Nucleosome deposition and DNA methylation at coding region boundaries

Nucleosomes and methylation have been observed to peak at both ends of protein coding units in a genome-wide survey

A Novel Technique of Morcellation Using a Pneumovesicum After Holmium Laser Enucleation of the Prostate in Complicated Situations: Our Initial Experience and Tips

Purpose To describe our initial experience with a novel method of adenoma retrieval using a pneumovesicum (PNV) after Holmium laser enucleation of the prostate (HoLEP). Methods From January 2016 to April 2018, a total of 93 consecutive patients treated with HoLEP were enrolled in this study. For tissue morcellation, we used the PNV morcellation technique for an initial series of 21 patients and the conventional technique (Lumenis VersaCut) for a consecutive series of 72 patients. We compared efficiency and safety between the novel technique and the traditional technique. Subgroup analysis was performed to assess the effectiveness of the current technique in the large prostate (>70 mL). Results There were significant differences in mean age and prostate volume between the 2 groups. However, there were no significant differences in the baseline characteristics and preoperative parameters in the subgroup analysis of large prostates (>70 mL). The mean morcellation efficiency was higher (8.50±1.94 minutes vs. 1.76±0.45 minutes, P<0.05) and the time of morcellation (7.81±1.25 minutes vs. 34.04±11.14 minutes, P<0.05) was shorter in the PNV group. Moreover, there were no significant differences between groups in hospitalization period (2.62±1.10 days vs. 2.90±1.26 days, P=0.852) and any other postoperative events, including recatheterization, reoperation, clot retention, and urethral stricture (P-value range, 0.194–0.447). In the PNV group, there were some cases of procedure-related complications, including postoperative extravesical leakage (5th case), clot retention (8th case), and recatheterization (9th case). Conclusions This method has a higher tissue retrieval efficacy, with the advantage of excellent visibility compared to conventional morcellation. The current method can be applied when a transurethral morcellator is out of order or cannot be used

Data of methylome and transcriptome derived from human dilated cardiomyopathy

AbstractAlterations in DNA methylation and gene expression have been implicated in the development of human dilated cardiomyopathy (DCM). Differentially methylated probes (DMPs) and differentially expressed genes (DEGs) were identified between the left ventricle (LV, a pathological locus for DCM) and the right ventricle (RV, a proxy for normal hearts). The data in this DiB are for supporting our report entitled “Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy” (Bong-Seok Jo, In-Uk Koh, Jae-Bum Bae, Ho-Yeong Yu, Eun-Seok Jeon, Hae-Young Lee, Jae-Joong Kim, Murim Choi, Sun Shim Choi, 2016) [1]

Identification of DNA methylation changes associated with human gastric cancer

<p>Abstract</p> <p>Background</p> <p>Epigenetic alteration of gene expression is a common event in human cancer. DNA methylation is a well-known epigenetic process, but verifying the exact nature of epigenetic changes associated with cancer remains difficult.</p> <p>Methods</p> <p>We profiled the methylome of human gastric cancer tissue at 50-bp resolution using a methylated DNA enrichment technique (methylated CpG island recovery assay) in combination with a genome analyzer and a new normalization algorithm.</p> <p>Results</p> <p>We were able to gain a comprehensive view of promoters with various CpG densities, including CpG Islands (CGIs), transcript bodies, and various repeat classes. We found that gastric cancer was associated with hypermethylation of 5' CGIs and the 5'-end of coding exons as well as hypomethylation of repeat elements, such as short interspersed nuclear elements and the composite element SVA. Hypermethylation of 5' CGIs was significantly correlated with downregulation of associated genes, such as those in the <it>HOX </it>and histone gene families. We also discovered long-range epigenetic silencing (LRES) regions in gastric cancer tissue and identified several hypermethylated genes (<it>MDM2</it>, <it>DYRK2</it>, and <it>LYZ</it>) within these regions. The methylation status of CGIs and gene annotation elements in metastatic lymph nodes was intermediate between normal and cancerous tissue, indicating that methylation of specific genes is gradually increased in cancerous tissue.</p> <p>Conclusions</p> <p>Our findings will provide valuable data for future analysis of CpG methylation patterns, useful markers for the diagnosis of stomach cancer, as well as a new analysis method for clinical epigenomics investigations.</p