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Nucleic Acids Research Papers on Transcriptome Timing Tool, Transcription Factor Variants, More

Researchers from the University of Wisconsin, Madison, and the University of California, Santa Barbara, present a statistical tool called TimeMeter for tracking temporal gene expression similarities and differences using RNA sequencing data. The team applied TimeMeter to mouse and axolotl models, searching for similar temporal patterns (STP) behind digit tip regeneration in the mouse and blastema differentiation in the axolotl. "Analysis of genes with similar temporal patterns in mouse digit regeneration and axolotl blastema differentiation reveals common gene groups for appendage regeneration," the team notes, "which have potential implications in regenerative medicine."

A pair of investigators from India take a look at transcription factor variants and their consequences for regulatory gene networks in bacteria. Following from prior studies suggesting bacterial transcription factors may be less conserved than target genes in some circumstances, the duo did whole-genome sequencing on naturally-occurring and lab-evolved Escherichia coli isolates, detecting more frequent transcription factor mutations in isolates from certain stages of adaptive evolutionary experiments in the lab. "Extrapolating the dynamics of genetic variation from long-term laboratory evolution to natural populations, we propose that point mutations, conferring large-scale gene expression changes, may drive the early stages of adaptation," they write, "but gene regulation is subjected to stronger purifying selection post adaptation."

Finally, investigators at Cornell University and elsewhere outline a pipeline known as TypeTE, designed to find and genotype insertions stemming from Alu retrotransposons and other mobile elements based on available whole-genome sequence data. The TypeTE appeared to compare favorably to PCR-based methods for genotyping hundreds of mobile element insertion loci in data from the 1000 Genomes Project. Moreover, they note, the strategy "can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics."