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Series GSE40121 Query DataSets for GSE40121
Status Public on Oct 10, 2012
Title Control of Somatic Tissue Differentiation by the Long Non-Coding RNA TINCR (HTS)
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7kb lncRNA, terminal differentiation-induced ncRNA (TINCR), controls human epidermal differentiation by a post-transcriptional mechanism. TINCR is required for high mRNA abundance of key differentiation genes, many of which are mutated in human skin diseases, including FLG, LOR, ALOXE3, ALOX12B, ABCA12, CASP14 and ELOVL3. TINCR-deficient epidermis lacked terminal differentiation ultrastructure, including keratohyalin granules and intact lamellar bodies. Genome-scale RNA interactome analysis revealed that TINCR interacts with a suite of differentiation mRNAs. TINCR-mRNA interaction occurs through a 25 nucleotide “TINCR box” motif which is strongly enriched in interacting mRNAs and required for TINCR binding. A high-throughput screen to analyze TINCR binding capacity to ~9,400 human recombinant proteins revealed direct binding of TINCR RNA to the Staufen1 (STAU1) protein. STAU1-deficient tissue recapitulated the impaired differentiation seen with TINCR depletion. Loss of UPF1 and UPF2, both of which are required for STAU1-mediated RNA decay (SMD), however, lacked differentiation impacts. Instead, the TINCR/STAU1 complex seems to mediate stabilization of differentiation mRNAs, such as KRT80. These data identify TINCR as a key lncRNA required for somatic tissue differentiation, which occurs through inducible lncRNA binding to differentiation mRNAs to ensure their expression.
 
Overall design Examination of TINCR-binding RNAs using two independent pools of TINCR-targeting oligos
 
Contributor(s) Ci C, Qu K
Citation(s) 23201690
Submission date Aug 14, 2012
Last update date Oct 11, 2022
Contact name Douglas Porter
Organization name Stanford
Department Dermatology
Lab Khavari
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (3)
GSM986007 Input RNA
GSM986008 TINCR RIAseq even pool
GSM986009 TINCR RIAseq odd pool
This SubSeries is part of SuperSeries:
GSE40123 Control of Somatic Tissue Differentiation by the Long Non-Coding RNA TINCR
GSE58161 Suppression of progenitor differentiation requires the long noncoding RNA ANCR
Relations
BioProject PRJNA172897
SRA SRP014847

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40121_ria_exon_100bp_enriched.txt.gz 154.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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