD of rAAV-ZFN, repair by targeted insertion occurred in 0.10%±0.09% and 0.25%±0.14% of SA1-ATZ transgenes, respectively, which increased to 5.2%±5.0% and 33%±13%, respectively, 6 months after treatment. Six months after rAAV-ZFN administration, there was a marked clearance of ATZ globules from hepatocytes, and resolution of liver fibrosis, along with reduction of hepatic TAZ/WWTR1, hedgehog ligands, Gli2, a TIMP, and collagen content. CONCLUSIONS: ZFN-mediated SA1-ATZ transgene disruption provides a proliferative advantage to ATZ-depleted hepatocytes, enabling them to repopulate the liver and reverse hepatic fibrosis

Chromatin Remodeling by BRG1 and SNF2H : Biochemistry and Function

Chromatin is a highly dynamic, regulatory component in the process of transcription, repair, recombination and replication. The BRG1 and SNF2H proteins are ATP-dependent chromatin remodeling proteins that modulate chromatin structure to regulate DNA accessibility for DNA-binding proteins involved in these processes. The BRG1 protein is a central ATPase of the SWI/SNF complexes involved in chromatin remodeling associated with regulation of transcription. SWI/SNF complexes are biochemically hetero-geneous but little is known about the unique functional characteristics of the various forms. We have shown that SWI/SNF activity in SW13 cells affects actin filament organization dependent on the RhoA signaling pathway. We have further shown that the biochemical composition of SWI/SNF complexes qualitatively affects the remodeling activity and that the composition of biochemically purified SWI/SNF complexes does not reflect the patterns of chromatin binding of individual subunits. Chromatin binding assays (ChIP) reveal variations among subunits believed to be constitutive, suggesting that the plasticity in SWI/SNF complex composition is greater than suspected. We have also discovered an interaction between BRG1 and the splicing factor Prp8, linking SWI/SNF activity to mRNA processing. We propose a model whereby parts of the biochemical heterogeneity is a result of function and that the local chromatin environment to which the complex is recruited affect SWI/SNF composition. We have also isolated the novel B-WICH complex that contains WSTF, SNF2H, the splicing factor SAP155, the RNA helicase II/Guα, the transcription factor Myb-binding protein 1a, the transcription factor/DNA repair protein CSB and the RNA processing factor DEK. The formation of this complex is dependent on active transcription and links chromatin remodeling by SNF2H to RNA processing. By linking chromatin remodeling complexes with RNA processing proteins our work has begun to build a bridge between chromatin and RNA, suggesting that factors in chromatin associated assemblies translocate onto the growing nascent RNA

E2f3b plays an essential role in myogenic differentiation through isoform-specific gene regulation

Current models posit that E2F transcription factors can be divided into members that either activate or repress transcription, in part through collaboration with the retinoblastoma (pRb) tumor suppressor family. The E2f3 locus encodes E2f3a and E2f3b proteins, and available data suggest that they regulate cell cycle-dependent gene expression through opposing transcriptional activating and repressing activities in growing and quiescent cells, respectively. However, the role, if any, of E2F proteins, and in particular E2f3, in myogenic differentiation is not well understood. Here, we dissect the contributions of E2f3 isoforms and other activating and repressing E2Fs to cell cycle exit and differentiation by performing genome-wide identification of isoform-specific targets. We show that E2f3a and E2f3b target genes are involved in cell growth, lipid metabolism, and differentiation in an isoform-specific manner. Remarkably, using gene silencing, we show that E2f3b, but not E2f3a or other E2F family members, is required for myogenic differentiation, and that this requirement for E2f3b does not depend on pRb. Our functional studies indicate that E2f3b specifically attenuates expression of genes required to promote differentiation. These data suggest how diverse E2F isoforms encoded by a single locus can play opposing roles in cell cycle exit and differentiation

