Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Pratibha Jagannatha, Alexandra T Tankka, Daniel A Lorenz, Tao Yu, Brian A Yee, Kristopher W Brannan, Cathy J Zhou, Jason G Underwood, Gene W Yeo
Genome research · 2024 · Vol. 34 (11) · pp. 2012-2024
Abstract
Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed an integrated computational and experimental framework called long-read Ribo-STAMP (LR-Ribo-STAMP) that capitalizes on advancements in long-read sequencing and RNA-base editing-mediated technologies to simultaneously profile translation and transcription at both the gene and mRNA isoform levels. We also developed the EditsC metric to quantify editing and leverage the single-molecule, full-length transcript information provided by long-read sequencing. Here, we report concordance between gene-level translation profiles obtained with long-read and short-read Ribo-STAMP. We show that LR-Ribo-STAMP successfully profiles translation of mRNA isoforms and links regulatory features, such as upstream open reading frames (uORFs), to translation measurements. We apply LR-Ribo-STAMP to discovering translational differences at both the gene and isoform levels in a triple-negative breast cancer cell line under normoxia and hypoxia and find that LR-Ribo-STAMP effectively delineates orthogonal transcriptional and translation shifts between conditions. We also discover regulatory elements that distinguish translational differences at the isoform level. We highlight <i>GRK6</i>, in which hypoxia is observed to increase expression and translation of a shorter mRNA isoform, giving rise to a truncated protein without the AGC Kinase domain. Overall, LR-Ribo-STAMP is an important advance in our repertoire of methods that measures mRNA translation with isoform sensitivity.
Linked datasets 8
Long-read Ribo-STAMP simultaneously measures transcription and translation at full length isoform resolution
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| APOBEC1_only_HEK293T_rep1_ccs.bam | RNA-Seq | 493.9 MB |
| APOBEC1_only_HEK293T_rep2_ccs.bam | RNA-Seq | 474.4 MB |
| APOBEC1_only_HEK293T_rep3_ccs.bam | RNA-Seq | 361.6 MB |
| Ribo_STAMP_HEK293T_rep1_ccs.bam | RNA-Seq | 763.2 MB |
| Ribo_STAMP_HEK293T_rep2_ccs.bam | RNA-Seq | 498.9 MB |
| Ribo_STAMP_HEK293T_rep3_ccs.bam | RNA-Seq | 477.0 MB |
| Ribo_STAMP_MDA_MB_231_CoCl2_rep1_ccs.bam | RNA-Seq | 1.7 GB |
| Ribo_STAMP_MDA_MB_231_CoCl2_rep2_ccs.bam | RNA-Seq | 1.6 GB |
| Ribo_STAMP_MDA_MB_231_NT_rep1_ccs.bam | RNA-Seq | 2.2 GB |
| Ribo_STAMP_MDA_MB_231_NT_rep2_ccs.bam | RNA-Seq | 1.9 GB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| NRBF_1_S3_L001_R1_001.fastq.gz | RIP-Seq | 567.9 MB |
| NRBF_2_S4_L001_R1_001.fastq.gz | RIP-Seq | 583.6 MB |
| NTIA_1_S1_L001_R1_001.fastq.gz | RIP-Seq | 636.0 MB |
| NTIA_2_S2_L001_R1_001.fastq.gz | RIP-Seq | 333.4 MB |
| PRBF_1_S9_L001_R1_001.fastq.gz | RIP-Seq | 1.0 GB |
| PRBF_1_S9_L001_R1_001.fastq.gz | RIP-Seq | 1.0 GB |
| PRBF_2_S10_L001_R1_001.fastq.gz | RIP-Seq | 888.1 MB |
| PRBF_2_S10_L001_R1_001.fastq.gz | RIP-Seq | 888.1 MB |
| PTIA_1_S7_L001_R1_001.fastq.gz | RIP-Seq | 597.6 MB |
| PTIA_2_S8_L001_R1_001.fastq.gz | RIP-Seq | 878.5 MB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes
Homo sapiens
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| TIA_293T.rep1_clip.r1.reformatted.fq.gz | RIP-Seq | 291.5 MB |
| TIA_293T.rep1_clip.r1.reformatted.fq.gz | RIP-Seq | 291.5 MB |
| TIA_293T.rep1_clip.r1.reformatted.fq.gz | RIP-Seq | 291.5 MB |
| TIA_293T.rep1_input.NIL.r1.fq.gz | RIP-Seq | 460.5 MB |
| TIA_293T.rep1_input.NIL.r1.fq.gz | RIP-Seq | 460.5 MB |
| TIA_293T.rep1_input.NIL.r1.fq.gz | RIP-Seq | 460.5 MB |
| TIA_293T.rep1_input.NIL.r1.fq.gz | RIP-Seq | 460.5 MB |
