Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures

Johnny C. Loke, Eric A. Stahlberg, David G. Strenski, Brian J. Haas, Paul Chris Wood, Quinn Li Qingshun

Research output: Contribution to journalArticle

138 Citations (Scopus)

Abstract

Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly (A) signals and to develop tools to predict 3′-ends for gene annotation.

Original languageEnglish (US)
Pages (from-to)1457-1468
Number of pages12
JournalPlant Physiology
Volume138
Issue number3
DOIs
StatePublished - 2005
Externally publishedYes

Fingerprint

Polyadenylation
3' Untranslated Regions
3' untranslated regions
Arabidopsis
Messenger RNA
Nucleotides
nucleotides
Molecular Sequence Annotation
Poly A
prediction
mutagenesis
Mutagenesis
Arabidopsis thaliana
Databases
RNA
mutation
Mutation
genes

ASJC Scopus subject areas

  • Plant Science

Cite this

Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. / Loke, Johnny C.; Stahlberg, Eric A.; Strenski, David G.; Haas, Brian J.; Wood, Paul Chris; Qingshun, Quinn Li.

In: Plant Physiology, Vol. 138, No. 3, 2005, p. 1457-1468.

Research output: Contribution to journalArticle

Loke, Johnny C. ; Stahlberg, Eric A. ; Strenski, David G. ; Haas, Brian J. ; Wood, Paul Chris ; Qingshun, Quinn Li. / Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. In: Plant Physiology. 2005 ; Vol. 138, No. 3. pp. 1457-1468.
@article{18e48ef8ead04c6b955d59a4e1e73cbe,
title = "Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures",
abstract = "Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10{\%} of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly (A) signals and to develop tools to predict 3′-ends for gene annotation.",
author = "Loke, {Johnny C.} and Stahlberg, {Eric A.} and Strenski, {David G.} and Haas, {Brian J.} and Wood, {Paul Chris} and Qingshun, {Quinn Li}",
year = "2005",
doi = "10.1104/pp.105.060541",
language = "English (US)",
volume = "138",
pages = "1457--1468",
journal = "Plant Physiology",
issn = "0032-0889",
publisher = "American Society of Plant Biologists",
number = "3",

}

TY - JOUR

T1 - Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures

AU - Loke, Johnny C.

AU - Stahlberg, Eric A.

AU - Strenski, David G.

AU - Haas, Brian J.

AU - Wood, Paul Chris

AU - Qingshun, Quinn Li

PY - 2005

Y1 - 2005

N2 - Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly (A) signals and to develop tools to predict 3′-ends for gene annotation.

AB - Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly (A) signals and to develop tools to predict 3′-ends for gene annotation.

UR - http://www.scopus.com/inward/record.url?scp=27244444905&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=27244444905&partnerID=8YFLogxK

U2 - 10.1104/pp.105.060541

DO - 10.1104/pp.105.060541

M3 - Article

C2 - 15965016

AN - SCOPUS:27244444905

VL - 138

SP - 1457

EP - 1468

JO - Plant Physiology

JF - Plant Physiology

SN - 0032-0889

IS - 3

ER -