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Series GSE75880 Query DataSets for GSE75880
Status Public on Jun 01, 2016
Title Unlinking a lncRNA from its associated cis element [Capture-C]
Organism Mus musculus
Experiment type Other
Summary Capture-C using probes at the Cdkn1b promoter and the Lockd promoter
Overall design Many long non-coding (lnc) RNAs are reported to regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (LncRNA downstream of Cdkn1b), a 434 bp polyadenylated lncRNA originating 4 kb 3’ to the Cdkn1b gene. Heterozygous and homozygous deletion of the 25 kb Lockd locus reduced Cdkn1b transcription by approximately 35 and 70% respectively in a mouse erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by > 90%, but had no effect on Cdkn1b transcription. The promoter of the Lockd gene contains a DNase hypersensitive site, binds numerous transcription factors (TFs), and physically associates with the Cdkn1b promoter in chromosomal conformation capture (NG Capture-C) studies. Thus, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element, while the lncRNA itself is dispensable. These findings demonstrate that the biological activities of a lncRNA cannot be inferred from phenotypes that arise after deleting the corresponding gene. Rather, the model of an inert transcript arising from a functional genomic cis element should be considered while investigating the biology of any lncRNA.
Contributor(s) Paralkar V, Weiss M
Citation(s) 27041223
Submission date Dec 10, 2015
Last update date May 15, 2019
Contact name Vikram Paralkar
Phone 215-590-0558
Organization name University of Pennsylvania
Street address 3400 Civic Center Boulevard, Perelman Center, 7th Floor, South Pavilion Extension
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (4)
GSM1969240 Cdkn1b promoter Capture, Rep 1
GSM1969241 Cdkn1b promoter Capture, Rep 2
GSM1969242 Lockd promoter Capture, Rep 1
This SubSeries is part of SuperSeries:
GSE75881 Unlinking a lncRNA from its associated cis element
BioProject PRJNA305603
SRA SRP067218

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Supplementary file Size Download File type/resource
GSE75880_Cdkn1b_promoter_capture.bedgraph.gz 62.8 Kb (ftp)(http) BEDGRAPH
GSE75880_Lockd_promoter_capture.bedgraph.gz 166.3 Kb (ftp)(http) BEDGRAPH
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