Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra

paper
Author

Zach Bengtsson

Published

May 29, 2023

Paper I Chose

Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra

Can find here

Background

  • Sampled gill tissue from snails located at 4 different sites along the central northern coast of Chile. 

  • Gill tissue was sampled in summer and winter

Sequencing and lncRNA Identification

  • RNA-seq

  • lncRNA ID process filters for >200 bp, coding potential (CPAT), and BLAST against Genbank protein sequence database for mussels

lncRNA filtering process

Analysis

  • Expression analysis for both lncRNAs and coding RNAs

  • PCA, differential expression, and expression correlation between lnc and coding RNAs

  • Differential expression of lncRNAs by season

PCA

  • More variability in expression over summer, less in winter

  • Punta Talca individuals most distinct from others

Co-expression

  • Correlation of lncRNA expression with known coding RNA expression

  • lncRNA upregulation (A) most associated with stress response

  • Downregulation (B) most associated with metabolism

My Main Takeaways

  • lncRNA expression showed seasonal variation as well as spatial variation–most notably in the case of a single site (thought to be due to more temperature variability at this site).

  • lncRNA expression appears to be very involved in stress response, translation, and metabolism–which play important roles during cases of environmental perturbation.

  • The author suggest that lncRNA genes may be more environmentally responsive than coding genes, implicating them more in rapid response to stress.