Population collapses in introduced non-indigenous crayfish

Invasive species often have instable population dynamics and are known to collapse or oscillate heavily after passing through the initial lag/growth phases. Long-term data-series documenting these fluctuations are however rare. We use long-term (starting in the early 1960s), semi-quantitative data on the invasive signal crayfish (Pacifastacus leniusculus), capturing its population development after introduction in 44 Swedish lakes. In total 18 (41 %) of these populations had experienced a collapse. A stepwise discriminant function analysis including 20 different ecological or physicochemical characteristics identified three variables explaining collapses in the following order: stocking year, population age and mean air temperature. Populations stocked in the 1980s were more likely to collapse than populations stocked in the 1970s. Lakes with collapses were located in areas with 0.4 A degrees C higher yearly mean air temperatures than the still viable populations. Collapses also depended on the time phase of the population and started to occur 12 years after stocking and were most frequent in the interval 16-20 years after stocking and after 11-15 years duration of the established phase with harvestable densities. An analysis of prevalence and pathogen load of Aphanomyces astaci was conducted in eight of the studied populations. A. astaci was present in all populations but neither the level of prevalence nor the pathogen load in infested specimens differed significantly between lakes with collapses and lakes without. Our results highlight the potential sensitivity and instability of introduced crayfish. The importance of density-dependence and temperature suggest that both climate variability and/or fisheries can influence these processes

Graphitic microstructure and performance of carbon fibre Li-ion structural battery electrodes

International audienceCarbon fibres (CFs), originally made for use in structural composites, have also been demonstrated as high capacity Li-ion battery negative electrodes. Consequently, CFs can be used as structural electrodes; simultaneously carrying mechanical load and storing electrical energy in multifunctional structural batteries. To date, all CF microstructural designs have been generated to realise a targeted mechanical property, e.g. high strength or stiffness, based on a profound understanding of the relationship between the graphitic microstructure and the mechanical performance. Here we further advance this understanding by linking CF microstructure to the lithium insertion mechanism and the resulting electrochemical capacity. Different PAN-based CFs ranging from intermediate- to high-modulus types with distinct differences in microstructure are characterised in detail by SEM and HR-TEM and electrochemical methods. Furthermore, the mechanism of Li-ion intercalation during charge/discharge is studied by in situ confocal Raman spectroscopy on individual CFs. Raman G band analysis reveals a Li-ion intercalation mechanism in the high-modulus fibre reminiscent of that in crystalline graphite. Also, the combination of a relatively low capacity of the high-modulus CFs (ca. 150 mAh g−1) is shown to be due to that the formation of a staged structure is frustrated by an obstructive turbostratic disorder. In contrast, intermediate-modulus CFs, which have significantly higher capacities (ca. 300 mAh g−1), have Raman spectra indicating a Li-ion insertion mechanism closer to that of partly disordered carbons. Based on these findings, CFs with improved multifunctional performance can be realised by tailoring the graphitic order and crystallite sizes

New insights into the human heart development using a combined spatial and single-cell transcriptomics approach

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The Mammalian Sin3 Proteins Are Required for Muscle Development and Sarcomere Specification▿ †

The highly related mammalian Sin3A and Sin3B proteins provide a versatile platform for chromatin-modifying activities. Sin3-containing complexes play a role in gene repression through deacetylation of nucleosomes. Here, we explore a role for Sin3 in myogenesis by examining the phenotypes resulting from acute somatic deletion of both isoforms in vivo and from primary myotubes in vitro. Myotubes ablated for Sin3A alone, but not Sin3B, displayed gross defects in sarcomere structure that were considerably enhanced upon simultaneous ablation of both isoforms. Massively parallel sequencing of Sin3A- and Sin3B-bound genomic loci revealed a subset of target genes directly involved in sarcomere function that are positively regulated by Sin3A and Sin3B proteins. Both proteins were coordinately recruited to a substantial number of genes. Interestingly, depletion of Sin3B led to compensatory increases in Sin3A recruitment at certain target loci, but Sin3B was never found to compensate for Sin3A loss. Thus, our analyses describe a novel transcriptional role for Sin3A and Sin3B proteins associated with maintenance of differentiated muscle cells