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Chanfreau, G.

Publications and source records attributed to Chanfreau, G..

2 recordsLinked to original sources

Formin tails act as a switch, inhibiting or enhancing processive actin elongation

Formins are large, multidomain proteins that nucleate new actin filaments and accelerate elongation through a processive interaction with the barbed end of filaments. Their actin assembly activity is generally attributed to their eponymous Formin Homology (FH) 1 and 2 domains; however, evidence is mounting that regions outside of the FH1FH2 stretch also tune actin assembly. Here, we explore the underlying contributions of the tail domain, which spans the sequence between the FH2 domain and the C-terminus of formins. Tails vary in length from [~]0 to >200 residues and contain a number of recognizable motifs. The most well-studied motif is the [~]15 residue long diaphanous autoregulatory domain (DAD). The DAD mediates all or nothing regulation of actin assembly through an intramolecular interaction with the diaphanous inhibitory domain (DID) in the N-terminal half of the protein. Multiple reports demonstrate that the tail can enhance both nucleation and processivity. In this study, we provide a high-resolution view of the alternative splicing encompassing the tail in the Formin Homology Domain-(Fhod) family of formins during development. While four distinct tails are predicted, we found significant levels of only two of these. We characterized the biochemical effects of the different tails. Surprisingly, the two highly expressed Fhod-tails inhibit processive elongation and diminish the nucleation and elongation rates, while a third supports activity. These findings demonstrate a new mechanism of modulating actin assembly by formins and support the model that splice variants are specialized to build distinct actin structures during development.

biochemistry↗

NanoBlot: A Simple Tool for Visualization of RNA Isoform Usage From Third Generation RNA-sequencing Data

RT-PCR and Northern blots have long been used to study RNA isoforms usage for single genes. Recently, advancements in long read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues we have developed NanoBlot, a simple, open-source, command line tool, which generates Northern blot and RT-PCR-like images from third generation sequencing data. NanoBlot accepts processed bam files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlots include: designing probes to visualize isoforms which would be impossible with traditional RT-PCR or Northern blots, excluding reads from the Nanoblots based on the presence or absence of a specified region and, multiplexing plots with multiple colors. We present examples of NanoBlots compared to actual northern blot data. In addition to traditional gel-like images, NanoBlot also outputs other visualizations such as violin plots. The use of Nanoblot should provide a simple answer to the challenge of visualization of long-read RNA sequencing data.

bioinformatics↗