Data availabilitySummary statistics generated by COVID-19 Host Genetics Initiative are available online (https://www.covid19hg.org/results/r6/). The analyses described here use the freeze 6 data. The COVID-19 Host Genetics Initiative continues to regularly release new data freezes. Summary statistics for samples from individuals of non-European ancestry are not currently available owing to the small individual sample sizes of these groups, but the results for 23 loci lead variants are reported in Supplementary Table 3. Individual-level data can be requested directly from the authors of the contributing studies, listed in Supplementary Table 1.

STUDY QUESTIONCan spontaneous premature ovarian failure (POF) patients derived from population-based biobanks reveal the association between copy number variations (CNVs) and POF?SUMMARY ANSWERCNVs can hamper the functional capacity of ovaries by disrupting key genes and pathways essential for proper ovarian function.WHAT IS KNOWN ALREADYPOF is defined as the cessation of ovarian function before the age of 40 years. POF is a major reason for female infertility, although its cause remains largely unknown.STUDY DESIGN, SIZE, DURATIONThe current retrospective CNV study included 301 spontaneous POF patients and 3188 control individuals registered between 2003 and 2014 at Estonian Genome Center at the University of Tartu (EGCUT) biobank.PARTICIPANTS/MATERIALS, SETTING, METHODSDNA samples from 301 spontaneous POF patients were genotyped by Illumina HumanCoreExome (258 samples) and HumanOmniExpress (43 samples) BeadChip arrays. Genotype and phenotype information was drawn from the EGCUT for the 3188 control population samples, previously genotyped with HumanCNV370 and HumanOmniExpress BeadChip arrays. All identified CNVs were subjected to functional enrichment studies for highlighting the POF pathogenesis. Real-time quantitative PCR was used to validate a subset of CNVs. Whole-exome sequencing was performed on six patients carrying hemizygous deletions that encompass genes essential for meiosis or folliculogenesis.MAIN RESULTS AND THE ROLE OF CHANCEEleven novel microdeletions and microduplications that encompass genes relevant to POF were identified. For example, FMN2 (1q43) and SGOL2 (2q33.1) are essential for meiotic progression, while TBP (6q27), SCARB1 (12q24.31), BNC1 (15q25) and ARFGAP3 (22q13.2) are involved in follicular growth and oocyte maturation. The importance of recently discovered hemizygous microdeletions of meiotic genes SYCE1 (10q26.3) and CPEB1 (15q25.2) in POF patients was also corroborated.LIMITATIONS, REASONS FOR CAUTIONThis is a descriptive analysis and no functional studies were performed. Anamnestic data obtained from population-based biobank lacked clinical, biological (hormone levels) or ultrasonographical data, and spontaneous POF was predicted retrospectively by excluding known extraovarian causes for premature menopause.WIDER IMPLICATIONS OF THE FINDINGSThe present study, with high number of spontaneous POF cases, provides novel data on associations between the genomic aberrations and premature menopause of ovarian cause and demonstrates that population-based biobanks are powerful source of biological samples and clinical data to reveal novel genetic lesions associated with human reproductive health and disease, including POF.STUDY FUNDING/COMPETING INTERESTThis study was supported by the Estonian Ministry of Education and Research (IUT20-43, IUT20-60, IUT34-16, SF0180027s10 and 9205), Enterprise Estonia (EU30020 and EU48695), Eureka's EUROSTARS programme (NOTED, EU41564), grants from European Union's FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP, SARM, |EU324509) and Ho...

MicroRNAs (miRNAs) are known post-transcriptional regulators of various biological processesincluding ovarian follicle development. We have previously identified miRNAs from human preovulatory ovarian granulosa cells that are expressed from the intronic regions of two key genes in normal follicular development: FSH receptor (FSHR) and CYP19A1, the latter encoding the aromatase enzyme. The present study aims to identify the target genes regulated by these miRNAs: hsa-miR-548ba and hsa-miR-7973, respectively. The miRNAs of interest were transfected into KGN cell line and the gene expression changes were analyzed by Affymetrix microarray. Potential miRNA-regulated genes were further filtered by bioinformatic target prediction algorithms and validated for direct miRNA:mRNA binding by luciferase reporter assay. LIFR, PTEN, NEO1 and SP110 were confirmed as targets for hsa-miR-548ba. Hsa-miR-7973 target genes ADAM19, PXDN and FMNL3 also passed all verification steps. Additionally, the expression pattern of the miRNAs was studied in human primary cumulus granulosa cell culture in relation to the expression of their host genes and fSH stimulation. Based on our findings we propose the involvement of hsa-miR-548ba in the regulation of follicle growth and activation via LIFR and PTEN. Hsa-miR-7973 may be implicated in the modulation of extracellular matrix and cell-cell interactions by regulating the expression of its identified targets.Granulosa cell functions are essential in follicular development, maturation, and atresia. Granulosa cells support oocyte growth via continuous bidirectional communication to ensure oocyte quality and developmental competence. Due to the close communication cumulus (CGC) and mural granulosa cells (MGC) may reflect the characteristics of the oocyte and an understanding of the patterns of expression and functions of miRNAs in those cells may lead to a better understanding of follicle maturation and its dysfunction 1,2 .MicroRNAs (miRNAs) are short non-coding RNA molecules approximately 22 nucleotides in length 3 . MicroRNAs bind to their target mRNA 3′ untranslated region (3′UTR) at sites complementary to the miRNA 5′ seed region. MicroRNA biding to the target gene regulates gene expression by destabilizing the mRNA and/or inhibiting its translation 4 . In a few cases, an increase in gene expression has also been observed 5 .MicroRNAs have key role in the post-transcriptional regulation of various important biological processes, including cell proliferation, differentiation, apoptosis, and hormone biosynthesis and secretion 6 . Functional ovary requires precise coordination of follicle recruitment, selection and ovulation processes. Development of ovarian follicles is a complex process including oocyte maturation, granulosa cell proliferation and differentiation. MicroRNAs expressed in the ovary have regulative roles in ovarian follicle development and the expression of miRNAs in the ovary varies within the specific cell type and function 7 . The overall role of miRNAs in ovarian functions has ...

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited. Here we describe a novel method called Restriction Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables global histone modification profiling from as few as 100 cells. The method is simple, cost-effective and takes a single day to complete. We demonstrate the sensitivity of the method by deriving the first genome-wide maps of histone H3K4me3 and H3K27me3 modifications of inner cell mass and trophectoderm of bovine blastocyst stage embryos.

No abstract