Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq analysis of C. elegans mina-1 mutants

ABSTRACT: Comparative transcriptomics study between C. elegans wild-type N2 and mina-1 mutants.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Michael Hengartner

PROVIDER: E-MTAB-7389 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans.

Sendoel Ataman A Subasic Deni D Ducoli Luca L Keller Martin M Michel Erich E Kohler Ines I Singh Kapil Dev KD Zheng Xue X Brümmer Anneke A Imig Jochen J Kishore Shivendra S Wu Yibo Y Kanitz Alexander A Kaech Andres A Mittal Nitish N Matia-González Ana M AM Gerber André P AP Zavolan Mihaela M Aebersold Ruedi R Hall Jonathan J Allain Frédéric H-T FH Hengartner Michael O MO

Cell death and differentiation 20190206 10

Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation, and stability. Defects in such regulation can lead to a wide range of human diseases from neurological disorders to cancer. Many RBPs are conserved between Caenorhabditis elegans and humans, and several are known to regulate apoptosis in the adult C. elegans germ line. ...[more]

PMID: 30728462

Similar Datasets

Project description:Purpose: The plant hormone abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. RNA-seq was employed to obtain differential expression data in response to ABA, dehydration and mannitol treatments in wild-type tissue. This was compared against the targeted gene knockout line PpanrKO. The ANR gene encodes a novel ABA regulator identified from ABA non-responsive (anr) mutant screens. Methods: RNA-seq on the Illumina HiSeq platform and mapping to the V3.0 genome and transcriptome assemblies using tophat2 enabled gene abundance data to be generated for differential gene expression analysis with edgeR in the Trinity package. Results: We observe a coordinated up-regulation of ca. 900 genes, with extensive overlaps between hormone and stress treatments as well as ca. 900 down-regulated genes. Of the up-regulated genes, those encoding LEA proteins, membrane channel proteins and transporters and oxidative-stress-associated genes comprised a significant fraction while those encoding growth-associated cell wall enzymes (e.g. expansins) and components of secondary metabolism (notably enzymes in the phenylpropanoid pathway) were prominent in the down-regulated genes. The ANR gene, a modular MAP3 kinase comprising an N-terminal PAS domain, a central EDR domain and a C-terminal MAPKKK-like domain unique to basal plant lineages, is found to play a central role in these responses with mutants failing to accumulate the wide spectrum of dehydration tolerance-associated gene products characteristic of the wild-type response and do not acquire ABA-dependent desiccation tolerance. Conclusions: Our study adds considerable data to the stress responses in bryophytes helping understand the mechanisms behind vegetative dehydration tolerance; an important trait for crop species. We also confirmed the vital role that PpANR plays in these responses in the moss Physcomitrella patens likely representing an ancestral mechanism for ABA-mediated dehydration tolerance vital in the conquest of land. RNA from 3 biological replicas was bulked per library. 8 libraries were generated from two genotypes, wild-type and PpanrkO, which included 3 treatments and a control sample for each.

Dataset Information

RNA-seq analysis of C. elegans mina-1 mutants

Publications

MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets