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.

Základní údaje

Originální název

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

Autoři

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

Genetika a molekulární biologie

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 29.648

Kód RIV

RIV/00216224:14740/13:00066454

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1038/ng.2684

UT WoS

000322374900011

Klíčová slova anglicky

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

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 25. 4. 2014 16:54, Olga Křížová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GBP501/12/G090, projekt VaV

Název: 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 a 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, roč. 45, č. 8, s. 891-"U228", 10 s. ISSN 1061-4036. Dostupné z: https://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 = {https://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 a 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, roč.~45, č.~8, s.~891-''U228'', 10 s. ISSN~1061-4036. Dostupné z: https://doi.org/10.1038/ng.2684.

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