Temporal-iCLIP captures co-transcriptional RNA-protein interactions

Ross A. Cordiner; Yuhui Dou; Rune Thomsen; Andrii Bugai; Sander Granneman; Torben Heick Jensen

doi:10.1038/s41467-023-36345-y

Temporal-iCLIP captures co-transcriptional RNA-protein interactions

Ross A. Cordiner, Yuhui Dou, Rune Thomsen, Andrii Bugai, Sander Granneman, Torben Heick Jensen^*

^*Corresponding author af dette arbejde

Institut for Molekylærbiologi og Genetik - RNA-biologi og -innovation

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

12 Citationer (Scopus)

Abstract

Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5′end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3′end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.

Originalsprog	Engelsk
Artikelnummer	696
Tidsskrift	Nature Communications
Vol/bind	14
Nummer	1
ISSN	2041-1723
DOI	https://doi.org/10.1038/s41467-023-36345-y
Status	Udgivet - dec. 2023

Adgang til dokumentet

10.1038/s41467-023-36345-y

Citationsformater

@article{94f476fad4664b7892c8ac112b4920ff,

title = "Temporal-iCLIP captures co-transcriptional RNA-protein interactions",

abstract = "Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5′end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3′end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.",

author = "Cordiner, {Ross A.} and Yuhui Dou and Rune Thomsen and Andrii Bugai and Sander Granneman and {Heick Jensen}, Torben",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s).",

year = "2023",

month = dec,

doi = "10.1038/s41467-023-36345-y",

language = "English",

volume = "14",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

TY - JOUR

T1 - Temporal-iCLIP captures co-transcriptional RNA-protein interactions

AU - Cordiner, Ross A.

AU - Dou, Yuhui

AU - Thomsen, Rune

AU - Bugai, Andrii

AU - Granneman, Sander

AU - Heick Jensen, Torben

PY - 2023/12

Y1 - 2023/12

N2 - Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5′end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3′end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.

AB - Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5′end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3′end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.

U2 - 10.1038/s41467-023-36345-y

DO - 10.1038/s41467-023-36345-y

M3 - Journal article

C2 - 36755023

AN - SCOPUS:85147666540

SN - 2041-1723

VL - 14

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 696

ER -

Temporal-iCLIP captures co-transcriptional RNA-protein interactions

Abstract

Adgang til dokumentet

Fingeraftryk

Citationsformater