Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.

<h4>Background</h4>Downstream targets for a large number of RNA-binding proteins remain to be identified. The Drosophila master sex-switch protein Sex-lethal (SXL) is an RNA-binding protein that controls splicing, polyadenylation, or translation of certain mRNAs to mediate female-specifi...

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Autores principales:	Hiren Banerjee, Ravinder Singh
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/639a3309b8234888b2adda66c5f1041c
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spelling	oai:doaj.org-article:639a3309b8234888b2adda66c5f1041c2021-12-02T20:05:33ZGenomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.1932-620310.1371/journal.pone.0250592https://doaj.org/article/639a3309b8234888b2adda66c5f1041c2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0250592https://doaj.org/toc/1932-6203<h4>Background</h4>Downstream targets for a large number of RNA-binding proteins remain to be identified. The Drosophila master sex-switch protein Sex-lethal (SXL) is an RNA-binding protein that controls splicing, polyadenylation, or translation of certain mRNAs to mediate female-specific sexual differentiation. Whereas some targets of SXL are known, previous studies indicate that additional targets of SXL have escaped genetic screens.<h4>Methodology/principal findings</h4>Here, we have used an alternative molecular approach of GEnomic Selective Enrichment of Ligands by Exponential enrichment (GESELEX) using both the genomic DNA and cDNA pools from several Drosophila developmental stages to identify new potential targets of SXL. Our systematic analysis provides a comprehensive view of the Drosophila transcriptome for potential SXL-binding sites.<h4>Conclusion/significance</h4>We have successfully identified new SXL-binding sites in the Drosophila transcriptome. We discuss the significance of our analysis and that the newly identified binding sites and sequences could serve as a useful resource for the research community. This approach should also be applicable to other RNA-binding proteins for which downstream targets are unknown.Hiren BanerjeeRavinder SinghPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0250592 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hiren Banerjee Ravinder Singh Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.
description	<h4>Background</h4>Downstream targets for a large number of RNA-binding proteins remain to be identified. The Drosophila master sex-switch protein Sex-lethal (SXL) is an RNA-binding protein that controls splicing, polyadenylation, or translation of certain mRNAs to mediate female-specific sexual differentiation. Whereas some targets of SXL are known, previous studies indicate that additional targets of SXL have escaped genetic screens.<h4>Methodology/principal findings</h4>Here, we have used an alternative molecular approach of GEnomic Selective Enrichment of Ligands by Exponential enrichment (GESELEX) using both the genomic DNA and cDNA pools from several Drosophila developmental stages to identify new potential targets of SXL. Our systematic analysis provides a comprehensive view of the Drosophila transcriptome for potential SXL-binding sites.<h4>Conclusion/significance</h4>We have successfully identified new SXL-binding sites in the Drosophila transcriptome. We discuss the significance of our analysis and that the newly identified binding sites and sequences could serve as a useful resource for the research community. This approach should also be applicable to other RNA-binding proteins for which downstream targets are unknown.
format	article
author	Hiren Banerjee Ravinder Singh
author_facet	Hiren Banerjee Ravinder Singh
author_sort	Hiren Banerjee
title	Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.
title_short	Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.
title_full	Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.
title_fullStr	Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.
title_full_unstemmed	Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.
title_sort	genomic and cdna selection-amplification identifies transcriptome-wide binding sites for the drosophila protein sex-lethal.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/639a3309b8234888b2adda66c5f1041c
work_keys_str_mv	AT hirenbanerjee genomicandcdnaselectionamplificationidentifiestranscriptomewidebindingsitesforthedrosophilaproteinsexlethal AT ravindersingh genomicandcdnaselectionamplificationidentifiestranscriptomewidebindingsitesforthedrosophilaproteinsexlethal
_version_	1718375486158012416

Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal.

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