NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing.
Li Jiang, Changwei Shao, Qi-Jia Wu, Geng Chen, Jie Zhou, Bo Yang, Hairi Li, Lan-Tao Gou, Yi Zhang, Yangming Wang, Gene W Yeo, Yu Zhou, Xiang-Dong Fu
Nature structural & molecular biology · 2017 · Vol. 24 (10) · pp. 816-824
Abstract
MicroRNA (miRNA) biogenesis is known to be modulated by a variety of RNA-binding proteins (RBPs), but in most cases, individual RBPs appear to influence the processing of a small subset of target miRNAs. Here, we report that the RNA-binding NONO-PSF heterodimer binds a large number of expressed pri-miRNAs in HeLa cells to globally enhance pri-miRNA processing by the Drosha-DGCR8 Microprocessor. NONO and PSF are key components of paraspeckles organized by the long noncoding RNA (lncRNA) NEAT1. We further demonstrate that NEAT1 also has a profound effect on global pri-miRNA processing. Mechanistic dissection reveals that NEAT1 broadly interacts with the NONO-PSF heterodimer as well as many other RBPs and that multiple RNA segments in NEAT1, including a 'pseudo pri-miRNA' near its 3' end, help attract the Microprocessor. These findings suggest a 'bird nest' model in which an lncRNA orchestrates efficient processing of potentially an entire class of small noncoding RNAs in the nucleus.
Linked datasets 1
The LncRNA NEAT1 Nests RNA Binding Proteins and the Microprocessor to Globally Enhance Pri-miRNA Processing
Homo sapiens
32 data files
| File | Type | Size |
|---|---|---|
| NONO-1.fastq.gz | OTHER | 933.8 MB |
| NONO-2.fastq.gz | OTHER | 1.6 GB |
| PSF-1.fastq.gz | OTHER | 2.2 GB |
| PSF-2.fastq.gz | OTHER | 1.5 GB |
| siGFP-1.fastq.gz | ncRNA-Seq | 57.9 MB |
| siGFP-2.fastq.gz | ncRNA-Seq | 776.7 MB |
| siNEAT1-1.fastq.gz | ncRNA-Seq | 860.8 MB |
| siNEAT1-2.fastq.gz | ncRNA-Seq | 804.7 MB |
| siNEAT1_V2-1.fastq.gz | ncRNA-Seq | 170.2 MB |
| siNEAT1_V2-2.fastq.gz | ncRNA-Seq | 1017.0 MB |
| siNONO-1.fastq.gz | ncRNA-Seq | 343.5 MB |
| siNONO-2.fastq.gz | ncRNA-Seq | 1.2 GB |
| siPSF-1.fastq.gz | ncRNA-Seq | 462.8 MB |
| siPSF-2.fastq.gz | ncRNA-Seq | 527.0 MB |
| siPSPC1-1.fastq.gz | ncRNA-Seq | 374.6 MB |
| siPSPC1-2.fastq.gz | ncRNA-Seq | 606.9 MB |
| SRR5060656_GSM2409885 | ncRNA-Seq | 57.0 MB |
| SRR5060657_GSM2409886 | ncRNA-Seq | 776.0 MB |
| SRR5060658_GSM2409887 | ncRNA-Seq | 860.0 MB |
| SRR5060659_GSM2409888 | ncRNA-Seq | 804.0 MB |
| SRR5060660_GSM2409889 | ncRNA-Seq | 170.0 MB |
| SRR5060661_GSM2409890 | ncRNA-Seq | 1016.0 MB |
| SRR5060662_GSM2409891 | ncRNA-Seq | 343.0 MB |
| SRR5060663_GSM2409892 | ncRNA-Seq | 1.2 GB |
| SRR5060664_GSM2409893 | ncRNA-Seq | 462.0 MB |
| SRR5060665_GSM2409894 | ncRNA-Seq | 526.0 MB |
| SRR5060666_GSM2409895 | ncRNA-Seq | 374.0 MB |
| SRR5060667_GSM2409896 | ncRNA-Seq | 606.0 MB |
| SRR5060668_GSM2409897 | OTHER | 933.0 MB |
| SRR5060669_GSM2409898 | OTHER | 1.6 GB |
| SRR5060670_GSM2409899 | OTHER | 2.2 GB |
| SRR5060671_GSM2409900 | OTHER | 1.5 GB |
Potentially related datasets 1
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
Analysis pipelines 1
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE90650 CLIP-seq Data Processing geo_data_processing | CLIP-seq | 6 | GSE90650 |
Funding 3 grants
| Grant | Funder |
|---|---|
| R01 HG004659 | NHGRI NIH HHS (United States) |
| R01 GM052872 | NIGMS NIH HHS (United States) |
| R01 GM049369 | NIGMS NIH HHS (United States) |