A biochemical model for measuring microRNA targeting efficiency is reported in Science this week. Developed by researchers from the Whitehead Institute for Biomedical Research, the model adapts RNA Bind-N-Seek — a high-throughput method for characterizing sequence and structural specificity of RNA binding proteins — to enable the measurement of relative binding affinities between six miRNA and their targets. They find noncanonical target sites unique to each miRNA and miRNA-specific differences in canonical target-site affinities, among other things. The scientists also use a convolutional neural network to extend their model to all miRNA sequences. The work, they write, "substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks."
A new strategy for performing high-throughput chemical screens at single-cell resolution is described in this week's Science. The approach, called Sci-Plex, combines single-cell combinatorial indexing with a hashing approach that relies on labeling nuclei with unmodified single-stranded DNA oligos. The study's authors use their method to screen three cancer cell lines exposed to 188 compounds, profiling around 650,000 single-cell transcriptomes across roughly 5,000 independent samples in a single experiment.
Using single-molecule imaging, a team led by scientists from the University of Texas at Austin shows how cohesin — a chromosome-bound multisubunit ATPase complex — uses loop extrusion to organize the genome. As reported in Science last week, the investigators demonstrate that a recombinant human cohesin-NIPBL complexes compact both naked and nucleosome-bound DNA by extruding DNA loops — a process that is force sensitive, requires ATP hydrolysis, and is processive over tens of kilobases at an average rate of 0.5 kb per second. Compaction of double-tethered DNA, meanwhile, suggests that a cohesin dimer extrudes DNA loops bidirectionally, which explains the observed and simulated Hi-C maps of chromosome loops, the authors write.