|
| Status |
Public on Apr 21, 2017 |
| Title |
A global view of RNA-protein interactions reveals novel root hair cell fate regulators |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. This analysis reveals distinct structural and protein binding patterns across both transcriptomes, allowing identification of differential RNA binding protein (RBP) recognition sites. Using these sequences, we identify two RBPs that regulate hair cell development. Specifically, we find that SERRATE functions in a microRNA-dependent manner to inhibit hair cell fate, while also terminating hair growth in differentiated hair cells independent of microRNAs. Additionally, we show that GLYCINE-RICH PROTEIN 8 alleviates phosphate starvation stress while promoting hair cell fate. In total, this global analysis reveals novel post-transcriptional regulators of plant root epidermal cell fate.
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| Overall design |
Protein interaction profile sequencing (PIP-seq) in the nuclei of Arabidopsis thaliana root hair or nonhair cells. 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) |
Foley SW, Gregory BD |
| Citation(s) |
28441533 |
| Submission date |
Sep 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn Foley |
| E-mail(s) |
foleys@mail.med.upenn.edu
|
| Phone |
2158980808
|
| Organization name |
University of Pennsylvania
|
| Street address |
433 S. University Ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19103 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
|
| Samples (16)
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|
| Relations |
| BioProject |
PRJNA341963 |
| SRA |
SRP086629 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE86459_hair_rep1_dsRNase_merged.CSAR_PPS_FDR05.bed.gz |
253.4 Kb |
(ftp)(http) |
BED |
| GSE86459_hair_rep1_ssRNase_merged.CSAR_PPS_FDR05.bed.gz |
152.5 Kb |
(ftp)(http) |
BED |
| GSE86459_hair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed.gz |
686.6 Kb |
(ftp)(http) |
BED |
| GSE86459_hair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt.gz |
13.2 Mb |
(ftp)(http) |
TXT |
| GSE86459_hair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt.gz |
18.2 Mb |
(ftp)(http) |
TXT |
| GSE86459_hair_rep2_dsRNase_merged.CSAR_PPS_FDR05.bed.gz |
255.0 Kb |
(ftp)(http) |
BED |
| GSE86459_hair_rep2_ssRNase_merged.CSAR_PPS_FDR05.bed.gz |
153.5 Kb |
(ftp)(http) |
BED |
| GSE86459_nonhair_rep1_dsRNase_merged.CSAR_PPS_FDR05.bed.gz |
233.0 Kb |
(ftp)(http) |
BED |
| GSE86459_nonhair_rep1_ssRNase_merged.CSAR_PPS_FDR05.bed.gz |
145.4 Kb |
(ftp)(http) |
BED |
| GSE86459_nonhair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed.gz |
769.5 Kb |
(ftp)(http) |
BED |
| GSE86459_nonhair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt.gz |
17.8 Mb |
(ftp)(http) |
TXT |
| GSE86459_nonhair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt.gz |
26.2 Mb |
(ftp)(http) |
TXT |
| GSE86459_nonhair_rep2_dsRNase_merged.CSAR_PPS_FDR05.bed.gz |
326.2 Kb |
(ftp)(http) |
BED |
| GSE86459_nonhair_rep2_ssRNase_merged.CSAR_PPS_FDR05.bed.gz |
133.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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