Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts

RATIONALE:Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers li...

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Veröffentlicht in:Circulation research 2011-12, Vol.109 (12), p.1332-1341
Hauptverfasser: Lee, Jae-Hyung, Gao, Chen, Peng, Guangdun, Greer, Christopher, Ren, Shuxun, Wang, Yibin, Xiao, Xinshu
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container_end_page 1341
container_issue 12
container_start_page 1332
container_title Circulation research
container_volume 109
creator Lee, Jae-Hyung
Gao, Chen
Peng, Guangdun
Greer, Christopher
Ren, Shuxun
Wang, Yibin
Xiao, Xinshu
description RATIONALE:Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level. OBJECTIVE:To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels. METHODS AND RESULTS:In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (ie, novel genes), and long noncoding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts after pressure-overload–induced by transaortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNA-Seq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations. CONCLUSIONS:Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. Applications of the methods may infer important new insights to gene regulation in normal and disease hearts in terms of exon utilization and potential involvement of novel components of cardiac transcriptome.
doi_str_mv 10.1161/CIRCRESAHA.111.249433
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Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level. OBJECTIVE:To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels. METHODS AND RESULTS:In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (ie, novel genes), and long noncoding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts after pressure-overload–induced by transaortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNA-Seq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations. CONCLUSIONS:Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. 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Psychology ; Gene Expression Profiling - methods ; Gene Expression Regulation - physiology ; Heart ; Heart - physiology ; Heart Failure - genetics ; Heart Failure - physiopathology ; Heart failure, cardiogenic pulmonary edema, cardiac enlargement ; High-Throughput Nucleotide Sequencing - methods ; Male ; Medical sciences ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Sequence Analysis, RNA - methods ; Transcription, Genetic - genetics ; Transcription, Genetic - physiology ; Vertebrates: cardiovascular system</subject><ispartof>Circulation research, 2011-12, Vol.109 (12), p.1332-1341</ispartof><rights>2011 American Heart Association, Inc.</rights><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5853-54be602582d40fcc7ce8edb88762a18ac3b61b110f115c52d2aac2429430cf953</citedby><cites>FETCH-LOGICAL-c5853-54be602582d40fcc7ce8edb88762a18ac3b61b110f115c52d2aac2429430cf953</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,3674,27901,27902</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&amp;idt=25280556$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22034492$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Jae-Hyung</creatorcontrib><creatorcontrib>Gao, Chen</creatorcontrib><creatorcontrib>Peng, Guangdun</creatorcontrib><creatorcontrib>Greer, Christopher</creatorcontrib><creatorcontrib>Ren, Shuxun</creatorcontrib><creatorcontrib>Wang, Yibin</creatorcontrib><creatorcontrib>Xiao, Xinshu</creatorcontrib><title>Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts</title><title>Circulation research</title><addtitle>Circ Res</addtitle><description>RATIONALE:Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level. OBJECTIVE:To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels. METHODS AND RESULTS:In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (ie, novel genes), and long noncoding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts after pressure-overload–induced by transaortic constriction. 