Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin.
Animals
Base Pairing
Binding Sites
Biotinylation
Chromatin
/ chemistry
Chromosome Mapping
Chromosomes, Insect
/ chemistry
Drosophila Proteins
/ genetics
Drosophila melanogaster
/ genetics
Heat-Shock Response
Nanotechnology
/ methods
Nucleic Acid Hybridization
Oligonucleotides
/ chemistry
RNA, Long Noncoding
/ chemistry
RNA-Binding Proteins
/ genetics
X Chromosome
/ chemistry
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
03 2020
03 2020
Historique:
received:
05
11
2019
accepted:
31
01
2020
entrez:
12
3
2020
pubmed:
12
3
2020
medline:
15
4
2020
Statut:
ppublish
Résumé
Understanding the targeting and spreading patterns of long non-coding RNAs (lncRNAs) on chromatin requires a technique that can detect both high-intensity binding sites and reveal genome-wide changes in spreading patterns with high precision and confidence. Here we determine lncRNA localization using biotinylated locked nucleic acid (LNA)-containing oligonucleotides with toehold architecture capable of hybridizing to target RNA through strand-exchange reaction. During hybridization, a protecting strand competitively displaces contaminating species, leading to highly specific RNA capture of individual RNAs. Analysis of Drosophila roX2 lncRNA using this approach revealed that heat shock, unlike the unfolded protein response, leads to reduced spreading of roX2 on the X chromosome, but surprisingly also to relocalization to sites on autosomes. Our results demonstrate that this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.
Identifiants
pubmed: 32157249
doi: 10.1038/s41594-020-0390-z
pii: 10.1038/s41594-020-0390-z
doi:
Substances chimiques
Chromatin
0
Drosophila Proteins
0
Oligonucleotides
0
Pabp2 protein, Drosophila
0
RNA, Long Noncoding
0
RNA-Binding Proteins
0
locked nucleic acid
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
297-304Subventions
Organisme : NICHD NIH HHS
ID : DP2 HD083992
Pays : United States
Commentaires et corrections
Type : ErratumIn
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