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Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3' UTR landscape in Drosophila [L1 CNS 3'seq]

UID: 10914

Author(s): Wei, Lu*, Lee, Seungjae*, Majumdar, Sonali*, Zhang, Binglong*, Sanfilippo, Piero*, Joseph, Brian*, Miura, Pedro*, Soller, Matthias, Lai, Eric C* * MSK affiliated

Description
Summary from GEO:

"The goal of this study is to perform quantitative comparison of transcriptome-wide 3'-end features of Drosophila melanogaster 1st instar larvae central neural system (L1CNS) from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant; Total RNAs were extracted from dissected L1CNS of Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant; 3'-end sequencing libraries were prepared using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina with replicates for each genotype; final cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with SE-50 mode. 3'-end sequencing data were mapped onto the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6) and 3′ end clusters were derived and quantified within a 25 bp window. We found that L1CNS from Canton-S expresses neural specific 3' UTR extensions like head, while in L1CNS from elav5 single mutant, global neural specific 3' UTR extensions are not significantly lost, but in elav5/fne double mutant L1CNS, there is a dramatic loss of neural specific 3' UTR extensions. We reported for the first time demonstration of trans-acting factors that globally maintain this very distinctive tissue-specific APA landscape."

Overall design from GEO:

"3'-end sequencing profiles from dissected Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant. Elav5 and fne mutants are deletion KO alleles."
Subject of Study
Drosophila melanogaster
Subject(s)
3' Untranslated Regions
ELAV Proteins
RNA 3' End Processing
RNA-Binding Proteins
Access via GEO


Accession #: GSE155531

Access via BioProject


Accession #: PRJNA650190

Access via SRA


Accession #: SRP275489

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus, BioProject, and SRA databases provide open access to these files.
Associated Publications
Wei L, Lee S, Majumdar S, Zhang B, Sanfilippo P, Joseph B, Miura P, Soller M, Lai E. Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3′ UTR landscape in drosophila. Molecular Cell. 2020; 80(1):140-155.e6.
Equipment Used
Illumina HiSeq 1000

High throughput sequencing system

Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit

All-in-one library preparation protocol designed to generate Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA.

Dataset Format(s)
CSV, TAR, BW
Dataset Size
535.9 KB (CSV), 244.3 MB (TAR)
Data Catalog Record Updated
2023-10-10