An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Annabelle Haudry, Adrian E. Platts, Emilio Vello, Douglas R. Hoen, Mickael Leclercq, Robert J. Williamson, Ewa Forczek, Zoé Joly-Lopez, Joshua G. Steffen, Khaled M. Hazzouri, Ken Dewar, John R. Stinchcombe, Daniel J. Schoen, Xiaowu Wang, Jeremy Schmutz, Christopher D. Town, Patrick P. Edger, J. Chris Pires, Karen S Schumaker, David E. Jarvis & 9 others Terezie Mandáková, Martin A. Lysak, Erik Van Den Bergh, M. Eric Schranz, Paul M. Harrison, Alan M. Moses, Thomas E. Bureau, Stephen I. Wright, Mathieu Blanchette

Research output: Contribution to journalArticle

163 Citations (Scopus)

Abstract

Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.

Original languageEnglish (US)
Pages (from-to)891-898
Number of pages8
JournalNature Genetics
Volume45
Issue number8
DOIs
StatePublished - Aug 2013

Fingerprint

Conserved Sequence
Atlases
Nucleic Acid Regulatory Sequences
Plant DNA
Genome
Arabidopsis
Capsella
Brassicaceae
Metagenomics
DNA
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Haudry, A., Platts, A. E., Vello, E., Hoen, D. R., Leclercq, M., Williamson, R. J., ... Blanchette, M. (2013). An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics, 45(8), 891-898. https://doi.org/10.1038/ng.2684

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. / Haudry, Annabelle; Platts, Adrian E.; Vello, Emilio; Hoen, Douglas R.; Leclercq, Mickael; Williamson, Robert J.; Forczek, Ewa; Joly-Lopez, Zoé; Steffen, Joshua G.; Hazzouri, Khaled M.; Dewar, Ken; Stinchcombe, John R.; Schoen, Daniel J.; Wang, Xiaowu; Schmutz, Jeremy; Town, Christopher D.; Edger, Patrick P.; Pires, J. Chris; Schumaker, Karen S; Jarvis, David E.; Mandáková, Terezie; Lysak, Martin A.; Van Den Bergh, Erik; Schranz, M. Eric; Harrison, Paul M.; Moses, Alan M.; Bureau, Thomas E.; Wright, Stephen I.; Blanchette, Mathieu.

In: Nature Genetics, Vol. 45, No. 8, 08.2013, p. 891-898.

Research output: Contribution to journalArticle

Haudry, A, Platts, AE, Vello, E, Hoen, DR, Leclercq, M, Williamson, RJ, Forczek, E, Joly-Lopez, Z, Steffen, JG, Hazzouri, KM, Dewar, K, Stinchcombe, JR, Schoen, DJ, Wang, X, Schmutz, J, Town, CD, Edger, PP, Pires, JC, Schumaker, KS, Jarvis, DE, Mandáková, T, Lysak, MA, Van Den Bergh, E, Schranz, ME, Harrison, PM, Moses, AM, Bureau, TE, Wright, SI & Blanchette, M 2013, 'An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions', Nature Genetics, vol. 45, no. 8, pp. 891-898. https://doi.org/10.1038/ng.2684
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics. 2013 Aug;45(8):891-898. https://doi.org/10.1038/ng.2684
Haudry, Annabelle ; Platts, Adrian E. ; Vello, Emilio ; Hoen, Douglas R. ; Leclercq, Mickael ; Williamson, Robert J. ; Forczek, Ewa ; Joly-Lopez, Zoé ; Steffen, Joshua G. ; Hazzouri, Khaled M. ; Dewar, Ken ; Stinchcombe, John R. ; Schoen, Daniel J. ; Wang, Xiaowu ; Schmutz, Jeremy ; Town, Christopher D. ; Edger, Patrick P. ; Pires, J. Chris ; Schumaker, Karen S ; Jarvis, David E. ; Mandáková, Terezie ; Lysak, Martin A. ; Van Den Bergh, Erik ; Schranz, M. Eric ; Harrison, Paul M. ; Moses, Alan M. ; Bureau, Thomas E. ; Wright, Stephen I. ; Blanchette, Mathieu. / An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. In: Nature Genetics. 2013 ; Vol. 45, No. 8. pp. 891-898.
@article{d28402c12eb3432fa8819e1ba1f09430,
title = "An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions",
abstract = "Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17{\%} of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.",
author = "Annabelle Haudry and Platts, {Adrian E.} and Emilio Vello and Hoen, {Douglas R.} and Mickael Leclercq and Williamson, {Robert J.} and Ewa Forczek and Zo{\'e} Joly-Lopez and Steffen, {Joshua G.} and Hazzouri, {Khaled M.} and Ken Dewar and Stinchcombe, {John R.} and Schoen, {Daniel J.} and Xiaowu Wang and Jeremy Schmutz and Town, {Christopher D.} and Edger, {Patrick P.} and Pires, {J. Chris} and Schumaker, {Karen S} and Jarvis, {David E.} and Terezie Mand{\'a}kov{\'a} and Lysak, {Martin A.} and {Van Den Bergh}, Erik and Schranz, {M. Eric} and Harrison, {Paul M.} and Moses, {Alan M.} and Bureau, {Thomas E.} and Wright, {Stephen I.} and Mathieu Blanchette",
year = "2013",
month = "8",
doi = "10.1038/ng.2684",
language = "English (US)",
volume = "45",
pages = "891--898",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "8",

}

TY - JOUR

T1 - An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

AU - Haudry, Annabelle

AU - Platts, Adrian E.

AU - Vello, Emilio

AU - Hoen, Douglas R.

AU - Leclercq, Mickael

AU - Williamson, Robert J.

AU - Forczek, Ewa

AU - Joly-Lopez, Zoé

AU - Steffen, Joshua G.

AU - Hazzouri, Khaled M.

AU - Dewar, Ken

AU - Stinchcombe, John R.

AU - Schoen, Daniel J.

AU - Wang, Xiaowu

AU - Schmutz, Jeremy

AU - Town, Christopher D.

AU - Edger, Patrick P.

AU - Pires, J. Chris

AU - Schumaker, Karen S

AU - Jarvis, David E.

AU - Mandáková, Terezie

AU - Lysak, Martin A.

AU - Van Den Bergh, Erik

AU - Schranz, M. Eric

AU - Harrison, Paul M.

AU - Moses, Alan M.

AU - Bureau, Thomas E.

AU - Wright, Stephen I.

AU - Blanchette, Mathieu

PY - 2013/8

Y1 - 2013/8

N2 - Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.

AB - Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.

UR - http://www.scopus.com/inward/record.url?scp=84881028642&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84881028642&partnerID=8YFLogxK

U2 - 10.1038/ng.2684

DO - 10.1038/ng.2684

M3 - Article

VL - 45

SP - 891

EP - 898

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 8

ER -