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This Week in Cell: May 6, 2015

A transmissible form of a leukemia-like disease that's been impacting soft-shell clam populations on the East Coast of North America since the 1970s appears to stem from a clonal cell line being passed from one clam to another, according to a Cell study. A group fromColumbiaUniversity and Environment Canada did PCR-based genotyping on mitochondrial SNPs and DNA microsatellites in nine soft-shell clams with the neoplasm and 11 without. Results from the analysis revealed that the neoplasms were all genetically related — and peppered with insertions by a retrotransposon called Steamer — but had distinct genetic features from those found in the host clams. GenomeWeb has more on the study, here

Researchers from the UK, Portugal, and Japan introduce mNET-seq, a method for profiling growing transcripts in mammalian cells. The scheme relies on antibodies that target phosphorylation on the extended C-terminal domain of the mammalian polymerase II large subunit to nab not only the Pol II enzyme by immunoprecipitation, but associated transcripts-in-progress. Using the mNET-seq approach, authors of that study demonstrated that they were able to sequence nascent RNA transcripts and pick up on features such as intron splicing cleavage in chromatin from HeLa cells. "[O]urextensive mNET-seq datasets provide a 'treasure trove' of detailed information on nascent transcription and co-transcriptional RNA processing in mammalian cells," they write.

Lastly, an independent Harvard University-led team describes its own method — known as human NET-seq — for sequencing native elongating transcripts produced by the Pol II enzyme in human cells with the help of Pol II antisera. In that study, the researchers applied human NET-seq to HeLa and another human cell line to profile Pol II pausing and gain information on the convergent sense and antisense transcription that characterizes many genes with relatively low expression. "We expect adaptation of human NET-seq to any human cell type to be straightforward, resulting in a tool to illuminate a variety of biological processes," the authors note. "Future applications include high-resolution analyses of transcription regulation across cell types, responses to signaling pathways, and cellular differentiation."