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Series GSE111951 Query DataSets for GSE111951
Status Public on Mar 17, 2018
Title 4sU metabolic labeled transcripts in mESCs
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary We carried out an extensive functional genomics analysis to elucidate the roles, if any, of splicing at enhancer-associated lincRNA loci (elincRNA). While we found little evidence supporting conservation of elincRNA exons, their splice sites and other splicing associated motifs accumulated significantly fewer mutations than neutrally evolving regions, suggesting that selection has acted to preserve their splicing. We showed that in contrast to other lincRNAs, not only were multi-exonic elincRNAs efficiently and rapidly spliced, they were also specifically associated with enhanced expression of proximal genes and increased local chromosomal interactions. Enrichment of chromatin signatures associated with high enhancer activity at these loci further supports the contribution of elincRNA splicing to enhancer function. Our results elucidate the previously observed evolutionary constraint at elincRNA splice sites, but not their exons, and corroborate the impact of elincRNA splicing modulation on neighboring gene expression regulation, highlighting an unexpected contribution of elincRNA splicing to enhancer function.
Overall design Mouse embryonic stem cells (mESCs) were labeled with 4-thiouridine for 15, 30 and 60 minutes in duplicates. Labeled and total RNA were sequenced on Illumina HiSeq 2500.
Contributor(s) Tan JY, Biasini A, Marques AC
Citation(s) 32086317, 32175319
Submission date Mar 16, 2018
Last update date Mar 23, 2020
Contact name Jennifer Yihong Tan
Phone +4121 692 5472
Organization name University of Lausanne
Department Department of Computational Biology
Lab Ana Marques
Street address Rue du Bugnon 27
City Lausanne
ZIP/Postal code 1005
Country Switzerland
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM3045638 totalRNA_15_R1
GSM3045639 totalRNA_30_R1
GSM3045640 totalRNA_60_R1
BioProject PRJNA438673
SRA SRP135882

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Supplementary file Size Download File type/resource
GSE111951_Processed_data_table.txt.gz 5.1 Mb (ftp)(http) TXT
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Processed data are available on Series record

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