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Genome Research Papers on Cryptosporidium, Mobile Element Insertions, Hirschsprung Disease

A team from the US and Australia presents findings from a sequencing and comparative genomics study of Cryptosporidium, which can infect waterways and lead to a diarrheal disease called cryptosporidiosis. With two long-read sequencing technologies, the researchers put together a new reference genome assembly for C. parvum, comparing it with C. hominis and C. tyzzeri sequences to find new coding and non-coding sequences, genetic variants, gene orthologs, and genes under positive selection. "[T]his systematic study reveals that the primary differences between the zoonotic C. parvum, the anthroponotic C. hominis, and the rodent-infecting C. tyzzeri are [single-nucleotide variants] and CNVs rather than differences in unique gene content," they write, noting that "within parasite and/or within population sub-telomeric amplification, and variation events in C. parvum reveal a new level of genome plasticity that will complicate some genetic manipulations and may affect the organisms' phenotype."

University of Maryland researchers report on endogenous mobile elements contributing to mutagenesis in tens of thousands of human whole-genome or exome sequences. Using a "mobile element locator tool" (MELT) and an updated, more scalable version of the tool known as CloudMELT, the team unearthed 104,230 distinct mobile element insertions in 57,919 genomes or exomes, and explored mobilization-promoting source elements such as L1, mobile element distributions in the population, and their potential mutagenic effects. "Our study provides new insights on the L1 source elements that drive [mobile element insertion] mutagenesis," the authors report, "and brings forth a better understanding of how this mutagenesis impacts human genomes."

Finally, investigators at New York University, Johns Hopkins University, and the University of Texas Health Science Center at Houston describe potential contributors to Hirschsprung disease, a congenital colon condition previously linked to several cis-regulatory elements that impact the RET receptor tyrosine kinase enzyme-coding gene. The team turned to small-interfering RNA, chromatin immunoprecipitation sequencing, and CRISPR-Cas9-based gene deletion experiments to search for additional Hirschsprung disease-associated variants that fall in regulatory elements influencing RET gene expression. Based on their findings, the authors suggest that "common sequence variants in at least 10 RET enhancer affect [Hirschsprung disease] risk …extending the known RET-EDNRB [gene regulatory network] to reveal an extensive regulatory code modulating disease risk at a single gene."