Wednesday, 20th June 2018

Genome Dynamics and Function

    DNA replication, cell division and chromatin




Crisanto Gutierrez






Research summary

Identifying DNA replication origins in a whole A. thaliana plant by massive sequencing of a purified sample of short nascent strands (SNS-seq). The replication origins identified here (4 dayl-old seedling) correspond to those active in all proliferating cell types.
The Arabidopsis genome (Chr 1) in 9 color-coded chromatin states.
Identification of histone H3.1 and H3.3 in teh Arabidopsis root.


The transition to multicellularity required the evolution of novel structures and mechanisms to coordinate cell division, acquisition of cell fates and the differentiation, and the establishment of complex regulatory networks. Our group is interested in understanding the mechanisms that control these processes and how epigenetic mechanisms affect such coordination. To that end, we use the model plant Arabidopsis thaliana that offers the possibility of carrying out molecular, cellular, genetic and genomic approaches. In addition, plant development, contrary to the situation in animals, is post-embryonic and occurs during the entire life of the organism. Our research is aimed at understanding fundamental questions on cell proliferation control, cellular homeostasis and genome replication in multicellular organisms.

Cell proliferation is crucial for organogenesis, which is determined by a strict control of gene expression patterns. We study chromatin dynamics along the cell cycle with special emphasis in two aspects: one, the regulation of cell proliferation potential, very related to the control of gene expression in G1 and G2, and the exit to differentiation, and another, related to genome replication.

This implies that not only DNA but chromatin needs to be duplicated every cell cycle. In turn, several stages of genome replication are associated with specific chromatin states. We have identified 9 distinct chromatin states that define the Arabidopsis genome based on specific combinations of epigenetic marks (signatures). We are also developing genomic strategies to study the functional properties of replication origins in all cell types of the whole organism to determine the influence of hormonal conditions, developmental signals and the environment. This approach is allowing us to use mutants to study genome replication.





Desvoyes, B.*, Vergara, Z.*, Sequeira-Mendes, J., Madeira, S., Gutierrez, C. (2017) A rapid and efficient ChIP protocol to profile chromatin binding proteins and epigenetic modifications in bulk Arabidopsis tissue. Methods Mol. Biol. 1675, 71-81. * shared 1st coauthorship.  

Desvoyes, B.*,+, Sequeira-Mendes, J.*, Vergara, Z., Madeira, S., Gutierrez, C+. (2017) Sequential ChIP protocol for profiling bivalent epigenetic modifications in the same chromatin fiber (ReChIP). Methods Mol. Biol. 1675, 83-97.  * shared 1st coauthorship, + Co-corespondent authors

Dvorackova, M., Raposo, B., Matula, P., Fuchs, J., Schubert, V., Peska, V., Desvoyes, B., Gutierrez, C., Fajkus, J. (2017)  Replication of Ribosomal RNA Genes in Arabidopsis thaliana Occurs both inside and outside of the Nucleolus during S-Phase Progression. J. Cell Sci. (in press; doi: 10.1242/jcs.202416).

Vergara, Z., Sequeira-Mendes, J., Morata, J., Hénaff, E., Peiró, R., Costas, C., Casacuberta, J.M., Gutierrez, C. (2017) Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. Nucleic Acids Res. 45, 8358-8368.

Fernandez-Marcos, M., Desvoyes, B., Manzano, C., Liberman, L.M., Benfey, P.N., del Pozo, J.C., Gutierrez, C. (2017) Control of Arabidopsis lateral root boundaries by MYB36. New Phytol. 213, 105-112.

Vergara, Z., Gutierrez, C. (2017) Emerging roles of chromatin in the maintenance of genome organization and function in plants. Genome Biol. 18, 96.


Gutierrez, C., Desvoyes, B., Vergara, Z., Otero, S., Sequeira-Mendes, J. (2016) Links of genome replication, transcriptional silencing and chromatin dynamics. Curr. Opin. Plant. Biol. 34, 92-99.

Desvoyes, B., Gutierrez, C. (2016) A plant solution to the CDK conundrum in the DNA damage response. EMBO J. 35, 2061-2063. 

Gutierrez, C. (2016) 25 years of cell cycle research: what’s ahead?  Trends Plant Sci. 21, 823-833.

Sequeira-Mendes, J., Gutierrez, C. (2016) Genome architecture: from linear organisation of chromatin to 3D assembly in the nucleus. Chromosoma 125, 455-469.

