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| Status |
Public on Feb 09, 2016 |
| Title |
Probing Xist RNA structure in cells using Targeted Structure-Seq |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.
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| Overall design |
Examination of dimethylsufate reactivity of Xist lncRNA and 18S rRNA in cells using targeted reverse transcription to determine reactivity, and comparisons with untreated control samples.
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| Contributor(s) |
Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD |
| Citation(s) |
26646615 |
| Submission date |
Apr 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew D Simon |
| E-mail(s) |
matthew.simon@yale.edu
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| Phone |
2037373274
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| Organization name |
Yale University Chemical Biology Instiute
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| Department |
Molecular Biophysics & Biochemistry
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| Lab |
Simon Lab
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| Street address |
600 West Campus Dr. MIC312
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| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA280605 |
| SRA |
SRP056972 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67667_Targeted_Structure_Seq_18S_rRNA_higher_DMS.wig.gz |
4.5 Kb |
(ftp)(http) |
WIG |
| GSE67667_Targeted_Structure_Seq_18S_rRNA_intermediate_DMS.wig.gz |
4.5 Kb |
(ftp)(http) |
WIG |
| GSE67667_Targeted_Structure_Seq_18S_rRNA_lower_DMS.wig.gz |
4.8 Kb |
(ftp)(http) |
WIG |
| GSE67667_Targeted_Structure_Seq_Xist_higher_DMS.wig.gz |
48.5 Kb |
(ftp)(http) |
WIG |
| GSE67667_Targeted_Structure_Seq_Xist_lower_DMS.wig.gz |
48.8 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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