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Cell Rep. 2017 Mar 21;18(12):2979-2990. doi: 10.1016/j.celrep.2017.02.080.

The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation.

Author information

1
Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA.
2
Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
3
Biostatistics and Datamining Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
4
European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands.
5
Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: markus.hafner@nih.gov.
6
Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands. Electronic address: s.a.juranek@umcg.nl.

Abstract

The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs. CNBP preferentially bound G-rich elements in the target mRNA coding sequences, most of which were previously found to form G-quadruplex and other stable structures in vitro. Functional analyses, including RNA sequencing, ribosome profiling, and quantitative mass spectrometry, revealed that CNBP binding did not influence target mRNA abundance but rather increased their translational efficiency. Considering that CNBP binding prevented G-quadruplex structure formation in vitro, we hypothesize that CNBP is supporting translation by resolving stable structures on mRNAs.

KEYWORDS:

CLIP-seq; PAR-CLIP; RNA binding protein; posttranscriptional gene regulation; ribosome profiling; translational regulation; zinc-finger

PMID:
28329689
PMCID:
PMC5393907
DOI:
10.1016/j.celrep.2017.02.080
[Indexed for MEDLINE]
Free PMC Article

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