CaltechAUTHORS
  A Caltech Library Service

A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration

Sierra, Noemie and Olsman, Noah and Yi, Lynn and Pachter, Lior and Goentoro, Lea and Gold, David A. (2021) A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210324-071454082

[img] PDF - Submitted Version
See Usage Policy.

4Mb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20210324-071454082

Abstract

Molecular studies of animal regeneration typically focus on conserved genes and signaling pathways that underlie morphogenesis. To date, a holistic analysis of gene expression across animals has not been attempted, as it presents a suite of problems related to differences in experimental design and gene homology. By combining orthology analysis with a novel statistical method for testing gene enrichment across large datasets, we are able to test whether biological processes across organisms share transcriptional regulation. We applied this method to six publicly available RNA-seq datasets from diverse examples of animal regeneration. We recovered 160 conserved orthologous gene clusters, which are enriched in structural genes as opposed to those regulating morphogenesis. A breakdown of gene presence/absence provides only limited support for the conservation of pathways typically implicated in regeneration, such as Wnt signaling and cell pluripotency. Specifically, these pathways are only conserved if we allow gene paralogs to be interchangeable through evolution. Overall, our analysis does not support the hypothesis that a shared set of ancestral genes underlie regeneration mechanisms in animals. The methods described in this paper will be broadly applicable for studying the genetic underpinnings of traits across distantly related organisms.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.03.22.434850DOIDiscussion Paper
https://doi.org/10.7910/DVN/LZK9DRDOIData
https://github.com/nsierra1/RNAseq_pValueAggregationRelated ItemCode
ORCID:
AuthorORCID
Olsman, Noah0000-0002-4351-3880
Yi, Lynn0000-0003-4575-0158
Pachter, Lior0000-0002-9164-6231
Goentoro, Lea0000-0002-3904-0195
Gold, David A.0000-0003-0135-4022
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. This version posted March 23, 2021. The authors have declared no competing interest.
DOI:10.1101/2021.03.22.434850
Record Number:CaltechAUTHORS:20210324-071454082
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210324-071454082
Official Citation:A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration. Noemie Sierra, Noah Olsman, Lynn Yi, Lior Pachter, Lea Goentoro, David A Gold. bioRxiv 2021.03.22.434850; doi: https://doi.org/10.1101/2021.03.22.434850
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108540
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:24 Mar 2021 19:53
Last Modified:19 Apr 2021 22:04

Repository Staff Only: item control page