In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides

It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several s...

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Autores principales:	Magali Naville, Samir Merabet
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	lncRNA smORF altORF ELM SLiM Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/41a91f9725584c88aa205953c7794462
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spelling	oai:doaj.org-article:41a91f9725584c88aa205953c77944622021-11-25T17:10:01ZIn-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides10.3390/cells101129832073-4409https://doaj.org/article/41a91f9725584c88aa205953c77944622021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4409/10/11/2983https://doaj.org/toc/2073-4409It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several selecting filters based on evolutionary conservation and annotations of previously characterized altORF peptides. Our work was performed in the <i>Bithorax-complex</i> (<i>BX-C</i>), which was one of the first genomic regions described to contain long non-coding RNAs in <i>Drosophila</i>. We showed that several altORFs could be predicted from coding and non-coding sequences of <i>BX-C</i>. In addition, the selected altORFs encode for proteins that contain several interesting molecular features, such as the presence of transmembrane helices or a general propensity to be rich in short interaction motifs. Of particular interest, one altORF encodes for a protein that contains a peptide sequence found in specific isoforms of two <i>Drosophila</i> Hox proteins. Our work thus suggests that several altORF proteins could be produced from a particular genomic region known for its critical role during <i>Drosophila</i> embryonic development. The molecular signatures of these altORF proteins further suggests that several of them could make numerous protein–protein interactions and be of functional importance in vivo.Magali NavilleSamir MerabetMDPI AGarticlelncRNAsmORFaltORFELMSLiMBiology (General)QH301-705.5ENCells, Vol 10, Iss 2983, p 2983 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	lncRNA smORF altORF ELM SLiM Biology (General) QH301-705.5
spellingShingle	lncRNA smORF altORF ELM SLiM Biology (General) QH301-705.5 Magali Naville Samir Merabet In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides
description	It is recognized that a large proportion of eukaryotic RNAs and proteins is not produced from conventional genes but from short and alternative (alt) open reading frames (ORFs) that are not captured by gene prediction programs. Here we present an in silico prediction of altORFs by applying several selecting filters based on evolutionary conservation and annotations of previously characterized altORF peptides. Our work was performed in the <i>Bithorax-complex</i> (<i>BX-C</i>), which was one of the first genomic regions described to contain long non-coding RNAs in <i>Drosophila</i>. We showed that several altORFs could be predicted from coding and non-coding sequences of <i>BX-C</i>. In addition, the selected altORFs encode for proteins that contain several interesting molecular features, such as the presence of transmembrane helices or a general propensity to be rich in short interaction motifs. Of particular interest, one altORF encodes for a protein that contains a peptide sequence found in specific isoforms of two <i>Drosophila</i> Hox proteins. Our work thus suggests that several altORF proteins could be produced from a particular genomic region known for its critical role during <i>Drosophila</i> embryonic development. The molecular signatures of these altORF proteins further suggests that several of them could make numerous protein–protein interactions and be of functional importance in vivo.
format	article
author	Magali Naville Samir Merabet
author_facet	Magali Naville Samir Merabet
author_sort	Magali Naville
title	In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides
title_short	In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides
title_full	In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides
title_fullStr	In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides
title_full_unstemmed	In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides
title_sort	in-depth annotation of the <i>drosophila bithorax-complex</i> reveals the presence of several alternative orfs that could encode for motif-rich peptides
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/41a91f9725584c88aa205953c7794462
work_keys_str_mv	AT magalinaville indepthannotationoftheidrosophilabithoraxcomplexirevealsthepresenceofseveralalternativeorfsthatcouldencodeformotifrichpeptides AT samirmerabet indepthannotationoftheidrosophilabithoraxcomplexirevealsthepresenceofseveralalternativeorfsthatcouldencodeformotifrichpeptides
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In-Depth Annotation of the <i>Drosophila Bithorax-Complex</i> Reveals the Presence of Several Alternative ORFs That Could Encode for Motif-Rich Peptides

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