Maize abnormal chromosome 10 (Ab10) encodes a classic example of true meiotic drive that converts heterochromatic regions called knobs into motile neocentromeres that are preferentially transmitted ...to egg cells. Here, we identify a cluster of eight genes on Ab10, called the Kinesin driver (Kindr) complex, that are required for both neocentromere motility and preferential transmission. Two meiotic drive mutants that lack neocentromere activity proved to be kindr epimutants with increased DNA methylation across the entire gene cluster. RNAi of Kindr induced a third epimutant and corresponding loss of meiotic drive. Kinesin gliding assays and immunolocalization revealed that KINDR is a functional minus-end-directed kinesin that localizes specifically to knobs containing 180 bp repeats. Sequence comparisons suggest that Kindr diverged from a Kinesin-14A ancestor ∼12 mya and has driven the accumulation of > 500 Mb of knob repeats and affected the segregation of thousands of genes linked to knobs on all 10 chromosomes.
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•A kinesin moves maize neocentromeres along spindles to cause meiotic drive•The causal gene (Kindr) has multiple copies on abnormal chromosome 10•Meiotic drive mutants are epimutants that repress all Kindr copies•KINDR is active in vitro and localizes in vivo to knobs containing 180 bp DNA repeats
Neocentromere activity in maize relies on a kinesin motor to drive non-Mendelian inheritance.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
DNA methylation is thought to be an important determinant of human phenotypic variation, but its inherent cell type specificity has impeded progress on this question. At exceptional genomic regions, ...interindividual variation in DNA methylation occurs systemically. Like genetic variants, systemic interindividual epigenetic variants are stable, can influence phenotype, and can be assessed in any easily biopsiable DNA sample. We describe an unbiased screen for human genomic regions at which interindividual variation in DNA methylation is not tissue-specific.
For each of 10 donors from the NIH Genotype-Tissue Expression (GTEx) program, CpG methylation is measured by deep whole-genome bisulfite sequencing of genomic DNA from tissues representing the three germ layer lineages: thyroid (endoderm), heart (mesoderm), and brain (ectoderm). We develop a computational algorithm to identify genomic regions at which interindividual variation in DNA methylation is consistent across all three lineages. This approach identifies 9926 correlated regions of systemic interindividual variation (CoRSIVs). These regions, comprising just 0.1% of the human genome, are inter-correlated over long genomic distances, associated with transposable elements and subtelomeric regions, conserved across diverse human ethnic groups, sensitive to periconceptional environment, and associated with genes implicated in a broad range of human disorders and phenotypes. CoRSIV methylation in one tissue can predict expression of associated genes in other tissues.
In addition to charting a previously unexplored molecular level of human individuality, this atlas of human CoRSIVs provides a resource for future population-based investigations into how interindividual epigenetic variation modulates risk of disease.
The epigenome is multidimensional, with individual molecular components operating on different levels to control transcriptional output. Techniques that combine measurements of these features can ...reveal their precise correspondence in genomic space, or temporal connectivity, to better understand how they jointly regulate genes. ATAC-Me is an integrated method to probe DNA methylation and chromatin accessibility from a single DNA fragment library. Intact nuclei undergo Tn5 transposition to isolate DNA fragments within nucleosome-free regions. Isolated fragments are exposed to sodium bisulfite before library amplification and sequencing. A typical ATAC-Me experiment detects ~60,000-75,000 peak regions (P < 0.05), covering ~3-4 million CpG sites with at least 5× coverage. These sites display a range of methylation values depending on the cellular and genomic context. The approach is well suited for time course studies that aim to capture chromatin and DNA methylation dynamics in tandem during cellular differentiation. The protocol is completed in 2 d with standard molecular biology equipment and expertise. Analysis of resulting data uses publicly available software requiring basic bioinformatics skills to interpret results.
