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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 01, 2013 |
| Title |
Trans-chromosomal regulation by a novel lincRNA required for adipogenesis that escapes X-chromosome inactivation |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Long noncoding RNAs (lncRNAs) have emerged as an important layer of genome regulation with common mechanistic themes including the formation of ribonucleoprotein complexes. Here, we present a novel X-linked lncRNA termed linc-Firre that escapes X-chromosome inactivation and forms trans-chromosomal interactions required for adipogenesis. Linc-Firre is exclusively nuclear and forms punctate expression foci on chromatin near its site of transcription on both X-chromosomes in human and mouse. Both the localization of linc-Firre and the association with the nuclear matrix protein hnRNPU require a conserved repeating RNA domain, R2D2. Collectively, these results reveal a lincRNA that escapes X-chromosome inactivation with a critical role in driving cell fate decisions by trans-chromosomal interactions.
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| Overall design |
Replicate RNA-Seq analyses of oligo-mediated knockdowns of linc-FIRRE and hnRNPU in two different cellular contexts; HeLa cells and mouse embryonic stem cells. Also included are Firre knockout and wild-type mouse embryonic stem cells.
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| Contributor(s) |
Hacisuleyman E, Goff LA, Trapnell C, Sauvageau M, McClanahan P, Kelley D, Cabili M, Hendrickson D, Engreitz J, Guttman M, Lennox K, Rigo F, Beal M, Johansson H, Orjalo A, Lander E, Lodish H, Sun L, Raj A, Rinn JL |
| Citation(s) |
24463464 |
| Submission date |
Mar 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Loyal A Goff |
| E-mail(s) |
loyalgoff@jhmi.edu
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| Organization name |
Johns Hopkins University
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| Department |
Institute of Genetic Medicine
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| Lab |
Goff
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| Street address |
733 N. Broadway Avenue
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (3) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA193156 |
| SRA |
SRP019270 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45157_HeLa_diff.tab.gz |
3.8 Mb |
(ftp)(http) |
TAB |
| GSE45157_mESC_KO_vs_WT_diff.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE45157_mESC_KO_vs_WT_fpkm.txt.gz |
340.2 Kb |
(ftp)(http) |
TXT |
| GSE45157_mESC_diff.tab.gz |
2.4 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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