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This Week in Genome Research: Jan 31, 2018

Researchers from Yonsei University and other centers in Korea search for guide RNAs to target specific KRAS mutations in cancer cells using the CRISPR-Cas9 genome-editing approach. After screening for effective KRAS-editing guide RNAs in a cell line containing a fluorescent reporter system, the team validated the most promising guide RNAs in cancer cell lines with wild type KRAS or versions of the gene containing mutations of interest. The authors note that successful KRAS mutation editing appeared to curb tumor growth to some extent, both in the cell line system and in tumor-bearing immunodeficient mice.

Investigators from the UK and Portugal explore the consequences of deleting a portion of the mouse genome that contains a 170,000 base array of long interspersed element (LINE-1) — one of many LINE arrays larger than 100,000 bases that they uncovered while scrutinizing the mouse genome. Although the LINE-1 array fell in a chromosome 12 region previously implicated in imprinting, the team did not detect phenotypic changes or imprinting after deleting one or both copies of the array in mouse moms or dads. "Our findings suggest that [the] presence of a 170kn LINE-1 array reflects the tolerance of the site for repeat insertion rather than an important genomic function in normal development," they write.

Finally, a Carnegie Mellon University-led team takes a look at methods for modeling organ development from single-cell RNA sequencing data, focusing on lung epithelial growth and differentiation in a mouse animal model. "We developed a new method which learns a probabilistic model for constructing regulatory networks from single cell time series expression data," the researchers say. For their proof-of-principle analysis, they used this approach to track mouse lung development based on available gene expression data for more than 150 individual mouse embryonic cells profiled at different stages of lung development.