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This Week in Genome Research: Jan 6, 2010

In the advance, online edition of Genome Research, a group of investigators from Japan, Australia, and the UK came up with methods to account for the cross-mapping of an RNA sequences to incorrect loci. By analyzing small RNA high-throughput sequencing libraries using this correction, the team found evidence that mature miRNA editing occurs only rarely in animals.

David MacAlpine and his Duke University team evaluated the genome-wide origin recognition complex or ORC distribution patterns in Drosophila. They found that the DNA replication initiation factor localizes to parts of the chromosome that correspond to open chromatin — and that this ORC binding may be needed for subsequent cohesin complex loading in fruit flies.

An American, Australian, and Canadian research team investigated the role that replication timing plays in mouse embryonic stem cell differentiation by coming up with genome-wide replication-timing profiles for nearly two dozen mouse cell lines at ten early development stages and assessing transcription at seven of these developmental stages. The researchers found cell-type specific replication profiles and came up with what they call a "comprehensive 'fate map' of replication-timing changes during early mouse development."

National Institutes of Health researchers Yabin Guo and Henry Levin used high-throughput pyrosequencing to sequence retrotransposon insertion sites in the fission yeast Schizosaccharomyces pombe. Their results suggest the long terminal repeat retrotransposon Tf1 targets RNA polymerase II transcribed gene promoters — especially promoters that respond to stress. "This targeting of stress response genes coupled with the ability of Tf1 to regulate the expression of adjacent genes suggests Tf1 may improve the survival of S. pombe when cells are exposed to environmental stress," the duo writes.

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.