|
| Status |
Public on Aug 20, 2018 |
| Title |
Global Profiling of hnRNP A2/B1-RNA Interactions on Chromatin Suggests Additional Roles Outside of Splicing |
| Organisms |
Homo sapiens; synthetic RNA |
| Experiment type |
Other
|
| Summary |
Long noncoding RNAs (lncRNAs) often carry out their functions through associations with adaptor proteins. We recently identified heterogeneous ribonucleoprotein (hnRNP) A2/B1 as an adaptor of the human HOTAIR lncRNA. hnRNP A2 and B1 are splice isoforms of the same gene. Spliced HOTAIR preferentially associates with the B1 isoform, which may contribute to a mechanism matching lncRNAs with RNA transcripts of target genes. In this study we used enhanced cross-linking immunoprecipitation (eCLIP) to map the complete set of direct interactions between A2/B1 and RNA in breast cancer cells. We identified multiple additional sites of isoform specificity that correlate with differences in binding motif enrichment. Surprisingly, a strong A2/B1 binding site occurs in the third intron of HOTAIR, which interrupts a known RNA-RNA interaction hotspot and is retained at a higher frequency than other HOTAIR introns. In vitro eCLIP experiments suggest that A2/B1 may redistribute to exonic binding sites once this intron is spliced. A2/B1 associates with multiple lncRNAs at regions that may contribute to downstream regulation and function of the lncRNA. Finally, we performed cellular fractionation experiments to characterize the pattern of RNA association of A2/B1 in chromatin, nucleoplasm, and cytoplasm and find that a majority of interactions occur on chromatin, even those that do not contribute to co-transcriptional splicing. Our data characterize the multiple functions of a repurposed splicing factor, including isoform-biased interactions, and highlight that the vast majority of these functions occur on chromatin-associated RNA.
|
| |
|
| Overall design |
eCLIP-seq in human MCF7 and MCF10A cells
|
| |
|
| Contributor(s) |
Nguyen ED, Johnson AM |
| Citation(s) |
29938567 |
| |
| Submission date |
Aug 28, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Aaron M Johnson |
| E-mail(s) |
aaron.m.johnson@ucdenver.edu
|
| Phone |
303-724-3224
|
| Organization name |
University of Colorado Denver
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
12801 E 17th Ave Research 1 South L18-10402G
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL25479 |
Illumina NextSeq 500 (synthetic RNA) |
|
| Samples (20)
|
|
| Relations |
| BioProject |
PRJNA400384 |
| SRA |
SRP116309 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE103165_B1HA_HAXB1.merged.r2.norm.pos.bw |
26.7 Kb |
(ftp)(http) |
BW |
| GSE103165_B1HA_HA_B1.merged.r2.norm.pos.bw |
88.3 Kb |
(ftp)(http) |
BW |
| GSE103165_MCF10A_A2B1_AIP.peaks.inorm.enriched.bed.gz |
150.3 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF10A_A2B1_BIP.peaks.inorm.sorted.bed.gz |
224.8 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF10A_B1_AIP.peaks.inorm.enriched.bed.gz |
264.3 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF10A_B1_BIP.peaks.inorm.sorted.bed.gz |
209.8 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF7_A2B1_AIP.peaks.inorm.enriched.bed.gz |
192.7 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF7_A2B1_BIP.peaks.inorm.enriched.bed.gz |
157.8 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF7_B1_AIP.peaks.inorm.enriched.bed.gz |
436.0 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF7_B1_BIP.peaks.inorm.enriched.bed.gz |
287.7 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF7_chromatin_IP.peaks.inorm.sorted.bed.gz |
531.9 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF7_cytoplasm_IP.peaks.inorm.sorted.bed.gz |
3.8 Kb |
(ftp)(http) |
BED |
| GSE103165_MCF7_nucleoplasm_IP.peaks.inorm.sorted.bed.gz |
5.2 Kb |
(ftp)(http) |
BED |
| GSE103165_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
Less...
More...