Identification of gene 3′ ends by automated EST cluster analysis

Abstract

The properties and biology of mRNA transcripts can be affected profoundly by the choice of alternative polyadenylation sites, making definition of the 3′ ends of transcripts essential for understanding their regulation. Here we show that 22–52% of sequences in commonly used human and murine “full-length” transcript databases may not currently end at bona fide polyadenylation sites. To identify probable transcript termini over the entire murine and human genomes, we analyzed the EST databases for positional clustering of EST ends. The analysis yielded 58,282 murine- and 86,410 human-candidate polyadenylation sites, of which 75% mapped to 23,091 known murine transcripts and 22,891 known human transcripts. The murine dataset correctly predicted 97% of the 3′ ends in a manually curated and experimentally supported benchmark transcript set. Of currently known genes, 15% had no associated prediction and 25% had only a single predicted termination site. The remaining genes had an average of 3–4 alternative polyadenylation sites predicted for each murine or human transcript, respectively. The results are made available in the form of tables and an interactive web site that can be mined for rapid assessment of the validity of 3′ ends in existing collections, enumeration of potential alternative 3′ polyadenylation sites of known transcripts, direct retrieval of terminal sequences for design of probes, and detection of polyadenylation sites not currently mapped to known genes.

Autoren

Enrique M Muro
Robert Herrington
Salima Janmohamed
Catherine Frelin
Miguel A Andrade-Navarro
Norman N Iscove

DOI

10.1073/pnas.0807813105

eISSN

1091-6490

ISSN

0027-8424

Ausgabe der Veröffentlichung

51

Zeitschrift

Proceedings of the National Academy of Sciences

Sprache

en

Online publication date

2008

Paginierung

20286 - 20290

Datum der Veröffentlichung

2008

Status

Published

Herausgeber

Proceedings of the National Academy of Sciences

Herausgeber URL

http://dx.doi.org/10.1073/pnas.0807813105

Datum der Datenerfassung

2022

Titel

Identification of gene 3′ ends by automated EST cluster analysis

Ausgabe der Zeitschrift

105

Data source: Crossref

Abstract

The properties and biology of mRNA transcripts can be affected profoundly by the choice of alternative polyadenylation sites, making definition of the 3' ends of transcripts essential for understanding their regulation. Here we show that 22-52% of sequences in commonly used human and murine "full-length" transcript databases may not currently end at bona fide polyadenylation sites. To identify probable transcript termini over the entire murine and human genomes, we analyzed the EST databases for positional clustering of EST ends. The analysis yielded 58,282 murine- and 86,410 human-candidate polyadenylation sites, of which 75% mapped to 23,091 known murine transcripts and 22,891 known human transcripts. The murine dataset correctly predicted 97% of the 3' ends in a manually curated and experimentally supported benchmark transcript set. Of currently known genes, 15% had no associated prediction and 25% had only a single predicted termination site. The remaining genes had an average of 3-4 alternative polyadenylation sites predicted for each murine or human transcript, respectively. The results are made available in the form of tables and an interactive web site that can be mined for rapid assessment of the validity of 3' ends in existing collections, enumeration of potential alternative 3' polyadenylation sites of known transcripts, direct retrieval of terminal sequences for design of probes, and detection of polyadenylation sites not currently mapped to known genes.

Addresses

Ottawa Health Research Institute, 501 Smyth Road, Ottawa, ON, Canada K1H 8L6.

Autoren

Enrique M Muro
Robert Herrington
Salima Janmohamed
Catherine Frelin
Miguel A Andrade-Navarro
Norman N Iscove

DOI

10.1073/pnas.0807813105

eISSN

1091-6490

Externe Identifier

PubMed Identifier: 19095794
PubMed Central ID: PMC2629301

Open access

false

ISSN

0027-8424

Ausgabe der Veröffentlichung

51

Zeitschrift

Proceedings of the National Academy of Sciences of the United States of America

Schlüsselwörter

Animals
Humans
Mice
Poly A
Cluster Analysis
Methods
Polyadenylation
3' Flanking Region
Expressed Sequence Tags

Sprache

eng

Medium

Print-Electronic

Online publication date

2008

Paginierung

20286 - 20290

Datum der Veröffentlichung

2008

Status

Published

Datum der Datenerfassung

2008

Titel

Identification of gene 3' ends by automated EST cluster analysis.

Sub types

Research Support, Non-U.S. Gov't
research-article
Journal Article

Ausgabe der Zeitschrift

105

Files

http://www.pnas.org/content/105/51/20286.full.pdf http://www.pnas.org/cgi/reprint/105/51/20286.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19095794/pdf/?tool=EBI https://europepmc.org/articles/PMC2629301?pdf=render

Data source: Europe PubMed Central

Abstract

The properties and biology of mRNA transcripts can be affected profoundly by the choice of alternative polyadenylation sites, making definition of the 3' ends of transcripts essential for understanding their regulation. Here we show that 22-52% of sequences in commonly used human and murine "full-length" transcript databases may not currently end at bona fide polyadenylation sites. To identify probable transcript termini over the entire murine and human genomes, we analyzed the EST databases for positional clustering of EST ends. The analysis yielded 58,282 murine- and 86,410 human-candidate polyadenylation sites, of which 75% mapped to 23,091 known murine transcripts and 22,891 known human transcripts. The murine dataset correctly predicted 97% of the 3' ends in a manually curated and experimentally supported benchmark transcript set. Of currently known genes, 15% had no associated prediction and 25% had only a single predicted termination site. The remaining genes had an average of 3-4 alternative polyadenylation sites predicted for each murine or human transcript, respectively. The results are made available in the form of tables and an interactive web site that can be mined for rapid assessment of the validity of 3' ends in existing collections, enumeration of potential alternative 3' polyadenylation sites of known transcripts, direct retrieval of terminal sequences for design of probes, and detection of polyadenylation sites not currently mapped to known genes.

Autoren

Enrique M Muro
Robert Herrington
Salima Janmohamed
Catherine Frelin
Miguel A Andrade-Navarro
Norman N Iscove

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/19095794

DOI

10.1073/pnas.0807813105

eISSN

1091-6490

Externe Identifier

PubMed Central ID: PMC2629301

Ausgabe der Veröffentlichung

51

Zeitschrift

Proc Natl Acad Sci U S A

Schlüsselwörter

3' Flanking Region
Animals
Cluster Analysis
Expressed Sequence Tags
Humans
Methods
Mice
Poly A
Polyadenylation

Sprache

eng

Country

United States

Paginierung

20286 - 20290

PII

0807813105

Datum der Veröffentlichung

2008

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2009

Titel

Identification of gene 3' ends by automated EST cluster analysis.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

105

Data source: PubMed

Identification of gene 3′ ends by automated EST cluster analysis

Files

Tools