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This Week in Genome Research: Mar 17, 2010

In Genome Research this week, researchers in Austria and the US review the practice of inferring population genetics from genome sequence variation. The authors review the challenges of analyzing whole-genome sequence polymorphism data, and "discuss the potential of these data to yield new insights concerning population history and the genomic prevalence of natural selection." They suggest that, since the costs of next-generation sequencing have fallen and computational analysis methods have improved, population genetics studies will become increasingly common in several organisms.

Researchers from various branches of the National Institutes of Health and from the University of Chicago report their method for the genome-wide discovery of human heart enhancers this week. In their paper, the authors describe a "strategy to systematically identify tissue-specific cis-regulatory elements that share combinations of sequence motifs." Using heart development as a model, the team was able to distinguish heart enhancers from a pool of random, non-coding sequences. The authors suggest that their results support the existence of cis-regulatory codes which dictate tissue-specific transcription in mammalian genomes.

In an advance, online publication of Genome Research this week, a pair of investigators at Penn State University report that Alu and L1 densities have been influenced by the integration of distinct local genome landscapes and the evolutionary dynamics of sex chromosomes in primates. To decipher this, the authors used a multiple regression framework and analyzed the chromosome versus autosome transposable element densitites. They found that sex-chromosome bias causes Alu to be preferentially integrated in the male germline.

In another preprint this week, an international research team reports that "age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer." In their analysis of the methylation status of more than 27,000 CpGs mapping to promoters of nearly 14,000 genes in human blood samples, they show that stem cell polycomb group protein target genes are "far more likely to become methylated with age than non-targets." They also identified a subset of 69 PCGT CpGs that undergo hypermethylation with age; the team writes that the "age-PCGT methylation signature is present in preneoplastic conditions and may drive gene expression changes associated with carcinogenesis."

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.