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Comparative Epigenomics – A classified approach to functionally annotate genomes

Comparative Epigenomics – A classified approach to functionally annotate genomes

In an article entitled, “Comparative Epigenomic Annotation of Regulatory DNA”, published in June 8, 2012, issue of Cell 149:1381–1392, the lead author Shu Xiao with twelve other associates from five research groups investigated on the evolutionary properties of the mammalian epigenome. The aim of the study was to elucidate co-evolutionary interactions within genomes, transcriptomes (set of all RNA molecules), and epigenomes which consequently showed that comparative epigenomics (the epigenome controls the differential expression of genes in specific cells) can use epigenomic information to functionally annotate genomes. The researchers focused their effort on three species: humans, mice, and pigs. They were able to create an epigenomic map for each by analyzing 9 epigenomic marks in pluripotent stem cells which they could then compare. Their data confirm that the degree of epigenomic conservation is not constantly correlated with the degree of genomic conservation but that epigenomic conservation can yield additional explanation to genomic conservation. Furthermore, the conservation levels of epigenomes are indicative of the conservation levels of gene expression. This suggests that epigenomic conservation may be applied in combination with sequence evaluation to classify absolutely preferred regions to explore functional sequences that make humans distinctive. These conserved epigenetic markers can be successfully employed to annotate the genome, clarifying the genome’s regulatory function. Moreover, the associated evolutionary changes of the epigenome, the transcriptome, and TF binding suggest the functional meaning of the epigenome in mammalian transcription networks (TNs). This may clarify the partial successes in human TN reconstruction using simply the information of DNA sequence motifs and gene expression. [Summarized by the graduate student, Samsad Razzaque]

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