Developmental regulation of canonical and small ORF translation from mRNAs

Patraquim, Pedro, Mumtaz, Muhammad Ali Shahzad, Pueyo, Jose Ignacio, Aspden, Julie Louise and Couso, Juan-Pablo (2020) Developmental regulation of canonical and small ORF translation from mRNAs. Genome Biology, 21. a128 1-26. ISSN 1474-760X

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Abstract

Background
Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it to Drosophila melanogaster embryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis.
Results
We obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5′ mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition.
Conclusions
We suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.

Item Type: Article
Keywords: Ribosomal profiling, Poly-Ribo-Seq, Ribosomal binding, Non-canonical translation, Regulation of translation, smORFs, sORFs, uORFs, Maternal to zygotic transition
Schools and Departments: Brighton and Sussex Medical School > Brighton and Sussex Medical School
Brighton and Sussex Medical School > Clinical and Experimental Medicine
Research Centres and Groups: Developmental Genetics Research Group
Subjects: Q Science > QH Natural history > QH0301 Biology > QH0324 Methods of research. Technique. Experimental biology > QH0324.2 Data processing. Bioinformatics. General works
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0447 Genes. Alleles. Genome
Depositing User: Jose Pueyo-Marques
Date Deposited: 06 May 2020 07:32
Last Modified: 02 Jun 2020 15:00
URI: http://sro.sussex.ac.uk/id/eprint/91169

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Project NameSussex Project NumberFunderFunder Ref
Molecular and cellular functions of membrane peptides encoded by small ORFsG1791BBSRC-BIOTECHNOLOGY & BIOLOGICAL SCIENCES RESEARCH COUNCILBB/N001753/1