Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation

<p>Heterogeneity of DNA methylation status among alleles is observed in various cell types and is involved in epigenetic gene regulation and cancer biology. However, the individual methylation profile within each allele has not yet been examined at the whole-genome level. In the present study, we applied linkage disequilibrium analysis to the DNA methylation data obtained from whole-genome bisulfite sequencing studies in mouse germline and other types of cells. We found that the methylation status of 2 consecutive CpG sites showed deviation from equilibrium frequency toward concordant linkage (both methylated or both unmethylated) in germline cells. In the imprinting loci where methylation of constituent alleles is known, our analysis detected the deviation toward the concordant linkage as expected. In addition, we applied this analysis to the transitional zone between methylated and unmethylated regions and to the cells undergoing epigenetic reprogramming. In both cases, deviation to the concordant-linked alleles was conspicuous, indicating that the methylation pattern is not random but rather concordant within each allele. These results will provide the key to understanding the mechanism underlying allelic heterogeneity.</p

Synthesis of Cyclic 1‑Alkenylboronates via Zr-Mediated Double Functionalization of Alkynylboronates and Sequential Ru-Catalyzed Ring-Closing Olefin Metathesis

Synthesis of novel cyclic 1-alkenylboronates is accomplished through the zirconium-mediated regio- and stereoselective double functionalization of 1-alkynylboronates and the subsequent ruthenium-catalyzed ring-closing metathesis (RCM). The obtained substituted cyclic 1-alkenylboronates are transformed into <i>o</i>-terphenyl and triphenylene derivatives

Additional file 1: of Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat

Table S1. Summary statistics for SNV and INDEL in various depths. Figure S1. Sequence coverage of the target regions for each rat strain. Figure S2. Number of homozygous SNVs identified in WTC/Kyo and PVG/Seac strains for each genomic region. Figure S3. Proportion of the number of SNVs in terms of the each class of regions in the target, i.e., CDS, UTR, CNS, and other regions, for each rat strain. Figure S4. The relationship between the phastCons conservation score and SNV density for each rat strain. (PDF 215 kb

Sema3E, but not Sema3A or -3B, exerted inhibitory actions on growing vdINVP.

<p>Transverse sections were prepared from highlighter ink-infused embryos. (A) Control electroporation with EGFP. Arrow shows vdINVP. (B) Electroporation with <i>Sema3E</i> inhibited INVP (arrowhead). (C, D) In situ hybridization for <i>Sema3E</i> mRNA in spinal cord at E4 (HH22). Motor columns were positive. (E, F) Electroporation with <i>Sema3A</i> or <i>Sema3B</i> yielded no effects on vdINVP formation (arrows). (G, H) <i>VEGF+EGFP</i>, or <i>VEGF+Sema3E</i> were electroporated into the neural tube. <i>Sema3E</i>-overexpression neutralized VEGF-induced hypervascularization of vdINVP (arrowhead in H). Except C and D, specimens were of E5/HH26 subjected to confocal microscopy for Z-stack of 70 μm thick. Top and bottom panels are identical views. Scale bars: 100 μm.</p

Implantation with VEGF-producing cells into the lumen of neural tube resulted in hemorrhage.

<p>(A) Experimental design showing that an aggregate of VEGF-producing COS cells was implanted into an E2 (HH14) embryo, which was harvested at E5/HH26. Production of VEGF was controlled by the tet-on system so that the expression started at E3 (HH18) by Dox administration. (B, C) Implanted VEGF-COS cells (yellow arrow in C) caused invasion of vdINVP into the progenitor zone (white arrows in C), whereas control COS cells (yellow arrow in B) yielded no effects. (D) Tuj-1 staining showed no gross effects on neural differentiation by VEGF-COS cells (yellow arrow in D). White arrows show ink-infused vdINVP in the progenitor zone. (E, F) Implanted VEGF-COS cells caused hemorrhage (arrow in F), whereas control COS cells yielded no effects (E). Scale bars: 100 μm.</p

mRNA expression patterns of <i>VEGF, VEGFR2</i>, and <i>FLT-1/VEGFR1</i> in growing vdINVP analyzed by section in situ hybridization.

<p>(A) <i>VEGF</i> mRNA. (B) <i>VEGFR2</i> mRNA. (C) <i>FLT-1/VEGFR1</i> mRNA. Probe I was prepared from <i>soluble FLT-1</i>, and probes II and -III detecting cytoplasmic region were from full length (fl) <i>FLT-1</i> cDNA. (D-K) Except F and G, which were of long coloration time to detect digoxigenin (5 days), coloration was terminated after 3 days. Probe I antisense yielded signals in INVP (D). Faint signals in the progenitor zone in F appears to be a noise since the sense probe also gave similar staining (G). Probes II and -III failed to give signals (H-K). Specimens are transverse sections of chicken spinal cord at E5/HH26.</p

Supple Fig:Table.pdf

This item contains supplementary figures and table of a manuscript 'Possible regulation of steroidogenic gene independent of Ad4BP/SF-1 (NR5A1)'