CRISPR-assisted detection of RNA-protein interactions in living cells.

We have developed CRISPR-assisted RNA-protein interaction detection method (CARPID), which leverages CRISPR-CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method's wide applicability in identifying RNA-binding proteins

Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: Implications for neurological diseases

10.3389/fnins.2012.00144Frontiers in NeuroscienceOCTArticle 14

Genetic mutations in RNA-binding proteins and their roles in ALS

10.1007/s00439-017-1830-7Human Genetics13691193-121

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9

10.1093/nar/gky348Nucleic Acids Research46147323-733

LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance

LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) targets. Through crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells and somatic cells expressing exogenous LIN28, we have defined discrete LIN28-binding sites in a quarter of human transcripts. These sites revealed that LIN28 binds to GGAGA sequences enriched within loop structures in mRNAs, reminiscent of its interaction with let-7 miRNA precursors. Among LIN28 mRNA targets, we found evidence for LIN28 autoregulation and also direct but differing effects on the protein abundance of splicing regulators in somatic and pluripotent stem cells. Splicing-sensitive microarrays demonstrated that exogenous LIN28 expression causes widespread downstream alternative splicing changes. These findings identify important regulatory functions of LIN28 via direct mRNA interactions.482195206UCSD Genetics Training Program through the National Institute of General Medical Sciences [T32 GM008666]National Science Foundation Graduate Research FellowshipGenentechUS National Institutes of Health [HG004659, GM084317, NS075449]California Institute for Regenerative Medicine [RB1-01413, RB3-05009]UCSD Genetics Training Program through the National Institute of General Medical Sciences [T32 GM008666]US National Institutes of Health [HG004659, GM084317, NS075449]California Institute for Regenerative Medicine [RB1-01413, RB3-05009

Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis

10.7554/eLife.40811eLife8e4081

Prejudice toward Muslims in New Zealand: insights from the New Zealand attitudes and values study

Following the March 15th Christchurch terrorist attack, members of our research team have been repeatedly asked to comment or provide summary statistics from the New Zealand Attitudes and Values Study (NZAVS) on prejudice toward Muslims. As the curators of the NZAVS, we think that these findings should be in the public domain and accessible to as wide an audience as possible. In this article, we aim to provide a comprehensive summary of what we know from the NZAVS about attitudes toward Muslims and prejudice in New Zealand more generally. From 2012 onwards, the NZAVS included a feeling thermometer rating of people’s level of warmth toward Muslims. Here, we summarize what we know from the NZAVS about levels of warmth toward Muslims in the New Zealand population. We describe the distribution of thermometer ratings of warmth toward Muslims annually from 2012 onward, and compare these with thermometer ratings of a range of other groups that we also track. We present a regression model documenting the extent to which a broad range of demographics and aspects of personality are associated with low levels of warmth toward Muslims, and present a parallel model assessing warmth ratings toward immigrants as a comparison. Finally, we present a series of growth curve models outlining the relative level and rate of change over time in warmth toward Muslims and other groups from 2012-2018. Results from these analyses indicate that over the 2012-2018 period, levels of warmth toward Muslims in New Zealand were comparatively low relative to warmth ratings of other groups. However, warmth toward Muslims has also been steadily but gradually increasing over time in New Zealand

Evasion of regulatory phosphorylation by an alternatively spliced isoform of Musashi2

The Musashi family of RNA binding proteins act to promote stem cell self-renewal and oppose cell differentiation predominantly through translational repression of mRNAs encoding pro-differentiation factors and inhibitors of cell cycle progression. During tissue development and repair however, Musashi repressor function must be dynamically regulated to allow cell cycle exit and differentiation. The mechanism by which Musashi repressor function is attenuated has not been fully established. Our prior work indicated that the Musashi1 isoform undergoes site-specific regulatory phosphorylation. Here, we demonstrate that the canonical Musashi2 isoform is subject to similar regulated site-specific phosphorylation, converting Musashi2 from a repressor to an activator of target mRNA translation. We have also characterized a novel alternatively spliced, truncated isoform of human Musashi2 (variant 2) that lacks the sites of regulatory phosphorylation and fails to promote translation of target mRNAs. Consistent with a role in opposing cell cycle exit and differentiation, upregulation of Musashi2 variant 2 was observed in a number of cancers and overexpression of the Musashi2 variant 2 isoform promoted cell transformation. These findings indicate that alternately spliced isoforms of the Musashi protein family possess distinct functional and regulatory properties and suggest that differential expression of Musashi isoforms may influence cell fate decisions