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| Status |
Public on May 01, 2017 |
| Title |
Regulatory and evolutionary footprints of messenger RNA secondary structure in primate transcriptomes |
| Organisms |
Macaca fascicularis; Macaca mulatta; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Messenger RNA secondary structure is critical to all aspects of post-transcriptional regulation. However, the global regulatory and evolutionary significance of mRNA secondary structure remains largely illusive. Here, we describe a transcriptome-wide analysis of RNA secondary structure in humans and two non-human primates, based on a high-throughput, nuclease-mediated, structure mapping approach. Using this methodology, we uncover global patterns of mRNA secondary structure, which we find to be conserved through primate evolution. We provide evidence for secondary structure-based regulatory pathways, which impact on gene expression through associations with translational machinery and RNA-binding proteins, including components of the microprocessor complex. Our results lend support to an unexpected, conserved mechanism by which highly structured regions of mRNAs serve as processing sites for small RNAs, resulting in subsequent turnover.
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| Overall design |
Global mRNA secondary structure analysis in primate transcriptomes using high-throughput, nuclease-mediated, structure mappinng approaches of dsRNA-seq and ssRNA-seq, also with polyA+ mRNA-seq, smRNA-seq (small RNA), and genome-wide mapping of uncapped and cleaved transcripts (GMUCT); these NGS-seq experiments were carried out in three primate brains as well as three different cell lines, both in in vitro and in vivo.
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| Contributor(s) |
Zheng Q, Silverman IM, Li F, Willmann MR, Berkowitz ND, Richards AL, Gregory BD |
| Citation missing |
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| |
| Submission date |
May 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Qi Zheng |
| E-mail(s) |
qi.zheng@nemours.org
|
| Phone |
3026515778
|
| Organization name |
Nemours Children's Health
|
| Street address |
1701 Rockland Road
|
| City |
Wilmington |
| State/province |
DE |
| ZIP/Postal code |
19803 |
| Country |
USA |
| |
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| Platforms (6)
|
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13766 |
Illumina Genome Analyzer IIx (Macaca mulatta) |
| GPL14954 |
Illumina HiSeq 2000 (Macaca mulatta) |
| GPL17720 |
Illumina Genome Analyzer IIx (Macaca fascicularis) |
| GPL18648 |
Illumina HiSeq 2000 (Macaca fascicularis) |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA246200 |
| SRA |
SRP041669 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57295_cynomolgus_ensGene_expr.txt.gz |
955.2 Kb |
(ftp)(http) |
TXT |
| GSE57295_cynomolgus_ensGene_mRNA_structScore.txt.gz |
22.2 Mb |
(ftp)(http) |
TXT |
| GSE57295_cynomolgus_ensGene_mRNA_struct_hotspot_anno.txt.gz |
448.5 Kb |
(ftp)(http) |
TXT |
| GSE57295_human_refGene_expr.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE57295_human_refGene_mRNA_invivo_HEK293T_structScore.txt.gz |
451.5 Mb |
(ftp)(http) |
TXT |
| GSE57295_human_refGene_mRNA_invivo_HEK293T_struct_hotspot_anno.txt.gz |
6.1 Mb |
(ftp)(http) |
TXT |
| GSE57295_human_refGene_mRNA_invivo_HeLa_structScore.txt.gz |
223.6 Mb |
(ftp)(http) |
TXT |
| GSE57295_human_refGene_mRNA_invivo_HeLa_struct_hotspot_anno.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE57295_human_refGene_mRNA_structScore.txt.gz |
48.5 Mb |
(ftp)(http) |
TXT |
| GSE57295_human_refGene_mRNA_struct_hotspot_anno.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
| GSE57295_rhesus_ensGene_expr.txt.gz |
991.3 Kb |
(ftp)(http) |
TXT |
| GSE57295_rhesus_ensGene_mRNA_structScore.txt.gz |
31.0 Mb |
(ftp)(http) |
TXT |
| GSE57295_rhesus_ensGene_mRNA_struct_hotspot_anno.txt.gz |
454.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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