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This Week in Genome Research: Sep 30, 2009

In Genome Research this week, NHGRI's Gary Temple details the progress of the Mammalian Gene Collection, an effort to clone every human and mouse gene with a RefSeq transcript and at least 6,200 rat genes. Scientists used directed RT-PCR cloning and DNA synthesis to clone 92 percent of human and 89 percent of mouse genes with RefSeq transcripts, in addition to more than 6,300 rat genes.

Gerald Schumann at the Paul-Ehrlich-Institut in Langen, Germany, is the senior author on a paper that studied the structural diversity of SVA retrotransposons across the human genome. Looking at 116 SVA elements on chromosome 19, his team classified SVA elements into seven structural variants, with 5'-transduced SVA elements making up about 8 percent. Their data, they say, "indicate that SVA-mediated 5' transduction events involve alternative RNA splicing at cryptic splice sites," and that these "represent a novel source of genomic rearrangements contributing to genomic diversity," they say in the abstract.

University of Pennsylvania researchers also studied the human retrotransposon SVA, finding a new subfamily of SVA, "which apparently formed after an alternative splicing event where the first exon of the MAST2 gene spliced into an intronic SVA and subsequently retrotransposed," they say in the abstract. Further experimentation showed that a number of functional 3' splice sites exist within many transcribed SVAs in both the human and chimpanzee genomes. "These data imply that an SVA residing within an intron in the same orientation as the gene may alter normal gene transcription either by gene-trapping or by introducing [premature termination codons] through exonization, possibly creating differences within and across species."

Scientists from the National University of Singapore, the University of Oxford, and the Genome Institute of Singapore report on the Singapore Genome Variation Project, a public database of 1.6 million SNPs spanning individuals of Chinese, Malay, and Indian descent in Southeast Asia. In this paper, they clustered data from the HapMap and Human Genome Diversity projects, "providing useful insights into the population structure of the three major population groups in Asia."

The Scan

Rise of BA.5

The New York Times reports that the Omicron subvariant BA.5 has become the dominant version of SARS-CoV-2 in the US.

UK Health Secretary Resigns

Sajid Javid, the UK health secretary, resigned along with Chancellor Rishi Sunak, saying they cannot work with Prime Minister Boris Johnson's government, CNN reports.

Clones From Freeze-Dried Cells

A team in Japan has cloned mice from freeze-dried skin cells, according to the Guardian.

Genome Research Papers on Craniosynostosis, Macaque Retrotransposition, More

In Genome Research this week: structural variants in craniosynostosis, LINE-1 activity in rhesus macaque brain, and more.