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A collection of conserved noncoding sequences to study gene regulation in flowering plants

Jan Van de Velde, Michiel Van Bel UGent, Dries Vaneechoutte UGent and Klaas Vandepoele UGent (2016) PLANT PHYSIOLOGY. 171(4). p.2586-2598
abstract
Transcription factors (TFs) regulate gene expression by binding cis-regulatory elements, of which the identification remains an ongoing challenge owing to the prevalence of large numbers of nonfunctional TF binding sites. Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences (CNSs), which are functionally constrained and can greatly help in reducing the number of false-positive elements. In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in 10 dicot plants, yielding 1,032,291 CNSs associated with 243,187 genes. To annotate CNSs with TF binding sites, we made use of binding site information for 642 TFs originating from 35 TF families in Arabidopsis (Arabidopsis thaliana). In three species, the identified CNSs were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. To identify ultraconserved CNSs, we included genomes of additional plant families and identified 715 binding sites for 501 genes conserved in dicots, monocots, mosses, and green algae. Additionally, we found that genes that are part of conserved mini-regulons have a higher coherence in their expression profile than other divergent gene pairs. All identified CNSs were integrated in the PLAZA 3.0 Dicots comparative genomics platform (http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
COEXPRESSION NETWORKS, DICOTYLEDONOUS PLANTS, FLAVONOID BIOSYNTHESIS, RNA-SEQ, TARGET GENES, COMPARATIVE GENOMICS, ARABIDOPSIS CELL-SUSPENSION, TRANSCRIPTION FACTOR-BINDING, EXPRESSION ANALYSIS, PROMOTER EVOLUTION
journal title
PLANT PHYSIOLOGY
Plant Physiol.
volume
171
issue
4
pages
2586 - 2598
Web of Science type
Article
Web of Science id
000381303700025
JCR category
PLANT SCIENCES
JCR impact factor
6.456 (2016)
JCR rank
11/211 (2016)
JCR quartile
1 (2016)
ISSN
0032-0889
DOI
10.1104/pp.16.00821
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
8113234
handle
http://hdl.handle.net/1854/LU-8113234
date created
2016-10-13 10:54:10
date last changed
2016-12-19 15:41:06
@article{8113234,
  abstract     = {Transcription factors (TFs) regulate gene expression by binding cis-regulatory elements, of which the identification remains an ongoing challenge owing to the prevalence of large numbers of nonfunctional TF binding sites. Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences (CNSs), which are functionally constrained and can greatly help in reducing the number of false-positive elements. In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in 10 dicot plants, yielding 1,032,291 CNSs associated with 243,187 genes. To annotate CNSs with TF binding sites, we made use of binding site information for 642 TFs originating from 35 TF families in Arabidopsis (Arabidopsis thaliana). In three species, the identified CNSs were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. To identify ultraconserved CNSs, we included genomes of additional plant families and identified 715 binding sites for 501 genes conserved in dicots, monocots, mosses, and green algae. Additionally, we found that genes that are part of conserved mini-regulons have a higher coherence in their expression profile than other divergent gene pairs. All identified CNSs were integrated in the PLAZA 3.0 Dicots comparative genomics platform (http://bioinformatics.psb.ugent.be/plaza/versions/plaza\_v3\_dicots/) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops.},
  author       = {Van de Velde, Jan and Van Bel, Michiel and Vaneechoutte, Dries and Vandepoele, Klaas},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  keyword      = {COEXPRESSION NETWORKS,DICOTYLEDONOUS PLANTS,FLAVONOID BIOSYNTHESIS,RNA-SEQ,TARGET GENES,COMPARATIVE GENOMICS,ARABIDOPSIS CELL-SUSPENSION,TRANSCRIPTION FACTOR-BINDING,EXPRESSION ANALYSIS,PROMOTER EVOLUTION},
  language     = {eng},
  number       = {4},
  pages        = {2586--2598},
  title        = {A collection of conserved noncoding sequences to study gene regulation in flowering plants},
  url          = {http://dx.doi.org/10.1104/pp.16.00821},
  volume       = {171},
  year         = {2016},
}

Chicago
Van de Velde, Jan, Michiel Van Bel, Dries Vaneechoutte, and Klaas Vandepoele. 2016. “A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.” Plant Physiology 171 (4): 2586–2598.
APA
Van de Velde, Jan, Van Bel, M., Vaneechoutte, D., & Vandepoele, K. (2016). A collection of conserved noncoding sequences to study gene regulation in flowering plants. PLANT PHYSIOLOGY, 171(4), 2586–2598.
Vancouver
1.
Van de Velde J, Van Bel M, Vaneechoutte D, Vandepoele K. A collection of conserved noncoding sequences to study gene regulation in flowering plants. PLANT PHYSIOLOGY. 2016;171(4):2586–98.
MLA
Van de Velde, Jan, Michiel Van Bel, Dries Vaneechoutte, et al. “A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.” PLANT PHYSIOLOGY 171.4 (2016): 2586–2598. Print.