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  A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers

Degl'Innocenti, A., Meloni, G., Mazzolai, B., & Ciofani, G. (2019). A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers. BMC Bioinformatics, 20(1): 474. doi:10.1186/s12859-019-3012-1.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-C4CC-9 Version Permalink: http://hdl.handle.net/21.11116/0000-0004-C4CD-8
Genre: Journal Article

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 Creators:
Degl'Innocenti, Andrea1, 2, Author              
Meloni, Gabriella3, 4, Author
Mazzolai, Barbara3, Author
Ciofani, Gianni2, Author
Affiliations:
1Department of Molecular Neurogenetics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068296              
2Smart Bio-Interfaces, Istituto Italiano di Tecnologia, Pontedera (Pisa), Italy, ou_persistent22              
3Center for Micro-BioRobotics, Istituto Italiano di Tecnologia, Pontedera (Pisa), Italy, ou_persistent22              
4The BioRobotics Institute ,Scuola Superiore Sant’Anna, Pontedera (Pisa), Italy, ou_persistent22              

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Free keywords: Cluster, Element, Enhancer, Minicluster, Odorant receptor, Odorant receptor gene choice, Prediction, Sfaktiria, Solitary gene, Vomeronasal receptor
 Abstract: BACKGROUND: In most mammals, a vast array of genes coding for chemosensory receptors mediates olfaction. Odorant receptor (OR) genes generally constitute the largest multifamily (> 1100 intact members in the mouse). From the whole pool, each olfactory neuron expresses a single OR allele following poorly characterized mechanisms termed OR gene choice. OR genes are found in genomic aggregations known as clusters. Nearby enhancers, named elements, are crucial regulators of OR gene choice. Despite their importance, searching for new elements is burdensome. Other chemosensory receptor genes responsible for smell adhere to expression modalities resembling OR gene choice, and are arranged in genomic clusters - often with chromosomal linkage to OR genes. Still, no elements are known for them. RESULTS: Here we present an inexpensive framework aimed at predicting elements. We redefine cluster identity by focusing on multiple receptor gene families at once, and exemplify thirty - not necessarily OR-exclusive - novel candidate enhancers. CONCLUSIONS: The pipeline we introduce could guide future in vivo work aimed at discovering/validating new elements. In addition, our study provides an updated and comprehensive classification of all genomic loci responsible for the transduction of olfactory signals in mammals.

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Language(s): eng - English
 Dates: 2018-11-262019-07-292019-09-14
 Publication Status: Published online
 Pages: 16
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1186/s12859-019-3012-1
BibTex Citekey: deglinnocenti_purely_2019
 Degree: -

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Title: BMC Bioinformatics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: BioMed Central
Pages: - Volume / Issue: 20 (1) Sequence Number: 474 Start / End Page: - Identifier: ISSN: 1471-2105
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905000