Computational Analysis of Cancer Epigenome and Transcriptome
Conference Recording May 28, 2013
About the Speaker
Dr. Kaifu Chen has extensive experiences in genome sequencing and analysis during his PhD training in the Beijing Institute of Genomics. He thenjoined the Wei Li lab at Baylor College of Medicine in 2009 as a postdoctoral fellow, with research focusing on bioinformatics in epigenomics. Dr. Kaifu Chen has been collaborating with dozens of labs on analyzing whole-genome profiling of nucleosomes, histone modifications, transcription factors, DNA repair machinery, as well as many other chromatin proteins. He is the major developer of the bioinformatics software DANPOS.Abstract
All Eukaryotic cells divide a finite number of times, termed replicative aging. Replicative aging in Saccharomyces cerevisiae is accompanied by decreased total histone protein levels. While genome profiling based on high throughput sequencing shows that nucleosome occupancy decreases 50% during replicative aging. Most nucleosome positions are maintained during aging although their positioning becomes fuzzier, while other nucleosomes move to sequences predicted to better accommodate histone octamers. Transcriptome analysis reveals that all yeast genes are induced during aging, while genes that are repressed in young cells are most induced, due to loss of unique nucleosome positioning patterns in promoters. Contrary to the loss of mitochondrial function during aging, mitochondrial DNA content increases significantly. Unprecedented levels of large-scale chromosomal alterations and increased retrotransposition were also observed during aging.