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This Week in Genome Biology: Oct 31, 2018

University of Chicago researchers report on results from a comparative genomic study of endoderm differentiation with induced pluripotent stem cells (iPSC) from humans and chimpanzees. Starting with half a dozen human and four chimp iPSC lines, the team used RNA sequencing to track gene expression and regulation in 32 samples per species, collected over four days as primary streak, endoderm progenitor, and definitive endoderm differentiated. Although species-specific events did occur, the sequence data suggests some 75 percent of genes profiled had comparable regulatory trajectories, including changes in regulatory variation at the transition between certain developmental stages.

A Zhejiang University-led team describes a single-cell sequencing method called Holo-seq that aims to pick up both small RNA and messenger RNAs in individual cells, while addressing complications related to pre-amplification bias and murky strand of origin information. When they used Holo-seq to assess small RNA and mRNA in 32 individual cells from a human hepatocellular carcinoma tumor, for example, the researchers identified a handful of single-cell subpopulations with distinct expression or super-enhancer features.

Researchers from the University of Kent and the University of London introduce new chromosome-level assemblies for three avians: the saker falcon, common budgerigar, and ostrich. After putting the assemblies together with the help of comparative sequence analyses, targeted PCR, and molecular cytogenetics, the team searched for within- and between-chromosome rearrangements in the bird genomes relative to an avian ancestor reference, exploring potential contributions that conserved non-coding elements make to these rearrangements. "We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced," the authors write, noting that the density of these elements was particularly low at fission evolutionary breakpoints and highest at intra-chromosomal evolutionary breakpoints.