DNA methylation and DNA methyltransferases

The prevailing views as to the form, function, and regulation of genomic methylation patterns have their origin many years in the past, at a time when the structure of the mammalian genome was only dimly perceived, when the number of protein-encoding mammalian genes was believed to be at least five times greater than the actual number, and when it was not understood that only ~10% of the genome is under selective pressure and likely to have biological function. We use more recent findings from genome biology and whole-genome methylation profiling to provide a reappraisal of the shape of genomic methylation patterns and the nature of the changes that they undergo during gametogenesis and early development. We observe that the sequences that undergo deep changes in methylation status during early development are largely sequences without regulatory function. We also discuss recent findings that begin to explain the remarkable fidelity of maintenance methylation. Rather than a general overview of DNA methylation in mammals (which has been the subject of many reviews), we present a new analysis of the distribution of methylated CpG dinucleotides across the multiple sequence compartments that make up the mammalian genome, and we offer an updated interpretation of the nature of the changes in methylation patterns that occur in germ cells and early embryos. We discuss the cues that might designate specific sequences for demethylation or de novo methylation during development, and we summarize recent findings on mechanisms that maintain methylation patterns in mammalian genomes. We also describe the several human disorders, each very different from the other, that are caused by mutations in DNA methyltransferase genes

Abnormal X chromosome inactivation and sex-specific gene dysregulation after ablation of FBXL10

BACKGROUND: Almost all CpG-rich promoters in the mammalian genome are bound by the multidomain FBXL10 protein (also known as KDM2B, JHDM1B, CXXC2, and NDY1). FBXL10 is expressed as two isoforms: FBXL10-1, a longer form that contains an N-terminal histone demethylase domain with C-terminal F-box, CXXC, PHD, RING, and leucine-rich repeat domains, and FBXL10-2, a shorter form that initiates at an alternative internal exon and which lacks the histone demethylase domain but retains all other annotated domains. Selective deletion of Fbxl10-1 had been reported to produce a low penetrance and variable phenotype; most of the mutant animals were essentially normal. We constructed mutant mouse strains that were either null for Fbxl10-2 but wild type for Fbxl10-1 or null for both Fbxl10-1 and Fbxl10-2. RESULTS: Deletion of Fbxl10-2 (in a manner that does not perturb expression of Fbxl10-1) produced a phenotype very different from the Fbxl10-1 mutant, with craniofacial abnormalities, neural tube defects, and increased lethality, especially in females. Mutants that lacked both FBXL10-1 and FBXL10-2 showed embryonic lethality and even more extreme sexual dimorphism, with more severe gene dysregulation in mutant female embryos. X-linked genes were most severely dysregulated, and there was marked overexpression of Xist in mutant females although genes that encode factors that bind to Xist RNA were globally downregulated in mutant female as compared to male embryos. CONCLUSIONS: FBXL10 is the first factor shown to be required both for the normal expression and function of the Xist gene and for normal expression of proteins that associate with Xist RNA; it is proposed that FBXL10 coordinates the expression of Xist RNA with proteins that associate with this RNA. The function of FBXL10 is largely independent of the histone demethylase activity of the long form of the protein. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13072-016-0069-1) contains supplementary material, which is available to authorized users

Molecular outflows in the young open cluster IC348

We present a wide-field survey of the young open cluster IC348 for molecular H2 outflows. Outflow activity is only found at its south-western limit, where a new subcluster of embedded sources is in an early phase of its formation. If the IC348 cluster had been built up by such subclusters forming at different times, this could explain the large age-spread that Herbig (1998) found for the IC348 member stars. In addition to several compact groups of H2 knots, our survey reveals a large north-south oriented outflow, and we identify the newly discovered far-infrared and mm-object IC348MMS as its source. New deep images in the 1-0 S(1) line of molecular hydrogen trace the HH211 jet and counterjet as highly-collimated chains of knots, resembling the interferometric CO and SiO jets. This jet system appears rotated counter-clockwise by about 3 degrees with respect to the prominent H2 bow shocks. Furthermore, we resolve HH211-mm as a double point-like source in the mm-continuum.Comment: 10 pages, 9 figures, accepted for publication in Ap

