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...
Gespeichert in:
Veröffentlicht in: | Circulation research 2011-12, Vol.109 (12), p.1332-1341 |
---|---|
Hauptverfasser: | , , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
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 |
format | Article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_926903866</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>911929629</sourcerecordid><originalsourceid>FETCH-LOGICAL-c5853-54be602582d40fcc7ce8edb88762a18ac3b61b110f115c52d2aac2429430cf953</originalsourceid><addsrcrecordid>eNqFkU1P3DAQhi3Uqiy0P4HKl4pTwOOPbHyMIugiAZWW7dlyHId1ceLFTkT335PVLnDkNJrRMzPvzIvQGZALgBwuq5tltbx6KBfllMMF5ZIzdoRmICjPuJjDFzQjhMhszhg5Ricp_SMEOKPyGzqmlDDOJZ0hVfbab5NLOLR4FXWfTHSbIXQWV6HbePvfDVu8WscwPq7x8r7ED_Z5tL1x_SN2Pb4PsdMe677B19r5XfVujK63eGF1HNJ39LXVPtkfh3iK_l5frapFdvvn901V3mZGFIJlgtc2J1QUtOGkNWZubGGbuijmOdVQaMPqHGoA0gIII2hDtTaU0-loYlop2Ck638_dxDDpS4PqXDLWe93bMCYlaS4JK_L8cxJAUplTOZFiT5oYUoq2VZvoOh23CojamaA-TJhyUHsTpr6fhw1j3dnmvevt6xPw6wDoZLRvp7cblz44QQsixE6q3HMvwQ82pic_vtio1lb7Yf2JiFcpoqHV</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>911929629</pqid></control><display><type>article</type><title>Analysis of Transcriptome Complexity Through RNA Sequencing in Normal and Failing Murine Hearts</title><source>MEDLINE</source><source>American Heart Association Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Journals@Ovid Complete</source><creator>Lee, Jae-Hyung ; Gao, Chen ; Peng, Guangdun ; Greer, Christopher ; Ren, Shuxun ; Wang, Yibin ; Xiao, Xinshu</creator><creatorcontrib>Lee, Jae-Hyung ; Gao, Chen ; Peng, Guangdun ; Greer, Christopher ; Ren, Shuxun ; Wang, Yibin ; Xiao, Xinshu</creatorcontrib><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.</description><identifier>ISSN: 0009-7330</identifier><identifier>EISSN: 1524-4571</identifier><identifier>DOI: 10.1161/CIRCRESAHA.111.249433</identifier><identifier>PMID: 22034492</identifier><identifier>CODEN: CIRUAL</identifier><language>eng</language><publisher>Hagerstown, MD: American Heart Association, Inc</publisher><subject>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</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&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. 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.</description><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Cardiology. 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 & 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. 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.</abstract><cop>Hagerstown, MD</cop><pub>American Heart Association, Inc</pub><pmid>22034492</pmid><doi>10.1161/CIRCRESAHA.111.249433</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0009-7330 |
ispartof | Circulation research, 2011-12, Vol.109 (12), p.1332-1341 |
issn | 0009-7330 1524-4571 |
language | eng |
recordid | cdi_proquest_miscellaneous_926903866 |
source | MEDLINE; American Heart Association Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Journals@Ovid Complete |
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 |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-30T23%3A40%3A01IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Analysis%20of%20Transcriptome%20Complexity%20Through%20RNA%20Sequencing%20in%20Normal%20and%20Failing%20Murine%20Hearts&rft.jtitle=Circulation%20research&rft.au=Lee,%20Jae-Hyung&rft.date=2011-12-09&rft.volume=109&rft.issue=12&rft.spage=1332&rft.epage=1341&rft.pages=1332-1341&rft.issn=0009-7330&rft.eissn=1524-4571&rft.coden=CIRUAL&rft_id=info:doi/10.1161/CIRCRESAHA.111.249433&rft_dat=%3Cproquest_cross%3E911929629%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=911929629&rft_id=info:pmid/22034492&rfr_iscdi=true |