Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms.
Angela L Nicholson-Shaw, Eric R Kofman, Gene W Yeo, Amy E Pasquinelli
Nucleic acids research · 2022 · Vol. 50 (8) · pp. 4685-4702
Abstract
The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved in the biogenesis and function of RNA. While it is well-established that the nuclear PABP (PABPN) binds newly synthesized poly(A)-tails and is replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A)-tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein-coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A)-tails and PABPC-enriched RNAs had longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A)-tail synthesis, maintenance, and function.
Linked datasets 3
Cytoplasmic and nuclear fractionation from HEK293T cells
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| Cyto_frac_Rep1_R1.fastq.gz | RIP-Seq | 1.7 GB |
| Cyto_frac_Rep2_R1.fastq.gz | RIP-Seq | 1.7 GB |
| Nuclear_frac_Rep1_R1.fastq.gz | RIP-Seq | 1.7 GB |
| Nuclear_frac_Rep2_R1.fastq.gz | RIP-Seq | 1.8 GB |
| SRR17771270_GSM5839352 | RIP-Seq | 1.7 GB |
| SRR17771271_GSM5839351 | RIP-Seq | 1.7 GB |
| SRR17771272_GSM5839350 | RIP-Seq | 1.8 GB |
| SRR17771272.lite | RIP-Seq | 1.8 GB |
| SRR17771273_GSM5839349 | RIP-Seq | 1.7 GB |
| SRR17771273.lite | RIP-Seq | 1.7 GB |
Ribo-STAMP reveals translation status of RNAs bound by PABPN and PABPC
Homo sapiens
34 data files
| File | Type | Size |
|---|---|---|
| Input_CntrlSTAMP_Rep1_R1.fastq.gz | RIP-Seq | 1.9 GB |
| Input_CntrlSTAMP_Rep2_R1.fastq.gz | RIP-Seq | 2.2 GB |
| Input_CntrlSTAMP_Rep3_R1.fastq.gz | RIP-Seq | 2.2 GB |
| Input_RPS2STAMP_Rep1_R1.fastq.gz | RIP-Seq | 1.9 GB |
| Input_RPS2STAMP_Rep2_R1.fastq.gz | RIP-Seq | 2.0 GB |
| Input_RPS2STAMP_Rep3_R1.fastq.gz | RIP-Seq | 2.2 GB |
| IP_PABPC_CntrlSTAMP_Rep1_R1.fastq.gz | RIP-Seq | 1.9 GB |
| IP_PABPC_CntrlSTAMP_Rep2_R1.fastq.gz | RIP-Seq | 2.1 GB |
| IP_PABPC_RPS2STAMP_Rep1_R1.fastq.gz | RIP-Seq | 1.6 GB |
| IP_PABPC_RPS2STAMP_Rep2_R1.fastq.gz | RIP-Seq | 2.0 GB |
| IP_PABPC_RPS2STAMP_Rep3_R1.fastq.gz | RIP-Seq | 2.0 GB |
| IP_PABPN_CntrlSTAMP_Rep1_R1.fastq.gz | RIP-Seq | 1.9 GB |
| IP_PABPN_CntrlSTAMP_Rep2_R1.fastq.gz | RIP-Seq | 2.1 GB |
| IP_PABPN_CntrlSTAMP_Rep3_R1.fastq.gz | RIP-Seq | 1.8 GB |
| IP_PABPN_RPS2STAMP_Rep1_R1.fastq.gz | RIP-Seq | 2.2 GB |
| IP_PABPN_RPS2STAMP_Rep2_R1.fastq.gz | RIP-Seq | 2.0 GB |
| IP_PABPN_RPS2STAMP_Rep3_R1.fastq.gz | RIP-Seq | 2.7 GB |
| SRR17771528_GSM5839369 | RIP-Seq | 2.0 GB |
| SRR17771529_GSM5839368 | RIP-Seq | 2.0 GB |
| SRR17771530_GSM5839367 | RIP-Seq | 1.6 GB |
| SRR17771531_GSM5839366 | RIP-Seq | 2.7 GB |
| SRR17771532_GSM5839364 | RIP-Seq | 2.2 GB |