Genetic models suggested that SMARCA5 was required for DNA-templated events including transcription, DNA replication, and DNA repair. We engineered a degron tag into the endogenous alleles of ...SMARCA5, a catalytic component of the imitation switch complexes in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6 h of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
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•Target-specific protein degradation of endogenous human SMARCA5•Degradation of SMARCA5 leads to a rapid loss in CTCF DNA binding•SMARCA5 regulates nucleosome repeat length independent of the cell cycle•CTCF and SMARCA5 co-localize at H2A.Z-containing sites
Bomber et al. utilize degron tagging of the endogenous human chromatin-remodeling enzyme SMARCA5, coupled with a multi-omics approach, to define the requirements for SMARCA5-mediated nucleosome sliding. SMARCA5 co-localized with H2A.Z and CTCF and was required for CTCF DNA binding, nucleosomal phasing at these sites, and maintaining nucleosome repeat length.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
DNA methylation of enhancers is dynamic, cell-type specific, and vital for cell fate progression. However, current models inadequately define its role within the hierarchy of gene regulation. ...Analysis of independent datasets shows an unanticipated overlap between DNA methylation and chromatin accessibility at enhancers of steady-state stem cells, suggesting that these two opposing features might exist concurrently. To define their temporal relationship, we developed ATAC-Me, which probes accessibility and methylation from single DNA library preparations. We identified waves of accessibility occurring rapidly across thousands of myeloid enhancers in a monocyte-to-macrophage cell fate model. Prolonged methylation states were observed at a majority of these sites, while transcription of nearby genes tracked closely with accessibility. ATAC-Me uncovers a significant disconnect between chromatin accessibility, DNA methylation status, and gene activity. This unexpected observation highlights the value of ATAC-Me in constructing precise molecular timelines for understanding the role of DNA methylation in gene regulation.
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•ATAC-Me simultaneously measures chromatin accessibility and DNA methylation (DNAme)•Enhancer accessibility and DNAme change independently during cell fate transitions•Loss of DNAme is delayed in nascent open chromatin regions•Transcriptional changes track with new enhancer accessibility despite prolonged DNAme
Barnett et al. describe ATAC-Me, an approach that captures chromatin accessibility and DNA methylation simultaneously from a single DNA fragment library. ATAC-Me was used to probe temporal relationships between epigenetic and gene regulatory changes at enhancers during myeloid differentiation of THP1 monocytes, revealing a decoupling of chromatin and DNA methylation changes at transitioning enhancers.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Histone deacetylase 3 (HDAC3) is the catalytic component of NCoR/SMRT corepressor complexes that mediate the actions of transcription factors implicated in the regulation of B-cell development and ...function. We crossed Hdac3 conditional knockout mice with Mb1-Cre knockin animals to delete Hdac3 in early progenitor B cells. The spleens of Hdac3F/− Mb1-Cre+/−
mice were virtually devoid of mature B cells, and B220⁺CD43⁺ B-cell progenitors accumulated within the bone marrow. Quantitative deep sequencing of the Ig heavy chain locus from B220⁺CD43⁺ populations identified a defect in VHDJH
recombination with a severe reduction in productive rearrangements, which directly corresponded to the loss of pre-B cells from Hdac3Δ/−
bone marrow. For Hdac3Δ/−
B cells that did show productive VDJ rearrangement, there was significant skewing toward the incorporation of proximal VH
gene segments and a corresponding reduction in distal VH
gene segment use. Although transcriptional effects within these loci were modest, Hdac3Δ/−
progenitor cells displayed global changes in chromatin structure that likely hindered effective distal V-DJ recombination. Reintroduction of wild-type Hdac3 restored normal B-cell development, whereas an Hdac3 point mutant lacking deacetylase activity failed to complement this defect. Thus, the deacetylase activity of Hdac3 is required for the generation of mature B cells.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Hysterectomy is the most common gynecologic surgical procedure performed in the United States. Although most hysterectomies proceed without incident, complications with serious consequences may ...occur. This chapter reviews the incidence, predisposing factors, intraoperative risk, diagnosis, and management and prevention of complications of hysterectomy. These include hemorrhage, infection, thromboembolism, injury to viscera, and neuropathy. The prepared surgeon is familiar with anatomy, surgical risk factors, current recommendations for prophylaxis and prevention, as well as modern management of complications of hysterectomy.
