TY  - JOUR
A1  - Kappel, Christian
A1  - Trost, Gerda
A1  - Czesnick, Hjördis
A1  - Ramming, Anna
A1  - Kolbe, Benjamin
A1  - Vi, Son Lang
A1  - Bispo, Claudia
A1  - Becker, Jörg D.
A1  - de Moor, Cornelia
A1  - Lenhard, Michael
T1  - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
JF  - PLoS Genetics : a peer-reviewed, open-access journal
N2  - The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
Y1  - 2015
U6  - https://doi.org/10.1371/journal.pgen.1005474
SN  - 1553-7390
SN  - 1553-7404
VL  - 11
IS  - 8
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - GEN
A1  - Kappel, Christian
A1  - Trost, Gerda
A1  - Czesnick, Hjördis
A1  - Ramming, Anna
A1  - Kolbe, Benjamin
A1  - Vi, Song Lang
A1  - Bispo, Cláudia
A1  - Becker, Jörg D.
A1  - de Moor, Cornelia
A1  - Lenhard, Michael
T1  - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
N2  - The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 259 
KW  - comprehensive analysis
KW  - cytoplasmic polyadenylation
KW  - differential expression analysis
KW  - gene-expression
KW  - mammalian-cells
KW  - messenger-rna polyadenylation
KW  - poly(a)-binding protein
KW  - specificity factor
KW  - tail-length
KW  - translational control
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-96400
SP  - 1
EP  - 30
ER  - 
TY  - JOUR
A1  - Kappel, Christian
A1  - Trost, Gerda
A1  - Czesnick, Hjördis
A1  - Ramming, Anna
A1  - Kolbe, Benjamin
A1  - Vi, Son Lang
A1  - Bispo, Cláudia
A1  - Becker, Jörg D.
A1  - de Moor, Cornelia
A1  - Lenhard, Michael
T1  - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
JF  - PLoS Genetics : a peer-reviewed, open-access journal
N2  - The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
KW  - messenger-rna polyadenylation
KW  - differential expression analysis
KW  - gene-expression
KW  - tail-length
KW  - cytoplasmic polyadenylation
KW  - poly(a)-binding protein
KW  - translational control
KW  - comprehensive analysis
KW  - specificity factor
KW  - mammalian-cells
Y1  - 2015
U6  - https://doi.org/10.1371/journal.pgen.1005474
SN  - 1553-7390
SN  - 1553-7404
VL  - 11
IS  - 8
PB  - Public Library of Science
CY  - San Francisco
ER  -