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| Status |
Public on Mar 11, 2020 |
| Title |
Harnessing enhanced nucleotide chemistry and toehold nanotechnology to reveal lncRNA spreading on chromatin |
| Organisms |
Drosophila melanogaster; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress. Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
Refer to individual Series
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| Contributor(s) |
Machyna M, Kiefer L, Simon MD |
| Citation missing |
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| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| DP2 HD083992 |
Integrating RNAs into signaling pathways by engineering covalent RNA modification |
YALE UNIVERSITY |
Matthew David Simon |
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| |
| Submission date |
Sep 19, 2018 |
| Last update date |
Mar 13, 2020 |
| Contact name |
Matthew D Simon |
| E-mail(s) |
matthew.simon@yale.edu
|
| Phone |
2037373274
|
| Organization name |
Yale University Chemical Biology Instiute
|
| Department |
Molecular Biophysics & Biochemistry
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| Lab |
Simon Lab
|
| Street address |
600 West Campus Dr. MIC312
|
| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516 |
| Country |
USA |
| |
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| Platforms (4)
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| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
| GPL21306 |
Illumina HiSeq 4000 (Drosophila melanogaster) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
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| Samples (34)
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| This SuperSeries is composed of the following SubSeries:
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| GSE120217 |
thCHART of roX2 lncRNA [DNA] |
| GSE120218 |
thCHART of roX2 lncRNA [RNA] |
| GSE120219 |
TT-TimeLaps-seq of S2 cells response to heat shock |
|
| Relations |
| BioProject |
PRJNA492138 |
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