Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.

Microbial transcriptomics are providing new insights into the functional processes of microbial communities. However, analysis of each sample is still expensive and time consuming. A rapid and low cost method that would allow the identification of the most interesting samples for posterior in-depth...

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Autores principales:	Montserrat Coll-Lladó, Silvia G Acinas, Cristina Pujades, Carlos Pedrós-Alió
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e8061c10125d442084287bf2334775c2
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spelling	oai:doaj.org-article:e8061c10125d442084287bf2334775c22021-11-18T06:48:26ZTranscriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.1932-620310.1371/journal.pone.0022950https://doaj.org/article/e8061c10125d442084287bf2334775c22011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21857972/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Microbial transcriptomics are providing new insights into the functional processes of microbial communities. However, analysis of each sample is still expensive and time consuming. A rapid and low cost method that would allow the identification of the most interesting samples for posterior in-depth metatranscriptomics analysis would be extremely useful. Here we present Transcriptome Fingerprinting Analysis (TFA) as an approach to fulfill this objective in microbial ecology studies. We have adapted the differential display technique for mRNA fingerprinting based on the PCR amplification of expressed transcripts to interrogate natural microbial eukaryotic communities. Unlike other techniques, TFA does not require prior knowledge of the mRNA sequences to be detected. We have used a set of arbitrary primers coupled with a fluorescence labeled primer targeting the poly(A) tail of the eukaryotic mRNA, with further detection of the resulting labeled cDNA products in an automated genetic analyzer. The output represented by electropherogram peak patterns allowed the comparison of a set of genes expressed at the time of sampling. TFA has been optimized by testing the sensitivity of the method for different initial RNA amounts, and the repeatability of the gene expression patterns with increasing time after sampling both with cultures and environmental samples. Results show that TFA is a promising approach to explore the dynamics of gene expression patterns in microbial communities.Montserrat Coll-LladóSilvia G AcinasCristina PujadesCarlos Pedrós-AlióPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e22950 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Montserrat Coll-Lladó Silvia G Acinas Cristina Pujades Carlos Pedrós-Alió Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.
description	Microbial transcriptomics are providing new insights into the functional processes of microbial communities. However, analysis of each sample is still expensive and time consuming. A rapid and low cost method that would allow the identification of the most interesting samples for posterior in-depth metatranscriptomics analysis would be extremely useful. Here we present Transcriptome Fingerprinting Analysis (TFA) as an approach to fulfill this objective in microbial ecology studies. We have adapted the differential display technique for mRNA fingerprinting based on the PCR amplification of expressed transcripts to interrogate natural microbial eukaryotic communities. Unlike other techniques, TFA does not require prior knowledge of the mRNA sequences to be detected. We have used a set of arbitrary primers coupled with a fluorescence labeled primer targeting the poly(A) tail of the eukaryotic mRNA, with further detection of the resulting labeled cDNA products in an automated genetic analyzer. The output represented by electropherogram peak patterns allowed the comparison of a set of genes expressed at the time of sampling. TFA has been optimized by testing the sensitivity of the method for different initial RNA amounts, and the repeatability of the gene expression patterns with increasing time after sampling both with cultures and environmental samples. Results show that TFA is a promising approach to explore the dynamics of gene expression patterns in microbial communities.
format	article
author	Montserrat Coll-Lladó Silvia G Acinas Cristina Pujades Carlos Pedrós-Alió
author_facet	Montserrat Coll-Lladó Silvia G Acinas Cristina Pujades Carlos Pedrós-Alió
author_sort	Montserrat Coll-Lladó
title	Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.
title_short	Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.
title_full	Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.
title_fullStr	Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.
title_full_unstemmed	Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.
title_sort	transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/e8061c10125d442084287bf2334775c2
work_keys_str_mv	AT montserratcollllado transcriptomefingerprintinganalysisanapproachtoexploregeneexpressionpatternsinmarinemicrobialcommunities AT silviagacinas transcriptomefingerprintinganalysisanapproachtoexploregeneexpressionpatternsinmarinemicrobialcommunities AT cristinapujades transcriptomefingerprintinganalysisanapproachtoexploregeneexpressionpatternsinmarinemicrobialcommunities AT carlospedrosalio transcriptomefingerprintinganalysisanapproachtoexploregeneexpressionpatternsinmarinemicrobialcommunities
_version_	1718424387889135616

Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.

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