Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota
Metagenomics and other metaomics approaches (including metatranscriptomics) provide insights into the composition and function of microbial communities living in different environments or animal hosts. Metatranscriptomics research provides an unprecedented opportunity to examine gene regulation for...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00896/full |
| _version_ | 1811298697006284800 |
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| author | Guanhui eBao Mingjie eWang Thomas G. Doak Yuzhen eYe |
| author_facet | Guanhui eBao Mingjie eWang Thomas G. Doak Yuzhen eYe |
| author_sort | Guanhui eBao |
| collection | DOAJ |
| description | Metagenomics and other metaomics approaches (including metatranscriptomics) provide insights into the composition and function of microbial communities living in different environments or animal hosts. Metatranscriptomics research provides an unprecedented opportunity to examine gene regulation for many microbial species simultaneously, and more importantly, for the majority that are unculturable microbial species, in their natural environments (or hosts). Current analyses of metatranscriptomic datasets focus on the detection of gene expression levels and the study of the relationship between changes of gene expression and changes of environment. As a demonstration of utilizing metatranscriptomics beyond these common analyses, we developed a computational and statistical procedure to analyze the antisense transcripts in strand-specific metatranscriptomic datasets. Antisense RNAs encoded on the DNA strand opposite a gene’s CDS have the potential to form extensive base-pairing interactions with the corresponding sense RNA, and can have important regulatory functions. Most studies of antisense RNAs in bacteria are rather recent, are mostly based on transcriptome analysis, and have been applied mainly to single bacterial species. Application of our approaches to human gut-associated metatranscriptomic datasets allowed us to survey antisense transcription for a large number of bacterial species associated with human beings. The ratio of protein coding genes with antisense transcription ranges from zero to 35.8% (median = 10.0%) among 47 species. Our results show that antisense transcription is dynamic, varying between human individuals. Functional enrichment analysis revealed a preference of certain gene functions for antisense transcription, and transposase genes are among the most prominent ones (but we also observed antisense transcription in bacterial house-keeping genes). |
| first_indexed | 2024-04-13T06:23:11Z |
| format | Article |
| id | doaj.art-e9fdf79d1b744d30846724a923bc4d2a |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-13T06:23:11Z |
| publishDate | 2015-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-e9fdf79d1b744d30846724a923bc4d2a2022-12-22T02:58:34ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-09-01610.3389/fmicb.2015.00896149568Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiotaGuanhui eBao0Mingjie eWang1Thomas G. Doak2Yuzhen eYe3Indiana UniversityIndiana UniversityIndiana UniversityIndiana UniversityMetagenomics and other metaomics approaches (including metatranscriptomics) provide insights into the composition and function of microbial communities living in different environments or animal hosts. Metatranscriptomics research provides an unprecedented opportunity to examine gene regulation for many microbial species simultaneously, and more importantly, for the majority that are unculturable microbial species, in their natural environments (or hosts). Current analyses of metatranscriptomic datasets focus on the detection of gene expression levels and the study of the relationship between changes of gene expression and changes of environment. As a demonstration of utilizing metatranscriptomics beyond these common analyses, we developed a computational and statistical procedure to analyze the antisense transcripts in strand-specific metatranscriptomic datasets. Antisense RNAs encoded on the DNA strand opposite a gene’s CDS have the potential to form extensive base-pairing interactions with the corresponding sense RNA, and can have important regulatory functions. Most studies of antisense RNAs in bacteria are rather recent, are mostly based on transcriptome analysis, and have been applied mainly to single bacterial species. Application of our approaches to human gut-associated metatranscriptomic datasets allowed us to survey antisense transcription for a large number of bacterial species associated with human beings. The ratio of protein coding genes with antisense transcription ranges from zero to 35.8% (median = 10.0%) among 47 species. Our results show that antisense transcription is dynamic, varying between human individuals. Functional enrichment analysis revealed a preference of certain gene functions for antisense transcription, and transposase genes are among the most prominent ones (but we also observed antisense transcription in bacterial house-keeping genes).http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00896/fullMetagenomeTransposasesantisense RNAhuman gut microbiotametatranscriptome |
| spellingShingle | Guanhui eBao Mingjie eWang Thomas G. Doak Yuzhen eYe Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota Frontiers in Microbiology Metagenome Transposases antisense RNA human gut microbiota metatranscriptome |
| title | Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota |
| title_full | Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota |
| title_fullStr | Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota |
| title_full_unstemmed | Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota |
| title_short | Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota |
| title_sort | strand specific community rna seq reveals prevalent and dynamic antisense transcription in human gut microbiota |
| topic | Metagenome Transposases antisense RNA human gut microbiota metatranscriptome |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00896/full |
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