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Series GSE149018 Query DataSets for GSE149018
Status Public on Feb 09, 2021
Title Alternative RNA Stuctures Formed During Transcription Depend on Elongation Rate and Modify RNA processing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Most RNA processing occurs co-transcriptionally. We interrogated nascent pol II transcripts by chemical and enzymatic probing, and determined how the “nascent RNA structureome” relates to splicing, A-I editing and transcription speed. RNA folding within introns and steep structural transitions at splice sites are associated with efficient co-transcriptional splicing. A slow pol II mutant elicits extensive remodeling into more folded conformations with increased A-I editing. Introns that become more structured at their 3’ splice sites get co-transcriptionally excised more efficiently. Slow pol II altered folding of intronic Alu elements where cryptic splicing and intron retention are stimulated, an outcome mimicked by UV which decelerates transcription. Slow transcription also remodeled RNA folding around alternative exons in distinct ways that predict whether skipping or inclusion is favored, even though it occurs post-transcriptionally. Hence co-transcriptional RNA folding modulates post-transcriptional alternative splicing. In summary the plasticity of nascent transcripts has widespread effects on RNA processing.
 
Overall design RNA pol II immunoprecipiation in isogenic HEK293 cells expressing a slow pol II mutant or wild type pol II was combinded with either in vivo chemical RNA structure probing using DMS or enzymatic probing using structure specific nuleases to identify cotranscriptional RNA structures
 
Contributor(s) Bentley D, Erickson B
Citation(s) 33631106
Submission date Apr 21, 2020
Last update date May 11, 2021
Contact name David Bentley
E-mail(s) David.Bentley@ucdenver.edu
Phone 3037243237
Organization name UCD AMC
Department BMG
Lab Bentley
Street address 12801 E. 17th Ave, RC1 So. RM 10401D
City Aurora
State/province Colorado
ZIP/Postal code 80045
Country USA
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (38)
GSM4487503 tNetSeq WT pol II Rep1
GSM4487504 tNetSeq WT pol II Rep2
GSM4487505 tNetSeq WT pol II Rep3
Relations
BioProject PRJNA627155
SRA SRP257709

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Supplementary file Size Download File type/resource
GSE149018_Processed_File-to-GSM_Mapping_README.xlsx 12.3 Kb (ftp)(http) XLSX
GSE149018_processed_data_files.tar.gz 5.6 Gb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record
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