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Vascular system</subject><subject>Disease Models, Animal</subject><subject>Exons - genetics</subject><subject>Exons - physiology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation - physiology</subject><subject>Heart</subject><subject>Heart - physiology</subject><subject>Heart Failure - genetics</subject><subject>Heart Failure - physiopathology</subject><subject>Heart failure, cardiogenic pulmonary edema, cardiac enlargement</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Male</subject><subject>Medical sciences</subject><subject>Mice</subject><subject>Mice, Inbred C57BL</subject><subject>Molecular Sequence Data</subject><subject>Sequence Analysis, RNA - methods</subject><subject>Transcription, Genetic - genetics</subject><subject>Transcription, Genetic - physiology</subject><subject>Vertebrates: cardiovascular system</subject><issn>0009-7330</issn><issn>1524-4571</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1P3DAQhi3Uqiy0P4HKl4pTwOOPbHyMIugiAZWW7dlyHId1ceLFTkT335PVLnDkNJrRMzPvzIvQGZALgBwuq5tltbx6KBfllMMF5ZIzdoRmICjPuJjDFzQjhMhszhg5Ricp_SMEOKPyGzqmlDDOJZ0hVfbab5NLOLR4FXWfTHSbIXQWV6HbePvfDVu8WscwPq7x8r7ED_Z5tL1x_SN2Pb4PsdMe677B19r5XfVujK63eGF1HNJ39LXVPtkfh3iK_l5frapFdvvn901V3mZGFIJlgtc2J1QUtOGkNWZubGGbuijmOdVQaMPqHGoA0gIII2hDtTaU0-loYlop2Ck638_dxDDpS4PqXDLWe93bMCYlaS4JK_L8cxJAUplTOZFiT5oYUoq2VZvoOh23CojamaA-TJhyUHsTpr6fhw1j3dnmvevt6xPw6wDoZLRvp7cblz44QQsixE6q3HMvwQ82pic_vtio1lb7Yf2JiFcpoqHV</recordid><startdate>20111209</startdate><enddate>20111209</enddate><creator>Lee, Jae-Hyung</creator><creator>Gao, Chen</creator><creator>Peng, Guangdun</creator><creator>Greer, Christopher</creator><creator>Ren, Shuxun</creator><creator>Wang, Yibin</creator><creator>Xiao, Xinshu</creator><general>American Heart Association, Inc</general><general>Lippincott Williams &amp; Wilkins</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TM</scope></search><sort><creationdate>20111209</creationdate><title>Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts</title><author>Lee, Jae-Hyung ; Gao, Chen ; Peng, Guangdun ; Greer, Christopher ; Ren, Shuxun ; Wang, Yibin ; Xiao, Xinshu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5853-54be602582d40fcc7ce8edb88762a18ac3b61b110f115c52d2aac2429430cf953</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>Cardiology. Vascular system</topic><topic>Disease Models, Animal</topic><topic>Exons - genetics</topic><topic>Exons - physiology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene Expression Regulation - physiology</topic><topic>Heart</topic><topic>Heart - physiology</topic><topic>Heart Failure - genetics</topic><topic>Heart Failure - physiopathology</topic><topic>Heart failure, cardiogenic pulmonary edema, cardiac enlargement</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Male</topic><topic>Medical sciences</topic><topic>Mice</topic><topic>Mice, Inbred C57BL</topic><topic>Molecular Sequence Data</topic><topic>Sequence Analysis, RNA - methods</topic><topic>Transcription, Genetic - genetics</topic><topic>Transcription, Genetic - physiology</topic><topic>Vertebrates: cardiovascular system</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lee, Jae-Hyung</creatorcontrib><creatorcontrib>Gao, Chen</creatorcontrib><creatorcontrib>Peng, Guangdun</creatorcontrib><creatorcontrib>Greer, Christopher</creatorcontrib><creatorcontrib>Ren, Shuxun</creatorcontrib><creatorcontrib>Wang, Yibin</creatorcontrib><creatorcontrib>Xiao, Xinshu</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Nucleic Acids Abstracts</collection><jtitle>Circulation research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lee, Jae-Hyung</au><au>Gao, Chen</au><au>Peng, Guangdun</au><au>Greer, Christopher</au><au>Ren, Shuxun</au><au>Wang, Yibin</au><au>Xiao, Xinshu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts</atitle><jtitle>Circulation research</jtitle><addtitle>Circ Res</addtitle><date>2011-12-09</date><risdate>2011</risdate><volume>109</volume><issue>12</issue><spage>1332</spage><epage>1341</epage><pages>1332-1341</pages><issn>0009-7330</issn><eissn>1524-4571</eissn><coden>CIRUAL</coden><abstract>RATIONALE:Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. 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subjects Animals
Biological and medical sciences
Cardiology. Vascular system
Disease Models, Animal
Exons - genetics
Exons - physiology
Fundamental and applied biological sciences. Psychology
Gene Expression Profiling - methods
Gene Expression Regulation - physiology
Heart
Heart - physiology
Heart Failure - genetics
Heart Failure - physiopathology
Heart failure, cardiogenic pulmonary edema, cardiac enlargement
High-Throughput Nucleotide Sequencing - methods
Male
Medical sciences
Mice
Mice, Inbred C57BL
Molecular Sequence Data
Sequence Analysis, RNA - methods
Transcription, Genetic - genetics
Transcription, Genetic - physiology
Vertebrates: cardiovascular system
title Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts
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