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

J 2013

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

HAUNDRY, Annabelle, Adrian E. PLATTS, Emilio VELLO, Douglas R. HOEN, Mickael LECLERCQ et. al.

Basic information

Original name

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

Authors

HAUNDRY, Annabelle (250 France), Adrian E. PLATTS (124 Canada), Emilio VELLO (124 Canada), Douglas R. HOEN (124 Canada), Mickael LECLERCQ (124 Canada), Robert J. WILLIAMSON (124 Canada), Ewa FORCZEK (124 Canada), Zoé JOLY-LOPEZ (124 Canada), Joshua G. STEFFEN (840 United States of America), Khaled M. HAZZOURI (124 Canada), Ken DEWAR (124 Canada), John R. STINCHCOMBE (124 Canada), Daniel J. SCHOEN (124 Canada), Xiaowu WANG (156 China), Jeremy SCHMUTZ (840 United States of America), Christopher D. TOWN (724 Spain), Patrick P. EDGER (840 United States of America), J. Chris PIRES (840 United States of America), Karen S. SCHUMAKER (840 United States of America), David E. JARVIS (840 United States of America), Terezie MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Martin LYSÁK (203 Czech Republic, guarantor, belonging to the institution), Erik VAN DEN BERGH (528 Netherlands), M. Eric SCHRANZ (528 Netherlands), Paul M. HARRISON (124 Canada), Alan M. MOSES (124 Canada), Thomas E. BUREAU (124 Canada), Stephen I. WRIGHT (124 Canada) and Mathieu BLANCHETTE (124 Canada)

Edition

Nature Genetics, New York, Nature Publishing Group, 2013, 1061-4036

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Genetics and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 29.648

RIV identification code

RIV/00216224:14740/13:00066454

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/ng.2684

UT WoS

000322374900011

Keywords in English

ARABIDOPSIS-THALIANA; HUMAN GENOME; DNA ELEMENTS; ULTRACONSERVED ELEMENTS; BRASSICA-OLERACEA; GENE-EXPRESSION; EVOLUTION; DROSOPHILA; SIZE; ANNOTATION

Abstract

V originále

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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

GBP501/12/G090, research and development project

Name: Evoluce a funkce komplexních genomů rostlin

Citovat

HAUNDRY, Annabelle, 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, Terezie MANDÁKOVÁ, Martin LYSÁK, Erik VAN DEN BERGH, M. Eric SCHRANZ, Paul M. HARRISON, Alan M. MOSES, Thomas E. BUREAU, Stephen I. WRIGHT and Mathieu BLANCHETTE. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics. New York: Nature Publishing Group, 2013, vol. 45, No 8, p. 891-"U228", 10 pp. ISSN 1061-4036. Available from: https://dx.doi.org/10.1038/ng.2684.

@article{1126887,
   author = {Haundry, Annabelle and Platts, Adrian E. and Vello, Emilio and Hoen, Douglas R. and Leclercq, Mickael and Williamson, Robert J. and Forczek, Ewa and JolyandLopez, Zoé and Steffen, Joshua G. and Hazzouri, Khaled M. and Dewar, Ken and Stinchcombe, John R. and Schoen, Daniel J. and Wang, Xiaowu and Schmutz, Jeremy and Town, Christopher D. and Edger, Patrick P. and Pires, J. Chris and Schumaker, Karen S. and Jarvis, David E. and Mandáková, Terezie and Lysák, Martin 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 Blanchette, Mathieu},
   article_location = {New York},
   article_number = {8},
   doi = {http://dx.doi.org/10.1038/ng.2684},
   keywords = {ARABIDOPSIS-THALIANA; HUMAN GENOME; DNA ELEMENTS; ULTRACONSERVED ELEMENTS; BRASSICA-OLERACEA; GENE-EXPRESSION; EVOLUTION; DROSOPHILA; SIZE; ANNOTATION},
   language = {eng},
   issn = {1061-4036},
   journal = {Nature Genetics},
   title = {An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions},
   url = {http://www.nature.com/ng/journal/v45/n8/ng.2684/metrics/blogs},
   volume = {45},
   year = {2013}
}

TY  - JOUR
ID  - 1126887
AU  - Haundry, 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 - Lysák, Martin - van den Bergh, Erik - Schranz, M. Eric - Harrison, Paul M. - Moses, Alan M. - Bureau, Thomas E. - Wright, Stephen I. - Blanchette, Mathieu
PY  - 2013
TI  - An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
JF  - Nature Genetics
VL  - 45
IS  - 8
SP  - 891-"U228"
EP  - 891-"U228"
PB  - Nature Publishing Group
SN  - 10614036
KW  - ARABIDOPSIS-THALIANA
KW  - HUMAN GENOME
KW  - DNA ELEMENTS
KW  - ULTRACONSERVED ELEMENTS
KW  - BRASSICA-OLERACEA
KW  - GENE-EXPRESSION
KW  - EVOLUTION
KW  - DROSOPHILA
KW  - SIZE
KW  - ANNOTATION
UR  - http://www.nature.com/ng/journal/v45/n8/ng.2684/metrics/blogs
L2  - http://www.nature.com/ng/journal/v45/n8/ng.2684/metrics/blogs
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.
ER  -

HAUNDRY, Annabelle, 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, Terezie MANDÁKOVÁ, Martin LYSÁK, Erik VAN DEN BERGH, M. Eric SCHRANZ, Paul M. HARRISON, Alan M. MOSES, Thomas E. BUREAU, Stephen I. WRIGHT and Mathieu BLANCHETTE. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. \textit{Nature Genetics}. New York: Nature Publishing Group, 2013, vol.~45, No~8, p.~891-''U228'', 10 pp. ISSN~1061-4036. Available from: https://dx.doi.org/10.1038/ng.2684.

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