| TIA_293T.rep2_clip.r1.reformatted.fq.gz | RIP-Seq | 178.8 MB |
| TIA_293T.rep2_clip.r1.reformatted.fq.gz | RIP-Seq | 178.8 MB |
| TIA_293T.rep2_clip.r1.reformatted.fq.gz | RIP-Seq | 178.8 MB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| RPS3-0_S5_L001_R1_001.fastq.gz | OTHER | 1.8 GB |
| RPS3-1000_S19_L002_R1_001.fastq.gz | OTHER | 1.8 GB |
| Sample_40_S68_L006_R1_001.fastq.gz | OTHER | 730.7 MB |
| Sample41_S41_merged.fastq.gz | OTHER | 63.0 MB |
| Sample42_S42_merged.fastq.gz | OTHER | 124.1 MB |
| TI_55_S13_L001_R1_001.fastq.gz | OTHER | 883.8 MB |
| TI_56_S14_L001_R1_001.fastq.gz | OTHER | 241.8 MB |
| TI_58_S15_L001_R1_001.fastq.gz | OTHER | 262.8 MB |
| TI_59_S16_L001_R1_001.fastq.gz | OTHER | 718.1 MB |
| TI_8_S6_L001_R1_001.fastq.gz | RNA-Seq | 958.8 MB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| control_STAMP_possorted_genome_bam.bam | RNA-Seq | 12.0 GB |
| control_STAMP_possorted_genome_bam.bam | RNA-Seq | 12.0 GB |
| NPC_HEK_control_STAMP_possorted_genome_bam.bam | RNA-Seq | 8.6 GB |
| NPC_HEK_control_STAMP_possorted_genome_bam.bam | RNA-Seq | 8.6 GB |
| NPC_HEK_RBFOX2_STAMP_possorted_genome_bam.bam | RNA-Seq | 8.6 GB |
| NPC_HEK_RBFOX2_STAMP_possorted_genome_bam.bam | RNA-Seq | 8.6 GB |
| RBP_STAMP_possorted_genome_bam.bam | RNA-Seq | 18.6 GB |
| RBP_STAMP_possorted_genome_bam.bam | RNA-Seq | 18.6 GB |
| RPS2_STAMP_possorted_genome_bam.bam | RNA-Seq | 12.3 GB |
| RPS2_STAMP_possorted_genome_bam.bam | RNA-Seq | 12.3 GB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| APOBEC_cDNA_all_pass.fastq.gz | RNA-Seq | 7.7 GB |
| APOBEC_cDNA_all_pass.fastq.gz | RNA-Seq | 7.7 GB |
| APOBEC_dRNA.fastq.gz | RNA-Seq | 545.2 MB |
| APOBEC_dRNA.fastq.gz | RNA-Seq | 545.2 MB |
| RBFOX2_cDNA_all_pass.fastq.gz | RNA-Seq | 21.1 GB |
| RBFOX2_cDNA_all_pass.fastq.gz | RNA-Seq | 21.1 GB |
| RBFOX2_dRNA.fastq.gz | RNA-Seq | 1.2 GB |
| RBFOX2_dRNA.fastq.gz | RNA-Seq | 1.2 GB |
| RBFOX2_dRNA.fastq.gz | RNA-Seq | 1.2 GB |
| SRR12389276.lite | RNA-Seq | 21.1 GB |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]
Homo sapiens
10 data files
| File | Type | Size |
|---|---|---|
| CCS_Demux_5759_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… | OTHER | 32.0 MB |
| CCS_Demux_5759_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… | OTHER | 29.7 MB |
| CCS_Demux_5759_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… | OTHER | 20.7 MB |
| CCS_Demux_5779_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… | OTHER | 327.6 MB |
| CCS_Demux_6465_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… | OTHER | 37.6 MB |
| CCS_Demux_6465_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… | OTHER | 55.7 MB |
| CCS_Demux_6465_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… | OTHER | 37.0 MB |
| CCS_Demux_6499_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… | OTHER | 43.8 MB |
| CCS_Demux_6499_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… | OTHER | 34.3 MB |
| CCS_Demux_6499_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… | OTHER | 28.8 MB |
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.
| Accession | Source | Title |
|---|---|---|
| PXD020630 | PXD · PRIDE | No title in the index |
Funding 9 grants
| Grant | Funder |
|---|---|
| U24 HG009889 | NHGRI NIH HHS (United States) |
| R01 HG004659 | NHGRI NIH HHS (United States) |
| RF1 MH126719 | NIMH NIH HHS (United States) |
| R01 HG011864 | NHGRI NIH HHS (United States) |
| T32 CA067754 | NCI NIH HHS (United States) |
| U41 HG009889 | NHGRI NIH HHS (United States) |
| R01 CA284315 | NCI NIH HHS (United States) |
| T32 GM145427 | NIGMS NIH HHS (United States) |
| K22 NS112678 | NINDS NIH HHS (United States) |