Details
| Original language | English |
|---|---|
| Article number | 914 |
| Journal | BMC GENOMICS |
| Volume | 22 |
| Issue number | 1 |
| Publication status | Published - 29 Dec 2021 |
Abstract
BACKGROUND: The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box.
RESULTS: To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets.
CONCLUSIONS: Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs.
Keywords
- Bacterial Proteins/genetics, Epigenesis, Genetic, Plant Diseases/genetics, Transcription Activator-Like Effectors/genetics, Xanthomonas/genetics, Chromatin, Computational prediction, Transcription activator-like effector, DNA methylation
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Genetics
- Biochemistry, Genetics and Molecular Biology(all)
- Biotechnology
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In: BMC GENOMICS, Vol. 22, No. 1, 914, 29.12.2021.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Epigenetic features improve TALE target prediction
AU - Erkes, Annett
AU - Mücke, Stefanie
AU - Reschke, Maik
AU - Boch, Jens
AU - Grau, Jan
N1 - Funding Information: We acknowledge the financial support of the Open Access Publication Fund of the Martin Luther University Halle-Wittenberg( https://www.uni-halle.de ). This work was supported by grants from the Deutsche Forschungsgemeinschaft ( http://www.dfg.de ) (BO 1496/8-1 to JB and GR 4587/1-1 to JG) and COST Action CA16107 “EuroXanth” ( https://euroxanth.eu ) to JB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Open Access funding enabled and organized by Projekt DEAL.
PY - 2021/12/29
Y1 - 2021/12/29
N2 - BACKGROUND: The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box.RESULTS: To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets.CONCLUSIONS: Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs.
AB - BACKGROUND: The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box.RESULTS: To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets.CONCLUSIONS: Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs.
KW - Bacterial Proteins/genetics
KW - Epigenesis, Genetic
KW - Plant Diseases/genetics
KW - Transcription Activator-Like Effectors/genetics
KW - Xanthomonas/genetics
KW - Chromatin
KW - Computational prediction
KW - Transcription activator-like effector
KW - DNA methylation
UR - http://www.scopus.com/inward/record.url?scp=85122109372&partnerID=8YFLogxK
U2 - 10.1186/s12864-021-08210-z
DO - 10.1186/s12864-021-08210-z
M3 - Article
C2 - 34965853
VL - 22
JO - BMC GENOMICS
JF - BMC GENOMICS
SN - 1471-2164
IS - 1
M1 - 914
ER -