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This Week in PNAS: Jun 6, 2017

In the early, online edition of the Proceedings of the National Academy of Sciences, a team from China and the US introduces a statistical method called paired gene expression and chromatin accessibility (PECA) for evaluating gene regulation and interpreting the genome. Using cis-regulatory element patterns, transcription factor profiles, information on target genes, and more, the PECA method provides a look at context-specific regulatory effects, the researchers note — an approach they applied to data from the mouse ENCODE effort for the study. "[B]y modeling matched expression and accessibility data across diverse cellular contexts," the authors write, "it is possible to recover a significant portion of the information in the missing data on binding locations and chromatin states and to achieve accurate inference of gene regulatory relations."

Researchers from the University of Southern California, Yale University, Carnegie Mellon University, and Baylor College of Medicine describe the paleogenomics-aided approach they used to assess gene regulatory networks in the sea urchin, Strongylocentrotus purpuratus. The team set out to explore the so-called double-negative gate in sea urchins — a gene regulatory subcircuit that positions developmental gene at appropriate spatial locales as the sea urchin embryos form, using comparative genomic, phylogenetic, fossil, and other data to reconstruct the ancestral state of this regulatory process. "This paleogenomic approach allowed us to estimate the age of the [double-negative gate] and to establish a timeline for [gene regulatory network] evolution in echinoids," the authors write.

Finally, a team from Carnegie Mellon University takes its own look at gene regulatory networks in the sea urchin, sea star, and other echinoderms, focusing on the evolution of networks involving a development-related Tbox transcription factor known as Tbrain. The researchers turned to chromatin immunoprecipitation sequencing, RNA sequencing, and other approaches to characterize Tbrain binding sites genome-wide over the course of sea star and sea urchin development. In the process, they saw signs that low-affinity secondary binding motifs shift over the course of echinoderm evolution, leaving conserved high-affinity motifs relatively unaltered and changing the regulatory contributions that Tbrain makes in the organisms considered.