|
| Status |
Public on Dec 16, 2014 |
| Title |
Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP binding site mapping approach on Arabidopsis seedling nuclei in vivo to globally profile these features within the nuclear compartment. We reveal opposing patterns of secondary structure and RBP binding levels throughout native messenger RNAs that demarcate alternative splicing and polyadenylation. We also uncover a collection of protein bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, we identify a nuclear role for the chloroplast RBP, CP29A. In total, we provide the first simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus.
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| |
|
| Overall design |
Protein interaction profile sequencing (PIP-seq) in Arabidopsis seedling nuclei. These are crosslinked with formaldehyde and treated with two RNases (ssRNase and dsRNase) with two replicates
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| |
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| Contributor(s) |
Gosai SJ, Foley SW, Gregory BD |
| Citation(s) |
25557549 |
| |
| Submission date |
Jul 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sager Jayesh Gosai |
| Organization name |
Universiry of Pennsylvania
|
| Department |
Biology
|
| Lab |
Brian Gregory
|
| Street address |
433 S University Ave.
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA254031 |
| SRA |
SRP043993 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE58974_At_total_refTAIR10_cleavage_invivo_structScore_TH010.txt.gz |
14.5 Mb |
(ftp)(http) |
TXT |
| GSE58974_At_total_refTAIR10_mRNA_invivo_structScore_TH100.txt.gz |
68.1 Mb |
(ftp)(http) |
TXT |
| GSE58974_At_total_refTAIR10_pri_mRNA_invivo_structScore_TH100.txt.gz |
125.1 Mb |
(ftp)(http) |
TXT |
| GSE58974_TAIR10_mRNA_intron_splicingReads.constitutive.first.bed.gz |
331.9 Kb |
(ftp)(http) |
BED |
| GSE58974_TAIR10_mRNA_intron_splicingReads.constitutive.last.bed.gz |
330.7 Kb |
(ftp)(http) |
BED |
| GSE58974_totalArab_nuc_rep3_dsRNase_mergedGapped.CSAR_PPS_FDR05.bed.peak.txt.gz |
329.0 Kb |
(ftp)(http) |
TXT |
| GSE58974_totalArab_nuc_rep3_ssRNase_mergedGapped.CSAR_PPS_FDR05.bed.peak.txt.gz |
69.5 Kb |
(ftp)(http) |
TXT |
| GSE58974_totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed.gz |
698.3 Kb |
(ftp)(http) |
BED |
| GSE58974_totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed.peak.txt.gz |
690.4 Kb |
(ftp)(http) |
TXT |
| GSE58974_totalArab_nuc_rep4_dsRNase_mergedGapped.CSAR_PPS_FDR05.bed.peak.txt.gz |
314.9 Kb |
(ftp)(http) |
TXT |
| GSE58974_totalArab_nuc_rep4_ssRNase_mergedGapped.CSAR_PPS_FDR05.bed.peak.txt.gz |
61.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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