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This Week in PNAS: May 29, 2018

A New York University team takes a look at retrotransposon expression and regulation in human cells using a "mapping repeat reads to a consensus" (MapRRCon) pipeline to trace transcription factors interacting with transposable element sequences. The MapRRCon approach relies on chromatin immunoprecipitation sequencing in combination with whole-genome alignment to track the proteins that bin to characteristic retrotransposon sequences, the researchers say. With the help of ChIP-seq data generated for human cells or tissues profiled for the ENCODE project, for example, they found 178 transcription products bound to LINE-1 (L1) retrotransposons in at least one of the biological conditions considered. From there, the authors looked more closely at L1 retrotransposon interactions with cancer-related transcription factors such as Myc and CTCF using MapRRCon and follow-up gene knockdown experiments. 

Researchers from the UK, Switzerland, and Japan describe convergent evolution in photoreceptor protein features in animals with or without bilateral symmetry. Using protein sequence data, computational biology, and spectroscopy experiments, the team examined opsin visual structures in the box jellyfish Carybdea rastonii, which show radial symmetry. Results from such experiments indicated that the box jellyfish opsin has a counterion similar to that used for visible light sensitivity by vertebrate animals with bilateral symmetry, though the position of this counterion is distinct, pointing to convergent opsin evolution. "[O]ur data establish the third only counterion site in animal opsins," the authors write, "and reveal convergent evolution of tertiary structure in opsins from distantly related species with advanced visual systems."

A team from Germany, France, and the Netherlands explores mutations contributing to circadian clock shifts in domesticated tomato plants. Starting with genome and/or transcriptome sequences for a wild tomato ancestor, another wild relative, and cultivated tomato, the researchers tracked down 11 deletion-containing genes in the domesticated plant, focusing in on a potential clock-related gene called LNK2. They subsequently analyzed LNK2 and EID1 — a gene previously implicated in circadian rhythm — in hundreds of tomato accessions, identifying signatures of selection coinciding with the circadian clock deceleration documented in cultivated tomatoes. "We show that the mutant alleles of both [LNK2 and EID1] arose in the earliest cultivated types and were selected during the domestication process," the authors report, noting that "both mutant alleles specifically affect light input to the clock, leading to a light-conditional clock deceleration."