TU Darmstadt / ULB / TUbiblio

Differential protein occupancy profiling of the mRNA transcriptome.

Schueler, Markus ; Munschauer, Mathias ; Gregersen, Lea Haarup ; Finzel, Ana ; Loewer, Alexander ; Chen, Wei ; Landthaler, Markus ; Dieterich, Christoph :
Differential protein occupancy profiling of the mRNA transcriptome.
In: Genome biology, 15 (1) R15. ISSN 1474-760X
[Artikel] , (2014)

Kurzbeschreibung (Abstract)

BACKGROUND

RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequencing. A comparison of such profiles from different biological conditions has the power to unravel dynamic changes in protein-contacted cis-regulatory mRNA regions without a priori knowledge of the regulatory protein component.

RESULTS

We compared protein occupancy profiles of polyadenylated transcripts in MCF7 and HEK293 cells. Briefly, we developed a bioinformatics workflow to identify differential crosslinking sites in cDNA reads of 4-thiouridine crosslinked polyadenylated RNA samples. We identified 30,000 differential crosslinking sites between MCF7 and HEK293 cells at an estimated false discovery rate of 10%. 73% of all reported differential protein-RNA contact sites cannot be explained by local changes in exon usage as indicated by complementary RNA-seq data. The majority of differentially crosslinked positions are located in 3' UTRs, show distinct secondary-structure characteristics and overlap with binding sites of known RBPs, such as ELAVL1. Importantly, mRNA transcripts with the most significant occupancy changes show elongated mRNA half-lives in MCF7 cells.

CONCLUSIONS

We present a global comparison of protein occupancy profiles from different cell types, and provide evidence for altered mRNA metabolism as a result of differential protein-RNA contacts. Additionally, we introduce POPPI, a bioinformatics workflow for the analysis of protein occupancy profiling experiments. Our work demonstrates the value of protein occupancy profiling for assessing cis-regulatory RNA sequence space and its dynamics in growth, development and disease.

Typ des Eintrags: Artikel
Erschienen: 2014
Autor(en): Schueler, Markus ; Munschauer, Mathias ; Gregersen, Lea Haarup ; Finzel, Ana ; Loewer, Alexander ; Chen, Wei ; Landthaler, Markus ; Dieterich, Christoph
Titel: Differential protein occupancy profiling of the mRNA transcriptome.
Sprache: Englisch
Kurzbeschreibung (Abstract):

BACKGROUND

RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequencing. A comparison of such profiles from different biological conditions has the power to unravel dynamic changes in protein-contacted cis-regulatory mRNA regions without a priori knowledge of the regulatory protein component.

RESULTS

We compared protein occupancy profiles of polyadenylated transcripts in MCF7 and HEK293 cells. Briefly, we developed a bioinformatics workflow to identify differential crosslinking sites in cDNA reads of 4-thiouridine crosslinked polyadenylated RNA samples. We identified 30,000 differential crosslinking sites between MCF7 and HEK293 cells at an estimated false discovery rate of 10%. 73% of all reported differential protein-RNA contact sites cannot be explained by local changes in exon usage as indicated by complementary RNA-seq data. The majority of differentially crosslinked positions are located in 3' UTRs, show distinct secondary-structure characteristics and overlap with binding sites of known RBPs, such as ELAVL1. Importantly, mRNA transcripts with the most significant occupancy changes show elongated mRNA half-lives in MCF7 cells.

CONCLUSIONS

We present a global comparison of protein occupancy profiles from different cell types, and provide evidence for altered mRNA metabolism as a result of differential protein-RNA contacts. Additionally, we introduce POPPI, a bioinformatics workflow for the analysis of protein occupancy profiling experiments. Our work demonstrates the value of protein occupancy profiling for assessing cis-regulatory RNA sequence space and its dynamics in growth, development and disease.

Titel der Zeitschrift, Zeitung oder Schriftenreihe: Genome biology
Band: 15
(Heft-)Nummer: 1
Fachbereich(e)/-gebiet(e): 10 Fachbereich Biologie
10 Fachbereich Biologie > Systems Biology of the Stress Response
Hinterlegungsdatum: 02 Sep 2015 08:30
Export:

Optionen (nur für Redakteure)

Eintrag anzeigen Eintrag anzeigen