| SRR17771533_GSM5839363 | RIP-Seq | 2.2 GB |
| SRR17771534_GSM5839362 | RIP-Seq | 2.0 GB |
| SRR17771535_GSM5839365 | RIP-Seq | 2.0 GB |
| SRR17771536_GSM5839361 | RIP-Seq | 1.9 GB |
| SRR17771537_GSM5839360 | RIP-Seq | 2.1 GB |
| SRR17771538_GSM5839359 | RIP-Seq | 1.9 GB |
| SRR17771539_GSM5839358 | RIP-Seq | 1.8 GB |
| SRR17771540_GSM5839357 | RIP-Seq | 2.1 GB |
| SRR17771541_GSM5839356 | RIP-Seq | 1.9 GB |
| SRR17771542_GSM5839355 | RIP-Seq | 2.2 GB |
| SRR17771543_GSM5839354 | RIP-Seq | 2.2 GB |
| SRR17771544_GSM5839353 | RIP-Seq | 1.9 GB |
Identification of different transcripts that favor the nuclear or cytoplasmic Poly(A) Binding Proteins (PABPs) through RNA immunoprecipitation
Homo sapiens
18 data files
| File | Type | Size |
|---|---|---|
| RIP_PABPC_Rep1.fastq.gz | RIP-Seq | 1.9 GB |
| RIP_PABPC_Rep2.fastq.gz | RIP-Seq | 1.3 GB |
| RIP_PABPC_Rep3.fastq.gz | RIP-Seq | 1.5 GB |
| RIP_PABPN_Rep1.fastq.gz | RIP-Seq | 1.5 GB |
| RIP_PABPN_Rep2.fastq.gz | RIP-Seq | 1.7 GB |
| RIP_PABPN_Rep3.fastq.gz | RIP-Seq | 1.6 GB |
| SRR17771363_GSM5839378 | RIP-Seq | 1.5 GB |
| SRR17771364_GSM5839377 | RIP-Seq | 1.3 GB |
| SRR17771365_GSM5839376 | RIP-Seq | 1.9 GB |
| SRR17771366_GSM5839375 | RIP-Seq | 1.6 GB |
| SRR17771367_GSM5839374 | RIP-Seq | 1.7 GB |
| SRR17771368_GSM5839373 | RIP-Seq | 1.5 GB |
| SRR17771369_GSM5839372 | RIP-Seq | 1.7 GB |
| SRR17771370_GSM5839371 | RIP-Seq | 1.7 GB |
| SRR17771371_GSM5839370 | RIP-Seq | 1.8 GB |
| TotalInput_Rep1.fastq.gz | RIP-Seq | 1.8 GB |
| TotalInput_Rep2.fastq.gz | RIP-Seq | 1.7 GB |
| TotalInput_Rep3.fastq.gz | RIP-Seq | 1.7 GB |
Potentially related datasets 3
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.
| Accession | Source | Title |
|---|---|---|
| GSE195493 | GSE · GEO GEO ↗ | Cytoplasmic and nuclear fractionation from HEK293T cells |
| GSE195495 | GSE · GEO GEO ↗ | Identification of different transcripts that favor the nuclear or cytoplasmic Poly(A) Binding Proteins (PABPs) through RNA immunoprecipitation |
| GSE195494 | GSE · GEO GEO ↗ | Ribo-STAMP reveals translation status of RNAs bound by PABPN and PABPC |
Analysis pipelines 3
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE195493 Data Processing geo_data_processing | — | 5 | GSE195493 |
| GSE195494 Data Processing geo_data_processing | — | 5 | GSE195494 |
| GSE195495 Data Processing geo_data_processing | — | 12 | GSE195495 |
Funding 5 grants
| Grant | Funder |
|---|---|
| S10 OD026929 | NIH HHS (United States) |
| R01 HG011864 | NHGRI NIH HHS (United States) |
| T32 GM007240 | NIGMS NIH HHS (United States) |
| T32 GM008806 | NIGMS NIH HHS (United States) |
| R35 GM127012 | NIGMS NIH HHS (United States) |