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Series GSE95567 Query DataSets for GSE95567
Status Public on Jul 19, 2017
Title In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding
Organism Escherichia coli
Experiment type Expression profiling by high throughput sequencing
Other
Summary Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates’ secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5΄-halves of long-range helices get sequestered into transient non-native interactions until their 3΄ counterparts have been transcribed. Together our work provides the first transcriptome-scale overview of RNA cotranscriptional folding in a living organism.
 
Overall design Transcritome-wide mapping of nascent RNA secondary structures in Escherichia coli
 
Contributor(s) Incarnato D, Morandi E, Anselmi F, Simon LM, Basile G, Oliviero S
Citation(s) 28934475
Submission date Mar 01, 2017
Last update date Oct 18, 2017
Contact name Danny Incarnato
E-mail danny.incarnato@hugef-torino.org
Organization name HuGeF
Department Epigenetics
Street address Via Nizza 52
City Torino
State/province Italy
ZIP/Postal code 10126
Country Italy
 
Platforms (2)
GPL16085 Illumina MiSeq (Escherichia coli)
GPL21222 Illumina NextSeq 500 (Escherichia coli)
Samples (10)
GSM2516397 3'-end RNA-seq, Cytosolic fraction, Replicate #1
GSM2516400 3'-end RNA-seq, Cytosolic fraction, Replicate #2
GSM2516401 3'-end RNA-seq, Nucleoid fraction, Replicate #1
Relations
BioProject PRJNA377536
SRA SRP100931

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE95567_DMS-seq.rc.tar.gz 10.6 Mb (ftp)(http) TAR
GSE95567_RAW.tar 29.9 Mb (http)(custom) TAR (of BEDGRAPH, TAR)
GSE95567_SPET-seq.rc.tar.gz 29.4 Mb (ftp)(http) TAR
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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