Transite: A computational motif-based analysis platform that identifies RNA-binding proteins modulating changes in gene expression

Abstract

RNA-binding proteins (RBPs) play critical roles in regulating gene expression by modulating splicing, RNA stability, and protein translation. In response to various stimuli, alterations in RBP function contribute to global changes in gene expression, but identifying which specific RBPs are responsible for the observed changes in gene expression patterns remains an unmet need. Here, we present Transite a multipronged computational approach that systematically infers RBPs influencing gene expression changes through alterations in RNA stability and degradation. As a proof of principle, we applied Transite to public RNA expression data from human patients with non-small cell lung cancer whose tumors were sampled at diagnosis, or after recurrence following treatment with platinum-based chemotherapy. Transite implicated known RBP regulators of the DNA damage response and identified hnRNPC as a new modulator of chemotherapeutic resistance, which we subsequently validated experimentally. Transite serves as a generalizable framework for the identification of RBPs responsible for gene expression changes that drive cell-state transitions and adds additional value to the vast wealth of publicly-available gene expression data.

Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes

“…We used the spectrum motif analysis (SPMA) approach from Transite (https://transite.mit.edu; ref. 23) to identify RNA binding proteins whose target transcripts are upregulated in low pH conditions. The original list of transcripts was sorted by the log 2 -fold change between the low pH and physiologic pH conditions in ascending order, subdivided into 40 bins and RBP motif enrichment was calculated for each bin with respect to the entire list of transcripts.…”

“…Additionally, local consistency scores (CS; ref. 23) were used to identify nonrandom arrangements of putative binding sites across the spectrum of fold change sorted transcripts. The Transite source code is hosted on GitHub (https://github.com/kkrismer/transite).…”

“…Targets of RNA binding proteins that interact with AU-rich motifs are enriched in low pH transcriptomic signature Given the major impact on the global deregulation of constitutive exons and changes in splicing patterns, we asked if a specific set of RNA binding proteins contributes to the global rewiring of the transcriptome in response to extracellular acidity. We took advantage of publicly available datasets to investigate how RBP targets are distributed across pH-induced transcriptomic changes in mouse and human, applying the "SPMA" approach from Transite, a novel bioinformatics platform (23). SPMA identified RBPs whose putative target transcripts were arranged in a nonrandom fashion across the sorted list of pH induced transcripts organized by their log 2 -fold change.…”

Members of the CUGBP Elav-Like Family of RNA-Binding Proteins are Expressed in Distinct Populations of Primary Sensory Neurons

“…Previous studies examining the expression profile and function of CELF members have determined that these proteins are expressed in the central nervous system during development and in the adult (Table 4 (Giudice et al, 2016; Krismer et al, 2020b; Samaras et al, 2020; Schmidt et al, 2018)). The RNA-binding motifs for all members are similar, with UG repeats (Table 4), suggesting that these proteins have the ability to bind similar transcripts.…”

“…All mRNAs detected by scRNA-Seq (see above) in TRPV1+ neurons were assessed for the presence of CELF4-binding motifs using the transite package (Krismer et al, 2020a) with bioconductor (Gentleman et al, 2004;Huber et al, 2015) in R statistical software. This list of genes with CELF4-binding motifs was inputted into the PANTHER gene ontology classification system (Mi et al, 2021) for statistical overrepresentation analysis.…”