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RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent
Pre-mRNAs and chromatin sites
#MMPMID25259926
Engreitz JM
; Sirokman K
; McDonel P
; Shishkin AA
; Surka C
; Russell P
; Grossman SR
; Chow AY
; Guttman M
; Lander ES
Cell
2014[Sep]; 159
(1
): 188-199
PMID25259926
show ga
Intermolecular RNA-RNA interactions are used by many noncoding RNAs (ncRNAs) to
achieve their diverse functions. To identify these contacts, we developed a
method based on RNA antisense purification to systematically map RNA-RNA
interactions (RAP-RNA) and applied it to investigate two ncRNAs implicated in RNA
processing: U1 small nuclear RNA, a component of the spliceosome, and Malat1, a
large ncRNA that localizes to nuclear speckles. U1 and Malat1 interact with
nascent transcripts through distinct targeting mechanisms. Using differential
crosslinking, we confirmed that U1 directly hybridizes to 5' splice sites and 5'
splice site motifs throughout introns and found that Malat1 interacts with
pre-mRNAs indirectly through protein intermediates. Interactions with nascent
pre-mRNAs cause U1 and Malat1 to localize proximally to chromatin at active
genes, demonstrating that ncRNAs can use RNA-RNA interactions to target specific
pre-mRNAs and genomic sites. RAP-RNA is sensitive to lower abundance RNAs as
well, making it generally applicable for investigating ncRNAs.
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