Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
Nicole M Martinez, Amanda Su, Margaret C Burns, Julia K Nussbacher, Cassandra Schaening, Shashank Sathe, Gene W Yeo, Wendy V Gilbert
Molecular cell · 2022 · Vol. 82 (3) · pp. 645-659.e9
Abstract
Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine profiling on chromatin-associated RNA from human cells, we identified pseudouridines in nascent pre-mRNA at locations associated with alternatively spliced regions, enriched near splice sites, and overlapping hundreds of binding sites for RNA-binding proteins. In vitro splicing assays establish a direct effect of individual endogenous pre-mRNA pseudouridines on splicing efficiency. We validate hundreds of pre-mRNA sites as direct targets of distinct pseudouridine synthases and show that PUS1, PUS7, and RPUSD4-three pre-mRNA-modifying pseudouridine synthases with tissue-specific expression-control widespread changes in alternative pre-mRNA splicing and 3' end processing. Our results establish a vast potential for cotranscriptional pre-mRNA pseudouridylation to regulate human gene expression via alternative pre-mRNA processing.
Linked datasets 1
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicingÂ
Homo sapiens
120 data files
| File | Type | Size |
|---|---|---|
| Control-1-Resub_R1_001.fastq.gz | OTHER | 14.9 GB |
| Control-2-Resub_R1_001.fastq.gz | OTHER | 9.3 GB |
| shPUS71_S1_L001_R1_001.fastq.gz | OTHER | 7.5 GB |
| shPUS72_S1_L001_R1_001.fastq.gz | OTHER | 7.1 GB |
| shPUS73_S1_L001_R1_001.fastq.gz | OTHER | 6.7 GB |
| shRPUSD4-1-Resub_R1_001.fastq.gz | OTHER | 11.1 GB |
| shRPUSD4-2-Resub_R1_001.fastq.gz | OTHER | 15.0 GB |
| SRR16967339_GSM5693557 | OTHER | 8.6 GB |
| SRR16967340_GSM5693558 | OTHER | 7.5 GB |
| SRR16967341_GSM5693559 | OTHER | 9.7 GB |
| SRR16967342_GSM5693560 | OTHER | 7.1 GB |
| SRR16967343_GSM5693561 | OTHER | 10.3 GB |
| SRR16967344_GSM5693562 | OTHER | 6.7 GB |
| SRR16967345_GSM5693563 | OTHER | 14.9 GB |
| SRR16967346_GSM5693564 | OTHER | 11.1 GB |
| SRR16967347_GSM5693565 | OTHER | 9.3 GB |
| SRR16967348_GSM5693566 | OTHER | 15.0 GB |
| SRR8311135 | OTHER | 756.3 MB |
| SRR8311135_GSM3507940 | OTHER | 756.0 MB |
| SRR8311136 | OTHER | 910.4 MB |
| SRR8311136_GSM3507941 | OTHER | 910.0 MB |
| SRR8311137 | OTHER | 766.5 MB |
| SRR8311137_GSM3507942 | OTHER | 766.0 MB |
| SRR8311138 | OTHER | 885.4 MB |
| SRR8311138_GSM3507943 | OTHER | 885.0 MB |
| SRR8311139 | OTHER | 506.5 MB |
| SRR8311139_GSM3507944 | OTHER | 506.0 MB |
| SRR8311140 | OTHER | 771.9 MB |
| SRR8311140_GSM3507945 | OTHER | 771.0 MB |
| SRR8311141 | OTHER | 798.2 MB |
| SRR8311141_GSM3507946 | OTHER | 798.0 MB |
| SRR8311142 | OTHER | 837.8 MB |
| SRR8311142_GSM3507947 | OTHER | 837.0 MB |
| SRR8311143 | OTHER | 642.9 MB |
| SRR8311143_GSM3507948 | OTHER | 642.0 MB |
| SRR8311144 | OTHER | 412.0 MB |
| SRR8311144_GSM3507949 | OTHER | 412.0 MB |
| SRR8311145 | OTHER | 814.3 MB |
| SRR8311145_GSM3507950 | OTHER | 814.0 MB |
| SRR8311146 | OTHER | 538.5 MB |
| SRR8311146_GSM3507951 | OTHER | 538.0 MB |
| SRR8311147 | OTHER | 646.5 MB |
| SRR8311147_GSM3507952 | OTHER | 646.0 MB |
| SRR8311148 | OTHER | 514.0 MB |
| SRR8311148_GSM3507953 | OTHER | 513.0 MB |
| SRR8311149 | OTHER | 477.4 MB |
| SRR8311149_GSM3507954 | OTHER | 477.0 MB |
| SRR8311150 | OTHER | 510.4 MB |
| SRR8311150_GSM3507955 | OTHER | 510.0 MB |
| SRR8311151 | OTHER | 661.5 MB |
| SRR8311151_GSM3507956 | OTHER | 661.0 MB |
| SRR8311152 | OTHER | 586.3 MB |
| SRR8311152_GSM3507957 | OTHER | 586.0 MB |
| SRR8311153 | OTHER | 738.0 MB |
| SRR8311153_GSM3507958 | OTHER | 738.0 MB |
| SRR8311154 | OTHER | 686.8 MB |
| SRR8311154_GSM3507959 | OTHER | 686.0 MB |
