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Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome

View ORCID ProfileJ. Sequeira-Mendes, View ORCID ProfileZ. Vergara, View ORCID ProfileR. Peiró, View ORCID ProfileJ. Morata, I. Aragüez, C. Costas, R. Mendez-Giraldez, View ORCID ProfileJ.M. Casacuberta, View ORCID ProfileU. Bastolla, View ORCID ProfileC. Gutierrez
doi: https://doi.org/10.1101/258301
J. Sequeira-Mendes
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
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Z. Vergara
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
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R. Peiró
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
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J. Morata
2Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
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I. Aragüez
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
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C. Costas
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
3Current address: Departamento de Química Física, Universidad de Vigo, 36310 Vigo, Spain
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R. Mendez-Giraldez
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
4Current address: Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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J.M. Casacuberta
2Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
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U. Bastolla
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
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  • For correspondence: cgutierrez@cbm.csic.es ubastolla@cbm.csic.es
C. Gutierrez
1Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco,28049 Madrid, Spain
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  • For correspondence: cgutierrez@cbm.csic.es ubastolla@cbm.csic.es
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SUMMARY

Full genome replication in eukaryotes depends on the function of thousands of DNA replication origins (ORIs) that constitute the originome. The identification of ORIs in cultured cells has served to define their basic DNA and chromatin features. However, a major challenge is to learn the biology of ORIs in adult organisms to understand their developmental plasticity. Here, we have determined the originome and chromatin landscape in Arabidopsis thaliana at two stages of vegetative development. We found that ORIs associate with multiple chromatin signatures including the most frequent at TSS but also at proximal and distal gene regulatory regions or repressed Polycomb (PcG) domains. In constitutive heterochromatin, a high fraction of ORIs colocalize with GC-rich retrotransposons. Quantitative analysis of ORI activity led us to conclude that strong ORIs possess high scores of local GC content and clusters of GGN trinucleotides that may form G quadruplexes and other G-rich structures. We also found that development primarily influences ORI firing strength rather than ORI location. Moreover, ORIs that preferentially fire at early vegetative stages colocalize with GC-rich heterochromatin whereas those at later stages associate with transcribed genes. Our study provides the first originome of an adult organism, which is a developmentally and genetically tractable, thus opening new avenues of studying the biology of ORIs in response to developmental cues, transcriptional programs, environmental challenges and mutant backgrounds.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 01, 2018.
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Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome
J. Sequeira-Mendes, Z. Vergara, R. Peiró, J. Morata, I. Aragüez, C. Costas, R. Mendez-Giraldez, J.M. Casacuberta, U. Bastolla, C. Gutierrez
bioRxiv 258301; doi: https://doi.org/10.1101/258301
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Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome
J. Sequeira-Mendes, Z. Vergara, R. Peiró, J. Morata, I. Aragüez, C. Costas, R. Mendez-Giraldez, J.M. Casacuberta, U. Bastolla, C. Gutierrez
bioRxiv 258301; doi: https://doi.org/10.1101/258301

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