NeuroUTRs

A public repository of code, data and figures for the publication:

Alternative 3′ UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments

Georgi Tushev, Caspar Glock, Maximilian Heumüller, Anne Biever, Marko Jovanovic, Erin M.Schuman

https://doi.org/10.1016/j.neuron.2018.03.030

abstract

Neurons localize mRNAs near synapses where their translation can be regulated by synaptic demand and activity. Differences in the 3′ UTRs of mRNAs can change their localization, stability, and translational regulation. Using 3′ end RNA sequencing of microdissected rat brain slices, we discovered a huge diversity in mRNA 3′ UTRs, with many transcripts showing enrichment for a particular 3′ UTR isoform in either somata or the neuropil. The 3′ UTR isoforms of localized transcripts are significantly longer than the 3′ UTRs of non-localized transcripts and often code for proteins associated with axons, dendrites, and synapses. Surprisingly, long 3′ UTRs add not only new, but also duplicate regulatory elements. The neuropil-enriched 3′ UTR isoforms have significantly longer half-lives than somata-enriched isoforms. Finally, the 3′ UTR isoforms can be significantly altered by enhanced activity. Most of the 3′ UTR plasticity is transcription dependent, but intriguing examples of changes that are consistent with altered stability, trafficking between compartments, or local “remodeling” remain.

overview

• /data contains raw data in form of tables in either TXT or MAT(matlab object) format. Data tables are used by the code to conduct analysis and render figures. It can be considered as an addition to the supplementary tables
• /figures contains figures generated from the code in the process of manuscript preparation and explorative analysis. Many plots did not end up in the final manuscript or they are an alternative representation of the data. Figure formats are either PNG of compressed SVG. Figures numbering might differs from the publication, but the title will guide to the type of data and analysis it represents.
• /libs contains additional code used to support data mining or figures rendering
• /pipeline is a description of the steps used in PASS prediction and annotation
• /revisit as part of a request by the Tchumatchenko group, an overview of 3'UTR isoform half-life prediction is provided, by two different models. We post a table and a code to compare those models and reconfirm findings.
• /sandbox contains Matlab source code to mine data and render figures.