Reliability of 2D ultrasound imaging associated with transient ShearWave Elastography method to analyze spastic gastrocnemius medialis muscle architecture and viscoelastic properties

PurposeThe aim of the study was to assess the reliability of pennation angle (PA) and muscle thickness (MT) 2D measurements and of shear elastic modulus measurement, using ultrasound imaging (US). Those measurements were made on spastic gastrocnemius medialis muscle at rest and at maximal passive stretching, in post-stroke hemiplegic patients. The paretic side measurements were compared to non-paretic side.Material and methodsFourteen patients took part in 2 inter-session reliability experiments, realized at a 7 days interval by the same operator. The Aixplorer® Supersonic US scanner with the transient ShearWave Elastography (SWE) software was used. The stretching experiments were made manually and controlled by a goniometer.ResultsThe reliability of the 2D measurements was good. The coefficient of variation (CV) was 6.30% for MT measurement at rest, 6.40% and 8.26% for PA at rest and at maximal passive stretching respectively. The reliability of the shear elastic modulus measurement in the sagittal plane was good only at rest with a CV of 9.86%, versus 40.58% at stretching. None of the shear elastic modulus measurements in the axial plane were good. At rest, MT and PA were weaker on the paretic side (14.25±3.12mm and 17.32±5.10°) versus non-paretic side (16.30±3.19mm and 21.08±5.05°) (P<0.0001 and P=0.006). At rest, there was a small difference in the shear elastic modulus between the paretic side and the non-paretic side (5.40±1.67kPa versus 6.20±2.18kPa, P=0.041).DiscussionThis is the first description of muscle spastic structure using SWE with Supersonic Shear Imaging. 2D US associated with SWE shows promise in terms of muscular atrophy quantification and muscle histological quality assessment. These structural properties reflect some of the functional abilities regardless of motor control. It should enable further research on therapies, which impact muscle tissue quality, such as botulinum neurotoxin injections

Star formation in the vicinity of the IC 348 cluster

Aims. We present molecular line observations of the southwestern part of the IC 348 young cluster, and we use them together with NIR and mm continuum data to determine the distribution of dense gas, search for molecular outflows, and analyze the ongoing star formation activity in the region. Methods. Our molecular line data consists of C18O(1--0) and N2H+(1--0) maps obtained with the FCRAO telescope at a resolution of about 50'' and CO(2--1) data obtained with the IRAM 30m telescope at a resolution of 11''. Results. The dense gas southwest of IC 348 is concentrated in two groups of dense cores, each of them with a few solar masses of material and indications of CO depletion at high density. One of the core groups is actively forming stars, while the other seems starless. There is evidence for at least three bipolar molecular outflows in the region, two of them powered by previously identified Class 0 sources, while the other one is powered by a still not well characterized low-luminosity object. The ongoing star formation activity is producing a small stellar subgroup in the cluster. Using the observed core characteristics and the star formation rate in the cluster we propose that that similar episodes of stellar birth may have produced the subclustering observed in the halo of IC 348.Comment: 10 pages, 6 figures, A&A accepte

NOD × 129.H2g7 Backcross Delineates 129S1/SvImJ-Derived Genomic Regions Modulating Type 1 Diabetes Development in Mice

