PuSH - Publication Server of Helmholtz Zentrum München

Export: TXT Text RIS Endnote (RIS) BIB BibTeX
Rot, G.* ; Wang, Z.* ; Huppertz, I.* ; Modic, M. ; Lenče, T.* ; Hallegger, M.* ; Haberman, N.* ; Curk, T.* ; von Mering, C.* ; Ule, J.*

High-resolution RNA maps suggest common principles of splicing and polyadenylation regulation by TDP-43.

Cell Rep. 19, 1056-1067 (2017)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Many RNA-binding proteins (RBPs) regulate both alternative exons and poly(A) site selection. To understand their regulatory principles, we developed expressRNA, a web platform encompassing computational tools for integration of iCLIP and RNA motif analyses with RNA-seq and 3' mRNA sequencing. This reveals at nucleotide resolution the "RNA maps" describing how the RNA binding positions of RBPs relate to their regulatory functions. We use this approach to examine how TDP-43, an RBP involved in several neurodegenerative diseases, binds around its regulated poly(A) sites. Binding close to the poly(A) site generally represses, whereas binding further downstream enhances use of the site, which is similar to TDP-43 binding around regulated exons. Our RNAmotifs2 software also identifies sequence motifs that cluster together with the binding motifs of TDP-43. We conclude that TDP-43 directly regulates diverse types of pre-mRNA processing according to common position-dependent principles.
Impact Factor
Scopus SNIP
Web of Science
Times Cited
Scopus
Cited By
Altmetric
8.282
1.749
41
42
Tags
Annotations
Special Publikation
Hide on homepage

Edit extra information
Edit own tags
Private
Edit own annotation
Private
Hide on publication lists
on hompage
Mark as special
publikation
Publication type Article: Journal article
Document type Scientific Article
Keywords 3′ Mrna Sequencing ; Rna Map ; Rnamotifs2 ; Tdp-43 ; Alternative Polyadenylation ; Alternative Splicing ; Clustered Sequence Motifs ; Expressrna ; Iclip ; Positional Regulatory Principles; Cleavage Factor-i; 3' Utr Length; Alternative Polyadenylation; Binding Proteins; Global Analyses; Prediction; Sequences; Insights; Reveals; Genes
Language english
Publication Year 2017
HGF-reported in Year 2017
ISSN (print) / ISBN 2211-1247
e-ISSN 2211-1247
Journal Cell Reports
Quellenangaben Volume: 19, Issue: 5, Pages: 1056-1067 Article Number: , Supplement: ,
Publisher Cell Press
Publishing Place Cambridge
Reviewing status Peer reviewed
Institute(s) Institute of Stem Cell Research (ISF)
POF-Topic(s) 30504 - Mechanisms of Genetic and Environmental Influences on Health and Disease
Research field(s) Stem Cell and Neuroscience
PSP Element(s) G-552400-001
PubMed ID 28467899
DOI 10.1016/j.celrep.2017.04.028
WOS ID WOS:000402124100016
Scopus ID 85018973071
Erfassungsdatum 2017-07-05
[➜Report correction]