Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation

This is the final version of the article. Available from Springer Nature via the DOI in this record.Raw data were submitted to the European Genome-phenome Archive (EGA) under accession EGAS00001001077.X-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-chromosome methylation. Through cis-eQTL expression analysis, we map these loci to the genes SMCHD1/METTL4, TRIM6/HBG2, and ZSCAN9. Low-expression alleles of the loci are predominantly associated with mild hypomethylation of CpG islands near genes known to variably escape XCI, implicating the autosomal genes in variable XCI. Together, these results suggest a genetic basis for variable escape from XCI and highlight the potential of a population genomics approach to identify genes involved in XCI.This research was financially supported by several institutions: BBMRI-NL, a Research Infrastructure financed by the Dutch government (NWO, numbers 184.021.007 and 184.033.111); the UK Medical Research Council; Wellcome (www.wellcome.ac.uk; [grant number 102215/2/13/2 to ALSPAC]); the University of Bristol to ALSPAC; the UK Economic and Social Research Council (www.esrc.ac.uk; [ES/N000498/1] to CR); the UK Medical Research Council (www.mrc.ac.uk; grant numbers [MC_UU_12013/1, MC_UU_12013/2 to JLM, CR]); the Helmholtz Zentrum München – German Research Center for Environmental Health, which is funded by the German Federal Ministry of Education and Research (BMBF) and by the State of Bavaria; the Munich Center of Health Sciences (MC-Health), Ludwig-Maximilians-Universität, as part of LMUinnovativ; the Wellcome Trust, Medical Research Council, European Union (EU), and the National Institute for Health Research (NIHR)- funded BioResource, Clinical Research Facility, and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London

Skewed X-inactivation is common in the general female population

X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. To this end, we analyzed blood-derived RNA and whole-genome sequencing data from 79 female children and their parents from the Genome of the Netherlands project. We calculated the median ratio of the paternal over total counts at all X-chromosomal heterozygous single-nucleotide variants with coverage ≥10. We identified two individuals where the same X-chromosome was inactivated in all cells. Imbalanced expression of the two X-chromosomes (ratios ≤0.35 or ≥0.65) was observed in nearly 50% of the population. The empirically observed skewing is explained by a theoretical model where X-inactivation takes place in an embryonic stage in which eight cells give rise to the hematopoietic compartment. Genes escaping X-inactivation are expressed from both alleles and therefore demonstrate less skewing than inactivated genes. Using this characteristic, we identified three novel escapee genes (SSR4, REPS2, and SEPT6), but did not find support for many previously reported escapee genes in blood. Our collective data suggest that skewed X-inactivation is common in the general population. This may contribute to manifestation of symptoms in carriers of recessive X-linked disorders. We recommend that X-inactivation results should not be used lightly in the interpretation of X-linked variants

Interspinous process device versus standard conventional surgical decompression for lumbar spinal stenosis: randomised controlled trial

STUDY QUESTION Is interspinous process device implantation more effective in the short term (eight weeks) than conventional surgical decompression for patients with intermittent neurogenic claudication due to lumbar spinal stenosis? SUMMARY ANSWER The use of interspinous implants did not result in a better outcome than conventional decompression, but the reoperation rate was significantly higher. WHAT IS KNOWN AND WHAT THIS PAPER ADDS Bony decompression and treatment with interspinous process devices are superior to conservative and non-surgical treatment for intermittent neurogenic claudication due to lumbar spinal stenosis. Interspinous implants surgery is not superior to bony decompression, and the reoperation rate is significantly higher

Higher Incidence of Hypospadias in Monochorionic Twins

Background: Hypospadias is associated with twinning. The incidence of hypospadias in monochorionic and dichorionic male twins is, however, yet to be determined. Methods: All medical records of monochorionic and dichorionic twins admitted to our neonatal nursery between January 2004 and August 2013 were reviewed for the presence of hypospadias. Results: A total of 350 monochorionic and 303 dichorionic male twins were included in the study. The incidence of hypospadias in monochorionic and dichorionic groups was 4% (14/350) and 1% (3/303) (p = .016) respectively. In 11 of the 15 twin couples, hypospadias occurred in the twin with the lowest birth weight. The rate of hypospadias in twin infants small-for-gestational-age group was 10% (6/60) compared with 2% (11/593) in the appropriate-for-gestational-age group (p = .002). In a multivariate analysis, both monochorionicity and small-for-gestational-age were independently associated with hypospadias, odds ratio 4.1 (95% confidence interval (CI): 1.1-14.7) and 6.1 (95% CI: 2.2-17.2) respectively. Conclusions: The incidence of hypospadias is four-fold higher in monochorionic twins compared with dichorionic twins. Hypospadias is also independently associated with small-for-gestationalage

IPD without bony decompression versus conventional surgical decompression for lumbar spinal stenosis: 2-year results of a double-blind randomized controlled trial

Interspinous process devices (IPDs) are implanted to treat patients with intermittent neurogenic claudication (INC) based on lumbar spinal stenosis. It is hypothesized that patients with lumbar spinal stenosis treated with IPD have a faster short-term recovery, an equal outcome after 2 years and less back pain compared with bony decompression. A randomized design with variable block sizes was used, with allocations stratified according to center. Allocations were stored in prepared opaque, coded and sealed envelopes, and patients and research nurses were blind throughout the follow-up. Five neurosurgical centers (including one academic and four secondary level care centers) included participants. 211 participants were referred to the Leiden-The Hague Spine Prognostic Study Group. 159 participants with INC based on lumbar spinal stenosis at one or two levels with an indication for surgery were randomized into two groups. Patients and research nurses were blinded for the allocated treatment throughout the study period. 80 participants received an IPD and 79 participants underwent spinal bony decompression. The primary outcome at long-term (2-year) follow-up was the score for the Zurich Claudication Questionnaire. Repeated measurement analyses were applied to compare outcomes over time. At two years, the success rate according to the Zurich Claudication Questionnaire for the IPD group [69 % (95 % CI 57-78 %)] did not show a significant difference compared with standard bony decompression [60 % (95 % CI 48-71 %) p value 0.2]. Reoperations, because of absence of recovery, were indicated and performed in 23 cases (33 %) of the IPD group versus 6 (8 %) patients of the bony decompression group (p < 0.01). Furthermore, long-term VAS back pain was significantly higher [36 mm on a 100 mm scale (95 % CI 24-48)] in the IPD group compared to the bony decompression group [28 mm (95 % CI 23-34) p value 0.04]. This double-blinded study could not confirm the advantage of IPD without bony decompression over conventional 'simple' decompression, two years after surgery. Moreover, in the IPD treatment arm, the reoperation rate was higher and back pain was even slightly more intense compared to the decompression treatment arm

Electron tomography of DJANGOS.

<p><b>A.</b> Tomographic slice of an EM thick section showing a nuclear pore-associated structure formed in HeLa cells expressing B12-HA. Cytoplasm and nucleus are labeled with “C” and “N,” respectively. The thick arrow points to an atypical nuclear pore structure in cross-section at the junction with the nuclear envelope; the thin arrow points to a classic nuclear pore in the double membrane inside the nucleus. <b>B.</b> End-on view of the atypical nuclear pore at the neck of the double-membrane structure. <b>C.</b> 3D rendering of the tomogram shows the NPCs in blue. Also see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094322#pone.0094322.s004" target="_blank">Movie S1</a>.</p