A role for palindromic structures in the cis-region of maize
Sirevirus LTRs in transposable element evolution and host
epigenetic response

J 2016

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

BOUSIOS, Alexandros, Concepcion M. DIEZ, Shohei TAKUNO, Vojtěch BYSTRÝ, Nikos DARZENTAS et. al.

Základní údaje

Originální název

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

Autoři

BOUSIOS, Alexandros (300 Řecko), Concepcion M. DIEZ (724 Španělsko), Shohei TAKUNO (392 Japonsko), Vojtěch BYSTRÝ (203 Česká republika, garant, domácí), Nikos DARZENTAS (300 Řecko, domácí) a Brandon S. GAUT (840 Spojené státy)

Vydání

Genome research, COLD SPRING HARBOR, COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2016, 1088-9051

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 11.922

Kód RIV

RIV/00216224:14740/16:00093652

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1101/gr.193763.115

UT WoS

000369341900008

Klíčová slova anglicky

DIRECTED DNA METHYLATION; SMALL RNAS; MESSENGER-RNA; PLANT RETROTRANSPOSON; ARABIDOPSIS-THALIANA; REGULATORY REGIONS; DIVERGENCE; GENOMES; SIRNAS; CONSERVATION

Štítky

rivok

Změněno: 23. 2. 2017 12:35, Mgr. Eva Špillingová

Anotace

V originále

Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length of TEs, yet this information may provide crucial insights into the dynamics between hosts and TEs. By focusing on 6456 carefully annotated, full-length Sirevirus LTR retro-transposons in maize, we show that their silencing associates with underlying characteristics of the TE sequence and also uncover three features of the host-TE interaction. First, siRNA mapping varies among families and among elements, but particularly along the length of elements. Within the cis-regulatory portion of the LTRs, a complex palindrome-rich region acts as a hotspot of both siRNA matching and sequence evolution. These patterns are consistent across leaf, tassel, and immature ear libraries, but particularly emphasized for floral tissues and 21-to 22-nt siRNAs. Second, this region has the ability to form hairpins, making it a potential template for the production of miRNA-like, hairpin-derived small RNAs. Third, Sireviruses are targeted by siRNAs as a decreasing function of their age, but the oldest elements remain highly targeted, partially by siRNAs that cross-map to the youngest elements. We show that the targeting of older Sireviruses reflects their conserved palindromes. Altogether, we hypothesize that the palindromes aid the silencing of active elements and influence transposition potential, siRNA targeting levels, and ultimately the fate of an element within the genome.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

ED3.2.00/08.0144, projekt VaV

Název: CERIT Scientific Cloud

EE2.3.20.0045, projekt VaV

Název: Podpora profesního růstu a mezinárodní integrace výzkumných týmů v oblasti molekulární medicíny

LM2010005, projekt VaV

Název: Velká infrastruktura CESNET (Akronym: VI CESNET)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Velká infrastruktura CESNET

7E13008, projekt VaV

Název: Next Generation Sequencing Platform for Targeted Personalized Therapy of Leukemia (Akronym: NGS-PTL)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Next Generation Sequencing Platform for Targeted Personalized Therapy of Leukemia

Citovat

BOUSIOS, Alexandros, Concepcion M. DIEZ, Shohei TAKUNO, Vojtěch BYSTRÝ, Nikos DARZENTAS a Brandon S. GAUT. A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response. Genome research. COLD SPRING HARBOR: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2016, roč. 26, č. 2, s. 226-237. ISSN 1088-9051. Dostupné z: https://dx.doi.org/10.1101/gr.193763.115.

@article{1373354,
   author = {Bousios, Alexandros and Diez, Concepcion M. and Takuno, Shohei and Bystrý, Vojtěch and Darzentas, Nikos and Gaut, Brandon S.},
   article_location = {COLD SPRING HARBOR},
   article_number = {2},
   doi = {http://dx.doi.org/10.1101/gr.193763.115},
   keywords = {DIRECTED DNA METHYLATION; SMALL RNAS; MESSENGER-RNA; PLANT RETROTRANSPOSON; ARABIDOPSIS-THALIANA; REGULATORY REGIONS; DIVERGENCE; GENOMES; SIRNAS; CONSERVATION},
   language = {eng},
   issn = {1088-9051},
   journal = {Genome research},
   title = {A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response},
   url = {http://genome.cshlp.org/content/26/2/226},
   volume = {26},
   year = {2016}
}

TY  - JOUR
ID  - 1373354
AU  - Bousios, Alexandros - Diez, Concepcion M. - Takuno, Shohei - Bystrý, Vojtěch - Darzentas, Nikos - Gaut, Brandon S.
PY  - 2016
TI  - A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response
JF  - Genome research
VL  - 26
IS  - 2
SP  - 226-237
EP  - 226-237
PB  - COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
SN  - 10889051
KW  - DIRECTED DNA METHYLATION
KW  - SMALL RNAS
KW  - MESSENGER-RNA
KW  - PLANT RETROTRANSPOSON
KW  - ARABIDOPSIS-THALIANA
KW  - REGULATORY REGIONS
KW  - DIVERGENCE
KW  - GENOMES
KW  - SIRNAS
KW  - CONSERVATION
UR  - http://genome.cshlp.org/content/26/2/226
L2  - http://genome.cshlp.org/content/26/2/226
N2  - Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length of TEs, yet this information may provide crucial insights into the dynamics between hosts and TEs. By focusing on 6456 carefully annotated, full-length Sirevirus LTR retro-transposons in maize, we show that their silencing associates with underlying characteristics of the TE sequence and also uncover three features of the host-TE interaction. First, siRNA mapping varies among families and among elements, but particularly along the length of elements. Within the cis-regulatory portion of the LTRs, a complex palindrome-rich region acts as a hotspot of both siRNA matching and sequence evolution. These patterns are consistent across leaf, tassel, and immature ear libraries, but particularly emphasized for floral tissues and 21-to 22-nt siRNAs. Second, this region has the ability to form hairpins, making it a potential template for the production of miRNA-like, hairpin-derived small RNAs. Third, Sireviruses are targeted by siRNAs as a decreasing function of their age, but the oldest elements remain highly targeted, partially by siRNAs that cross-map to the youngest elements. We show that the targeting of older Sireviruses reflects their conserved palindromes. Altogether, we hypothesize that the palindromes aid the silencing of active elements and influence transposition potential, siRNA targeting levels, and ultimately the fate of an element within the genome.
ER  -

BOUSIOS, Alexandros, Concepcion M. DIEZ, Shohei TAKUNO, Vojtěch BYSTRÝ, Nikos DARZENTAS a Brandon S. GAUT. A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response. \textit{Genome research}. COLD SPRING HARBOR: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2016, roč.~26, č.~2, s.~226-237. ISSN~1088-9051. Dostupné z: https://dx.doi.org/10.1101/gr.193763.115.

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