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| Status |
Public on Feb 20, 2014 |
| Title |
Expression of novel long noncoding RNAs during erythro-megakaryopoiesis and GATA1-induced erythroid differentiation using RNA-seq |
| Project |
Mouse ENCODE
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| Sample organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Mammals express thousands of long noncoding (lnc) RNAs, a few of which are shown to function in tissue development. However, the entire repertoire of lncRNAs and the extent to which they regulate biological processes in different tissues and species are not defined. Indeed, most lncRNAs are not conserved between species, raising questions about function. We used RNA-Seq to identify lncRNAs in primary murine fetal liver erythroblasts expressing the lineage marker TER119, megakaryocytes (CD41+) cultured from embryonic day (E) 14.5 murine fetal liver and megakaryocyte erythroid progenitors (MEPs) isolated from mouse bone marrow. Strand-specific, paired-end, deep sequencing was performed on polyA+ mRNA from biological replicates of each sample. We assembled the transcriptomes using the Cufflinks package and generated a high-confidence transcriptome of 13,131 genes expressed in the three cell types. We identified 683 and 594 polyadenylated lncRNAs expressed in red blood cell (erythroid) precursors of mice and humans, respectively. More than one half of erythroid lncRNAs are un-annotated, emphasizing the opportunity for new discovery through studies of specialized cell types. Analysis of the murine erythroid lncRNA transcriptome indicates that ~75% arise from promoters and 25% from enhancers, many of which are regulated by the key erythroid transcription factors GATA1 and SCL/TAL1. Erythroid lncRNA expression is largely conserved among 8 different mouse strains, yet only 15% of mouse lncRNAs are expressed in humans and vice versa, reflecting dramatically greater species-specificity than coding genes. We investigated potential functions of 21 relatively abundant erythroid-specific murine lncRNAs (both conserved and non-conserved) by RNA interference in primary mouse erythroid precursors, and identified 7 whose knockdown inhibited features of terminal erythroid maturation including cell size reduction and enucleation. Strikingly, at least 6 of the 7 lncRNAs have no detectable expression in human erythroblasts, demonstrating that lack of conservation between mammalian species does not predict lack of function. These results reflect marked evolutionary differences between protein-coding genes and lncRNAs and indicate that the latter exert tissue- and species-specific roles in development.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
Strand-specific polyA+ RNA profiles from megakaryocyte erythroid progenitors (MEP), CD41+ megakaryocytes, TER119+ erythroblasts and estradiol-induced G1E-ER4 cells were generated in duplicate using deep sequencing on the Illumina HiSeq 2000. Long noncoding RNAs were identified from a high-confidence transcriptome assembled using MEP, megakaryocytes and erythroblasts. Transcripts that passed several filters for coding potential and lacked long open reading frames (>300 nt) were defined as long noncoding RNAs. Expression was estimated in MEP, megakaryocytes, erythroblasts and additionally in the estradiol-inducible GATA1 knockout and rescue system, G1E-ER4 cells over a 30-hour time-course after induction. Expression levels of lncRNAs were estimated using Cufflinks. Raw sequence data have been deposited in GEO record GSE40522 as part of the Mouse ENCODE Project. From GSE40522, samples GSM995525, GSM995533 and GSM995537 were used to assemble transcripts and identify lncRNAs. Expression of lncRNAs in response to GATA1 restoration was also measured using GSE40522 samples GSM995527, GSM995531, GSM995532, GSM995538, GSM995539 & GSM995541.
Data processing details are provided in the 'README.txt'.
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| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| Contributor(s) |
Paralkar VR, Mishra T, Giardine BM, Keller CA, Luan J, Yao Y, Kossenkov A, Pimkin M, Gore M, Sun D, Konuthula N, An X, Mohandas N, Bodine DM, Hardison RC, Weiss MJ |
| Citation(s) |
24497530 |
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| Submission date |
Oct 24, 2013 |
| Last update date |
Aug 08, 2016 |
| Contact name |
Ross Hardison |
| E-mail(s) |
rch8@psu.edu
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| Organization name |
Pennsylvania State University
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| Street address |
303 Wartik Lab
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| This SubSeries is part of SuperSeries: |
| GSE52555 |
Long noncoding RNA expression in several hematopoietic progenitor and differentiated cell populations |
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| Relations |
| Reanalysis of |
GSM995525 |
| Reanalysis of |
GSM995537 |
| Reanalysis of |
GSM995533 |
| Reanalysis of |
GSM995532 |
| Reanalysis of |
GSM995538 |
| Reanalysis of |
GSM995531 |
| Reanalysis of |
GSM995527 |
| Reanalysis of |
GSM995529 |
| Reanalysis of |
GSM995541 |
| BioProject |
PRJNA224576 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE51667_LncRNAGeneExprsDEcallsAllCats.txt.gz |
546.3 Kb |
(ftp)(http) |
TXT |
| GSE51667_README.txt |
2.0 Kb |
(ftp)(http) |
TXT |
| GSE51667_mm9_EryMegMEP_HighConfidenceTranscriptome.gtf.gz |
9.3 Mb |
(ftp)(http) |
GTF |
| Processed data are available on Series record |
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