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Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis

Jan Van de Velde (UGent) , Ken Heyndrickx (UGent) and Klaas Vandepoele (UGent)
(2014) PLANT CELL. 26(7). p.2729-2745
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Transcriptional regulation plays an important role in establishing gene expression profiles during development or in response to (a) biotic stimuli. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity, and the identification of individual TFBS in genome sequences is a major goal to inferring regulatory networks. We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 dicot plants. Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence divergence between related species. We identified 69,361 footprints associated with 17,895 genes. Through the integration of known TFBS obtained from the literature and experimental studies, we used the CNSs to compile a gene regulatory network in Arabidopsis thaliana containing 40,758 interactions, of which two-thirds act through binding events located in DNase I hypersensitive sites. This network shows significant enrichment toward in vivo targets of known regulators, and its overall quality was confirmed using five different biological validation metrics. Finally, through the integration of detailed expression and function information, we demonstrate how static CNSs can be converted into condition-dependent regulatory networks, offering opportunities for regulatory gene annotation.
Keywords
DNA ELEMENTS, FACTOR-BINDING-SITES, FLORAL TRANSITION, STAMEN DEVELOPMENT, DICOTYLEDONOUS PLANTS, TARGET GENES, PLANT GENOMES, SECONDARY WALL FORMATION, GENOME-WIDE IDENTIFICATION, CIS-REGULATORY ELEMENTS

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Citation

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Chicago
Van de Velde, Jan, Ken Heyndrickx, and Klaas Vandepoele. 2014. “Inference of Transcriptional Networks in Arabidopsis Through Conserved Noncoding Sequence Analysis.” Plant Cell 26 (7): 2729–2745.
APA
Van de Velde, Jan, Heyndrickx, K., & Vandepoele, K. (2014). Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. PLANT CELL, 26(7), 2729–2745.
Vancouver
1.
Van de Velde J, Heyndrickx K, Vandepoele K. Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. PLANT CELL. 2014;26(7):2729–45.
MLA
Van de Velde, Jan, Ken Heyndrickx, and Klaas Vandepoele. “Inference of Transcriptional Networks in Arabidopsis Through Conserved Noncoding Sequence Analysis.” PLANT CELL 26.7 (2014): 2729–2745. Print.
@article{5738431,
  abstract     = {Transcriptional regulation plays an important role in establishing gene expression profiles during development or in response to (a) biotic stimuli. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity, and the identification of individual TFBS in genome sequences is a major goal to inferring regulatory networks. We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 dicot plants. Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence divergence between related species. We identified 69,361 footprints associated with 17,895 genes. Through the integration of known TFBS obtained from the literature and experimental studies, we used the CNSs to compile a gene regulatory network in Arabidopsis thaliana containing 40,758 interactions, of which two-thirds act through binding events located in DNase I hypersensitive sites. This network shows significant enrichment toward in vivo targets of known regulators, and its overall quality was confirmed using five different biological validation metrics. Finally, through the integration of detailed expression and function information, we demonstrate how static CNSs can be converted into condition-dependent regulatory networks, offering opportunities for regulatory gene annotation.},
  author       = {Van de Velde, Jan and Heyndrickx, Ken and Vandepoele, Klaas},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {DNA ELEMENTS,FACTOR-BINDING-SITES,FLORAL TRANSITION,STAMEN DEVELOPMENT,DICOTYLEDONOUS PLANTS,TARGET GENES,PLANT GENOMES,SECONDARY WALL FORMATION,GENOME-WIDE IDENTIFICATION,CIS-REGULATORY ELEMENTS},
  language     = {eng},
  number       = {7},
  pages        = {2729--2745},
  title        = {Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis},
  url          = {http://dx.doi.org/10.1105/tpc.114.127001},
  volume       = {26},
  year         = {2014},
}

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