Background
Early childhood (0–3 years) is a critical period for obesity prevention, when tendencies in eating behaviors and physical activity are established. Yet, little is understood about how the ...environment shapes children's genetic predisposition for these behaviors during this time. The Baylor Infant Twin Study (BITS) is a two phase study, initiated to study obesity risk factors from infancy. Data collection has been completed for Phase 1 in which three sub‐studies pilot central measures for Phase 2. A novel infant temperament assessment, based on observations made by trained researchers was piloted in Behavior Observation Pilot Protocol (BOPP) study, a new device for measuring infant feeding parameters (the “orometer”) in the Baylor Infant Orometer (BIO), and methods for analyzing DNA methylation in twins of unknown chorionicity in EpiTwin.
Methods
EpiTwin was a cross‐sectional study of neonatal twins, while up to three study visits occurred for the other studies, at 4‐ (BOPP, BIO), 6‐ (BOPP), and 12‐ (BOPP, BIO) of age. Measurements for BOPP and BIO included temperament observations, feeding observations, and body composition assessments while EpiTwin focused on collecting samples of hair, urine, nails, and blood for quantifying methylation levels at 10 metastable epialleles. Additional data collected include demographic information, zygosity, chorionicity, and questionnaire‐based measures of infant behaviors.
Results
Recruitment for all three studies was completed in early 2020. EpiTwin recruited 80 twin pairs (50% monochorionic), 31 twin pairs completed the BOPP protocol, and 68 singleton infants participated in BIO.
Conclusions
The psychometric properties of the data from all three studies are being analyzed currently. The resulting findings will inform the development of the full BITS protocol, with the goal of completing assessments at 4‐, 6‐, 12‐, and 14‐month of age for 400 twin pairs.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Hysteroscopic sterilization is growing in popularity. Nearly 500,000 women have been sterilized using this method, and an increasing number of physicians are now performing this procedure in the ...office setting. The office setting can provide a cost-effective, convenient, and safe environment for hysteroscopic sterilization. Patients may benefit from avoiding hospital preoperative visits, excessive laboratory evaluation, operating room wait times, and expense associated with hospital care. Physicians may improve productivity through remaining in their office or avoiding operating room delays. This article reviews office-hysteroscopic sterilization with the Essure microinsert system.
Objective: To determine the usefulness of salivary E
2 and progesterone for noninvasive assessment of ovarian function.
Design: Prospective study of salivary hormone levels in women planning a ...pregnancy.
Setting: Department of Obstetrics and Gynecology at Northwestern University Medical School in Chicago, Illinois.
Patient(s): Fourteen women aged 23–39 years with regular menstrual cycles who were planning a pregnancy.
Intervention(s): None.
Main Outcome Measure(s): Salivary estradiol and progesterone concentrations.
Result(s): The sensitivity of the E
2 assay is 2.0 pmol/L; the interassay coefficient of variation was 5.2% (mean value 17 pmol/L). Recovery of E
2 added to saliva was 106%. The correlation with simultaneous serum samples was 0.71. Menstrual cycle patterns contained a preovulatory depression and a midcycle surge. By comparison with nonconception cycles, the luteal phases of conception cycles had significantly elevated salivary E
2 within the first 5 days after ovulation. Salivary progesterone was significantly elevated but not until 10 days after ovulation.
Conclusion(s): Salivary measurements of E
2 and progesterone can be used as noninvasive methods for assessment of ovarian function. Salivary specimens can be collected at home and brought to the laboratory for analysis, obviating the need for frequent phlebotomy. The sensitivity and precision of the salivary E
2 assay make it comparable with assays of serum E
2 for assessing changes in hormone levels.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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