Global Transcriptome Profiling of Genes that Are Differentially Regulated During Differentiation of Mouse Embryonic Neural Stem Cells into Astrocytes
JOURNAL OF MOLECULAR NEUROSCIENCE
Authors: Han, Dalmuri; Choi, Mi Ran; Jung, Kyoung Hwa; Kim, Namshin; Kim, Se Kye; Chai, Jin Choul; Lee, Young Seek; Chai, Young Gyu
Abstract
Many genes are associated with the differentiation of neural stem cells (NSCs) into astrocytes, the most abundant and functionally diverse population of glial cells in the central nervous system, particularly in the brain. In the present study, we differentiated NSCs from the forebrain of embryonic day 14.5 mouse embryos into astrocytes over 1 and 7 days. We identified transcriptomes of NSCs and astrocytes using RNA sequencing and analyzed enriched gene networks, signal pathways, and ontology. To identify important regulators of differentiation, we performed gene clustering according to expression patterns and promoter CG types. Our data show that genes related to system development, including Fbln2, Bcan, Ncam1, Itih3, Tnr, and Vcan, regulate NSC differentiation through WNT/beta-catenin and epithelial to mesenchymal transition pathways. We identified many CG-rich promoter genes related to basic cellular maintenance such as transcription, translation, and structural components and CG-poor promoter genes that are highly associated with cell-type-specific functions or play important roles during development. Our study provides a foundation for further research on NSC differentiation and the future application of stem cells.
The Relationship Between DNA Methylation in Key Region and the Differential Expressions of Genes in Human Breast Tumor Tissue
DNA AND CELL BIOLOGY
Authors: Jin, Wen; Li, Qian-Zhong; Zuo, Yong-Chun; Cao, Yan-Ni; Zhang, Lu-Qiang; Hou, Rui; Su, Wen-Xia
Abstract
Breast cancer has a high mortality rate for females. Aberrant DNA methylation plays a crucial role in the occurrence and progression of breast carcinoma. By comparing DNA methylation differences between tumor breast tissue and normal breast tissue, we calculate and analyze the distributions of the hyper- and hypomethylation sites in different function regions. Results indicate that enhancer regions are often hypomethylated in breast cancer. CpG islands (CGIs) are mainly hypermethylated, while the flanking CGI (shores and shelves) is more easily hypomethylated. The hypomethylation in gene body region is related to the upregulation of gene expression, and the hypomethylation of enhancer regions is closely associated with gene expression upregulation in breast cancer. Some key hypomethylation sites in enhancer regions and key hypermethylation sites in CGIs for regulating key genes are, respectively, found, such as oncogenes ESR1 and ERBB2 and tumor suppressor genes FBLN2, CEBPA, and FAT4. This suggests that the recognizing methylation status of these genes will be useful for the diagnosis of breast cancer.