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Hundreds of putatively functional small open reading frames in Drosophila

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posted on 2023-06-08, 12:10 authored by Emmanuel Ladoukakis, Vini Pereira, Emile G Magny, Adam Eyre-WalkerAdam Eyre-Walker, Juan Pablo Couso
Background: The relationship between DNA sequence and encoded information is still an unsolved puzzle. The number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. Functional small open reading frames (smORFs) are known to exist in several organisms. However, coding sequence detection methods are biased against detecting such very short open reading frames. Thus, a substantial number of non-canonical coding regions encoding short peptides might await characterization. Results: Using bio-informatics methods, we have searched for smORFs of less than 100 amino acids in the putatively non-coding euchromatic DNA of Drosophila melanogaster, and initially identified nearly 600,000 of them. We have studied the pattern of conservation of these smORFs as coding entities between D. melanogaster and Drosophila pseudoobscura, their presence in syntenic and in transcribed regions of the genome, and their ratio of conservative versus non-conservative nucleotide changes. For negative controls, we compared the results with those obtained using random short sequences, while a positive control was provided by smORFs validated by proteomics data. Conclusions: The combination of these analyses led us to postulate the existence of at least 401 functional smORFs in Drosophila, with the possibility that as many as 4,561 such functional smORFs may exist.

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Publication status

  • Published

File Version

  • Published version

Journal

Genome Biology

ISSN

1465-6914

Publisher

BioMed Central

Issue

11

Volume

12

Page range

R118

Department affiliated with

  • Clinical and Experimental Medicine Publications

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2012-08-06

First Open Access (FOA) Date

2019-06-13

First Compliant Deposit (FCD) Date

2019-07-01

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