TY - JOUR
T1 - Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks
AU - Costas, Celina
AU - De La Paz Sanchez, Maria
AU - Stroud, Hume
AU - Yu, Yanchun
AU - Oliveros, Juan Carlos
AU - Feng, Suhua
AU - Benguria, Alberto
AU - López-Vidriero, Irene
AU - Zhang, Xiaoyu
AU - Solano, Roberto
AU - Jacobsen, Steven E.
AU - Gutierrez, Crisanto
N1 - Funding Information:
We thank E. Martinez-Salas, J.A. Tercero and E. Caro for comments and discussions, S. Diaz-Triviño and P. Hernandez for initial efforts in origin mapping, and M. Gomez and J. Sequeira-Mendes for advice with the purification and analysis of nascent DNA strands. The technical help of V. Mora-Gil is deeply acknowledged. M.P.S. and C.C. are recipients of JAE-Doc contracts from CSIC. S.F. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation. This research has been supported by grants BFU2006-5662, BFU2009-9783 and CSD2007-00057-B (Spain Ministry of Science and Education) and P2006/GEN0191 (Comunidad de Madrid) to C.G., by an institutional grant from Fundación Ramón Areces to C.B.M., by grant GM60398 (US National Institutes of Health) to S.E.J., by grant 0960425 (US National Science Foundation) to X.Z. and by grants BIO2004-02502, BIO2007-66935, GEN2003-20218-C02-02 and CSD2007-00057-B (Spain Ministry of Science and Innovation) and GR/SAL/0674/2004 (Comunidad de Madrid) to R.S. S.E.J. is an investigator of the Howard Hughes Medical Institute.
PY - 2011/3
Y1 - 2011/3
N2 - Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ∼1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5' half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.
AB - Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ∼1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5' half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.
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U2 - 10.1038/nsmb.1988
DO - 10.1038/nsmb.1988
M3 - Article
C2 - 21297636
AN - SCOPUS:79952359976
SN - 1545-9993
VL - 18
SP - 395
EP - 400
JO - Nature Structural and Molecular Biology
JF - Nature Structural and Molecular Biology
IS - 3
ER -