In Nucleic Acids Research this week, Prathima Iengar from the Indian Institute of Science in Bangalore discusses substitutions and indels in cancer genes. She analyzed such cancer-related mutations found in the COSMIC database and found that "the most frequent substitutions were c→t, g→a, g→t, and the most frequent codon changes were to termination codons." In addition, she notes that deletions are more common than insertions and most indels cause frameshifts. "The study examines, at the nt level, the variety and preferred kinds of mutations that occur over the time-scale of cancer," Iengar writes. "It is hoped that the study will add perspective, in the effort to understand cancer mutations."
Also in Nucleic Acids Research, researchers led by Bruce Howard at the Eunice Kennedy Shriver National Institute of Child Health and Human Development report on their evaluation of genomic regions that undergo post-natal or age-related changes to their methylation patterns. Using MeDIP-Seq, they compared methylation patterns found in cord blood from newborns to those found in peripheral blood samples from adults. "Regions of interest that emerged from the analysis included tandem or interspersed-tandem gene sequence repeats (PCDHG, FAM90A, HRNR, ECEL1P2), and genes with strong homology to other family members elsewhere in the genome (FZD1, FZD7 and FGF17)," Howard and his colleagues write. "Our results raise the possibility that selected gene sequences with highly homologous copies may serve to facilitate, perhaps even provide a clock-like function for, developmental and age-related epigenome remodeling."
Finally, University of Copenhagen researchers say that they have sequenced about 99 percent of the three unfinished sequence gaps of human chromosome 20 using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing, and chromatin, methylation, and expression analyses. They found that the gaps contained conserved non-coding RNAs and five novel CPG islands, among other characteristics. "Our study shows that unfinished euchromatic gaps in the human genome may harbor specific epigenetic domains and contain conserved genomic elements with regulatory potential, including differentially methylated CpG-islands and other functional elements, as well as ncRNA genes, the function of which is now open for further study," the researchers add.