OBJECTIVE: Introduction of genes targeted in 129/Sv embryonic stem (ES) cells into NOD mice brings about linked genes that may modulate type 1 diabetes. Our objective was to identify 129S1/SvJ non-MHC regions contributing type 1 diabetes resistance or susceptibility in backcross to NOD/LtJ. RESEARCH DESIGN AND METHODS: After congenic transfer of the NOD H2(g7) haplotype onto 129S1/Sv, 310 females were produced by NOD x (NOD x 129.H2(g7))F1 backcross (N2). A genome scan for quantitative trait locus (QTL) affecting clinical diabetes, age of diabetes onset, and insulitis severity was performed using subphenotype characteristics to improve power and resolution for detection of diabetes susceptibility loci. RESULTS: Thirty-six of 310 (11.6%) N2 females developed type 1 diabetes between 14 and 40 weeks. Significant evidence of linkage for only a single previously reported Idd complex locus (Idd10/17/18, chromosome [Chr] 3) was indicated for clinical diabetes. The quantitative traits of insulitis either alone or combined with age at type 1 diabetes onset were significantly linked to known Idd regions on Chr 1 (Idd5 region), Chr 4 (Idd9 region), Chr 8 (Idd22), Chr 11 (Idd4.3), and proximal Chr 17 (Idd16 region). Significant 129S1/Sv resistance contributions were identified on Chr 1, 15 (two loci), and 19, with suggestive evidence for additional novel 129/Sv resistance QTL on Chr 5 and 17 and susceptibility on Chr 2. CONCLUSIONS: The 129S1/SvJ genome harbors collections of both known and potentially novel non-MHC Idd loci. Investigators targeting 129/Sv genes mapping within chromosomal regions reported herein or elsewhere in the genome need to exclude potential contributions from linked Idd loci by generating a NOD.129 control strain expressing the nontargeted allele

Root temperature and energy consumption at different cable depths in electrically heated substrates

A finite element method-based model of a substrate heated by an electric heating cable buried in a thermal isolated container was experimentally validated with root mean square error values of root zone temperature ranging 0.25 to 0.62 ºC. The two-dimensional transient model allowed variations in the physical properties of the substrate with temperature, water content and depth. The operation of nine configurations of a heating cable buried in sand at different depths (50 to 450 mm, at 50 mm intervals) at 200 mm spacing was simulated and assessed. The validated model was used to perform 24-h simulations applying boundary conditions, and substrate moisture content was experimentally obtained at a mean substrate surface temperature of 13.98 ºC. Such simulations reproduced the operation of the heating system by setting a reference temperature of 20 ºC at the control point in the root zone. Burying the heating cable in the surface layers of the substrate caused large temperature gradients and high heat losses through the substrate surface. Accordingly, average temperature in the root zone increased with heating cable depth, up to the 200 mm depth. For greater depths, temperature in the root zone was constant. The ON/OFF control was most effective with the heating cable buried in the root zone and at control point temperatures of 20 ± 1 ºC. Burying the heating cable in the surface layers required higher energy consumption, up to 28 % at 50 mm. The most efficient heating cable depth was 350 mm, with a daily energy consumption of 6750 kJ m-2

A Study of the Luminosity and Mass Functions of the Young IC 348 Cluster using FLAMINGOS Wide-Field Near-Infrared Images

We present wide-field near-infrared (JHK) images of the young, 2 Myr IC 348 cluster taken with FLAMINGOS. We use these new data to construct an infrared census of sources, which is sensitive enough to detect a 10 Mjup brown dwarf seen through an extinction of Av=7mag. We examine the cluster's structure and relationship to the molecular cloud and construct the cluster's K band luminosity function. Using our model luminosity function algorithm, we derive the cluster's initial mass function throughout the stellar and substellar regimes and find that the IC 348 IMF is very similar to that found for the Trapezium Cluster with both cluster IMFs having a mode between 0.2 - 0.08 Msun. In particular we find that, similar to our results for the Trapezium, brown dwarfs constitute only 1 in 4 of the sources in the IC 348 cluster. We show that a modest secondary peak forms in the substellar IC 348 KLF, corresponding to the same mass range responsible for a similar KLF peak found in the Trapezium. We interpret this KLF peak as either evidence for a corresponding secondary IMF peak at the deuterium burning limit, or as arising from a feature in the substellar mass-luminosity relation that is not predicted by current theoretical models. Lastly, we find that IC 348 displays radial variations of its sub-solar (0.5 - 0.08 Msun) IMF on a parsec scale. Whatever mechanism that is breaking the universality of the IMF on small spatial scales in IC 348 does not appear to be acting upon the brown dwarf population, whose relative size does not vary with distance from the cluster center.Comment: 53 pages, 20 figures, AASTeX5.0. Color version of Figure 1 made available in jpg format. Figure(s) 2,3,5 are reduced in resolution. Accepted 14 Jan 2003 to the Astronomical Journa