Genome-wide DNA methylation profiling of the regenerative MRL/MpJ mouse and two normal strains.

Aim: We aimed to identify the pivotal differences in the DNA methylation profiles between the regeneration capable MRL/MpJ mouse and reference mouse strains.

Materials & Methods: Global DNA methylation profiling was performed in ear pinnae, bone marrow, spleen, liver and heart from uninjured adult females of the MRL/MpJ and C57BL/6J and BALB/c.

Results & Conclusion: A number of differentially methylated regions (DMRs) distinguishing between the MRL/MpJ mouse and both references were identified.

The methylome and transcriptome of fetal skin: implications for scarless healing.

Aim: Fetal skin is known to heal without scarring. In mice, the phenomenon is observed until the 16-17 day of gestation - the day of transition from scarless to normal healing. The study aims to identify key methylome and transcriptome changes following the transition.

Molecular bases of aberrant miR-182 expression in ovarian cancer.

The molecular bases of miR-182 deregulation in epithelial ovarian cancers (EOCs) remain unknown and its diagnostic or prognostic role in EOCs is still unclear. We performed miR-182 expression analysis using a microarray approach and real-time PCR (qPCR). We also used array comparative genomic hybridization and methylated DNA immunoprecipitation to study copy number changes and methylation aberrations within coding locus/promoter sequences of miR-182 in EOC tissues, respectively.

Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse.

Background: The MRL/MpJ mouse is a laboratory inbred strain known for regenerative abilities which are manifested by scarless closure of ear pinna punch holes. Enhanced healing responses have been reported in other organs. A remarkable feature of the strain is that the adult MRL/MpJ mouse retains several embryonic biochemical characteristics, including increased expression of stem cell markers.

Concurrent DNA Copy-Number Alterations and Mutations in Genes Related to Maintenance of Genome Stability in Uninvolved Mammary Glandular Tissue from Breast Cancer Patients.

Somatic mosaicism for DNA copy-number alterations (SMC-CNAs) is defined as gain or loss of chromosomal segments in somatic cells within a single organism. As cells harboring SMC-CNAs can undergo clonal expansion, it has been proposed that SMC-CNAs may contribute to the predisposition of these cells to genetic disease including cancer. Herein, the gross genomic alterations (>500 kbp) were characterized in uninvolved mammary glandular tissue from 59 breast cancer patients and matched samples of primary tumors and lymph node metastases.

Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells.

Background: Signal transducer and activator of transcription 3 (STAT3) is constitutively activated in many human tumors, including gliomas, and regulates the expression of genes implicated in proliferation, survival, apoptosis, angiogenesis and immune regulation. Only a small fraction of those genes has been proven to be direct STAT3 targets. In gliomas, STAT3 can play tumor suppressive or oncogenic roles depending on the tumor genetic background with target genes being largely unknown.

The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia.

Unlabelled: Most neurological diseases are associated with chronic inflammation initiated by the activation of microglia, which produce cytotoxic and inflammatory factors. Signal transducers and activators of transcription (STATs) are potent regulators of gene expression but contribution of particular STAT to inflammatory gene expression and STAT-dependent transcriptional networks underlying brain inflammation need to be identified. In the present study, we investigated the genomic distribution of Stat binding sites and the role of Stats in the gene expression in lipopolysaccharide (LPS)-activated primary microglial cultures.

Epigenetic basis of regeneration: analysis of genomic DNA methylation profiles in the MRL/MpJ mouse.

Epigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. To investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration known to exhibit enhanced regeneration response in different organs. We report the comparative analysis of genomic DNA methylation profiles of the MRL/MpJ and the control C57BL/6J mouse.

A genome-wide transcriptional profiling of sporulating Bacillus subtilis strain lacking PrpE protein phosphatase.

The sporulation process is a complex genetic developmental program leading to profound changes in global gene expression profile. In this work, we have applied genome-wide microarray approach for transcriptional profiling of Bacillus subtilis strain lacking a gene coding for PrpE protein phosphatase. This protein was previously shown to be involved in the regulation of germination of B.

Regeneration of comparative genomic hybridization oligonucleotide microarrays with dimethylurea.

Reuse of materials in DNA hybridization-based methods has been known since the advent of Southern membranes. Array-based comparative genomic hybridization is essentially Southern hybridization with multiple probes immobilized on a solid surface. We show that comparative genomic hybridization microarrays fabricated with maskless array synthesizer technology can be used up to four times with the application of 1,3-dimethylurea as an array-stripping agent.

Age-related somatic structural changes in the nuclear genome of human blood cells.

Structural variations are among the most frequent interindividual genetic differences in the human genome. The frequency and distribution of de novo somatic structural variants in normal cells is, however, poorly explored. Using age-stratified cohorts of 318 monozygotic (MZ) twins and 296 single-born subjects, we describe age-related accumulation of copy-number variation in the nuclear genomes in vivo and frequency changes for both megabase- and kilobase-range variants.