| SRR8311155 | OTHER | 831.4 MB |
| SRR8311155_GSM3507960 | OTHER | 831.0 MB |
| SRR8311156 | OTHER | 815.6 MB |
| SRR8311156_GSM3507961 | OTHER | 815.0 MB |
| SRR8311157 | OTHER | 681.4 MB |
| SRR8311157_GSM3507962 | OTHER | 681.0 MB |
| SRR8311158 | OTHER | 654.3 MB |
| SRR8311158_GSM3507963 | OTHER | 654.0 MB |
| SRR8311159 | OTHER | 511.0 MB |
| SRR8311159_GSM3507964 | OTHER | 511.0 MB |
| SRR8311160 | OTHER | 528.6 MB |
| SRR8311160_GSM3507965 | OTHER | 528.0 MB |
| SRR8311161 | OTHER | 704.9 MB |
| SRR8311161_GSM3507966 | OTHER | 704.0 MB |
| SRR8311162 | OTHER | 449.8 MB |
| SRR8311162_GSM3507967 | OTHER | 449.0 MB |
| SRR8311163 | OTHER | 880.6 MB |
| SRR8311163_GSM3507968 | OTHER | 880.0 MB |
| SRR8311164 | OTHER | 643.6 MB |
| SRR8311164_GSM3507969 | OTHER | 643.0 MB |
| SRR8311165 | OTHER | 929.9 MB |
| SRR8311165_GSM3507970 | OTHER | 929.0 MB |
| SRR8311166 | OTHER | 725.9 MB |
| SRR8311166_GSM3507971 | OTHER | 725.0 MB |
| SRR8311167 | OTHER | 742.7 MB |
| SRR8311167_GSM3507972 | OTHER | 742.0 MB |
| SRR8311168 | OTHER | 1.1 GB |
| SRR8311168_GSM3507973 | OTHER | 1.1 GB |
| SRR8311169 | OTHER | 1.1 GB |
| SRR8311169_GSM3507974 | OTHER | 1.1 GB |
| SRR8311170 | OTHER | 514.7 MB |
| SRR8311170_GSM3507975 | OTHER | 514.0 MB |
| SRR8311171 | OTHER | 559.9 MB |
| SRR8311171_GSM3507976 | OTHER | 559.0 MB |
| SRR8311172 | OTHER | 1.2 GB |
| SRR8311172_GSM3507977 | OTHER | 1.2 GB |
| SRR8311173 | OTHER | 1.1 GB |
| SRR8311173_GSM3507978 | OTHER | 1.1 GB |
| SRR8311174 | OTHER | 1001.8 MB |
| SRR8311174_GSM3507979 | OTHER | 1001.0 MB |
| SRR8311175 | OTHER | 1.3 GB |
| SRR8311175_GSM3507980 | OTHER | 1.3 GB |
| SRR8311176 | OTHER | 1.2 GB |
| SRR8311176_GSM3507981 | OTHER | 1.2 GB |
| SRR8311177 | OTHER | 869.1 MB |
| SRR8311177_GSM3507982 | OTHER | 869.0 MB |
| SRR8311178 | OTHER | 885.8 MB |
| SRR8311178_GSM3507983 | OTHER | 885.0 MB |
| SRR8311179 | OTHER | 758.7 MB |
| SRR8311179_GSM3507984 | OTHER | 758.0 MB |
| SRR8311180 | OTHER | 1022.5 MB |
| SRR8311180_GSM3507985 | OTHER | 1022.0 MB |
| SRR8311181 | RNA-Seq | 4.6 GB |
| SRR8311181_GSM3507986 | RNA-Seq | 4.6 GB |
| SRR8311182 | RNA-Seq | 4.9 GB |
| SRR8311182_GSM3507987 | RNA-Seq | 4.9 GB |
| SRR8311183 | RNA-Seq | 5.3 GB |
| SRR8311183_GSM3507988 | RNA-Seq | 5.3 GB |
| SRR8311184 | RNA-Seq | 5.6 GB |
| SRR8311184_GSM3507989 | RNA-Seq | 5.6 GB |
| WT1_S1_L001_R1_001.fastq.gz | OTHER | 8.6 GB |
| WT2_S1_L001_R1_001.fastq.gz | OTHER | 9.7 GB |
| WT3_S1_L001_R1_001.fastq.gz | OTHER | 10.3 GB |
Potentially related datasets 6
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 |
|---|---|---|
| GSE90963 | GSE · GEO GEO ↗ | Transcriptome-wide Profiling of Multiple RNA Modifications Simultaneously at Single-base Resolution |
| GSM2418443 | GSM · GEO | No title in the index |
| GSM2418439 | GSM · GEO | No title in the index |
| GSM2418444 | GSM · GEO | No title in the index |
| GSM2418440 | GSM · GEO | No title in the index |
| GSE123613 | GSE · GEO GEO ↗ | Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing |
Analysis pipelines 2
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE123613 RNA-seq Data Processing geo_data_processing | RNA-seq | 9 | GSE123613 |
| GSE90963 Data Processing geo_data_processing | — | 35 | GSE90963 |
Funding 8 grants
| Grant | Funder |
|---|---|
| U24 HG009889 | NHGRI NIH HHS (United States) |
| R01 HG004659 | NHGRI NIH HHS (United States) |
| U41 HG009889 | NHGRI NIH HHS (United States) |
| R00 GM135537 | NIGMS NIH HHS (United States) |
| R01 GM101316 | NIGMS NIH HHS (United States) |
| T32 DK007541 | NIDDK NIH HHS (United States) |
| K99 GM135537 | NIGMS NIH HHS (United States) |
| T32 GM087237 | NIGMS NIH HHS (United States) |