Otero, S*., Desvoyes, B.*, Peiró, R., Gutierrez, C. (2016) Histone H3 dynamics uncovers domains with distinct proliferation potential in the Arabidopsis root. Plant Cell 28, 1361-1371 * 1st coauthors.              Plant Cell 28, 1235 (2016) In Brief- Hofmann, N. Last exit to differentiation: histone variants as signspots.

Mauri, N., Fernandez-Marcos, M., Costas, C., Desvoyes, B., Pichel, A., Caro, E., Gutierrez, C. (2016) GEM, a member of the GRAM domain family of proteins, is part of the ABA signaling pathway. Sci. Rep. 6, 22660.

García-Cruz, K., García-Ponce, B., Garay-Arroyo, A., Sanchez, M.P., Ugartechea-Chirino, Y., Desvoyes, B., Pacheco-Escobedo, M., Tapia-López, R., Ransom-Rodriguez, I., Gutierrez, C., Alvarez-Buylla, E. (2016) The MADS-box XAANTAL1 Increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell cycle components. Ann. Bot.117, 787-796.

Havlová, K., Dvořáčková, M., Peiro, R, Abia, D., Mozgová, I., Vansáčová, L., Gutierrez, C., Fajkus, J. (2016) Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana. Plant. Mol. Biol. 92, 457-471.


Gutierrez, C., Puchta H. (2015) Chromatin and Development: s Special issue. Editorial. Plant J. 83, 1-3.

Sequeira-Mendes, J., Gutierrez, C. (2015) Links between genome replication control and chromatin landscapes. Plant J. 83, 38-51.

Rodriguez-Mega, E., Pyñeiro-Nelson, A., Gutierrez, C., Garcia-Ponce, B., Sanchez, M.P., Zluhen-Martinez, E., Alvarez-Buylla, E.R., Garay-Arroyo, A. (2015) The role of transcriptional regulation in the evolution of plant phenotype. Dev. Dyn. 244, 1074–1095.


Desvoyes, D., Fernandez-Marcos, M., Sequeira-Mendes, J., Otero, S., Vergara, Z., Gutierrez, C. (2014) Looking at plant cell cycle from the chromatin window. Frontiers Plant Sci. 5, 369.

Sequeira-Mendes, J., Aragüez, I., Peiró, R., Zhang, X., Jacobsen, S.E., Bastolla, U., Gutierrez, C. (2014) The Functional Topography of the Arabidopsis Genome is organized in a reduced Number of linear Motifs of Chromatin states. Plant Cell 26, 2351-2366.

Otero, S., Desvoyes, B., Gutierrez, C. (2014) Histone H3 dynamics in plant cell cycle and development. Cytogenet. Genomic Res. 143, 114-124.

Edgar, B.A., Zielke, N., Gutierrez, C. (2014) Endocycles: a recurrent evolutionary innovation for post-mitotic cell growth. Nature Rev Cell Mol. Biol. 15, 197-210.

Coego, A., Brizuela, E., Castillejo, P., Ruiz, S., Koncz, C., del Pozo, J.C., Piñeiro, M., Jarillo, J.A., Paz-Ares, J., Leon J., and the TRANSPLANTA Consortium. (2014) The TRANSPLANTA Collection of Arabidopsis Lines: A resource for Functional Analysis of Transcription Factors based on their conditional Overexpression. Plant J. 77, 944-953.

Desvoyes, B., de Mendoza, A., Ruiz-Trillo, I., Gutierrez, C. (2014) Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. J. Exp. Bot. 65, 2657-2666.

Hénaff, E., Vives, C., Desvoyes, B., Chaurasia, A., Payet, J., Gutierrez, C., Casacuberta, JM. (2014) Extensive amplification of the E2F transcription factor binding sites by transposons during evolution of Brassica species. Plant J. 77, 852-862.


Lario, L., Ramirez-Parra, E., Gutierrez, C., Spampinato, C., Casati, P. (2013) ANTI-SILENCING FUNCTION1 proteins are involved in ultraviolet-induced DNA damage repair and are cell cycle regulated by E2F transcription factors in Arabidopsis. Plant Physiol. 162, 1164-1177.

Triviño, M., Martín-Trillo, M., Ballesteros I., Delgado D., de Marcos, A., Desvoyes, B., Gutierrez, C., Mena, M., Fenoll, C. (2013) Timely expression of Arabidopsis stoma-fate master regulator MUTE is required for specification of other epidermal cell types. Plant J. 75, 808-822.

Gutierrez, C., Sequeira-Mendes, J., Aragüez, I. (2013) Replication of Plant genomes. In: The Plant Sciences: Molecular Biology. M. Tester, R. A. Jorgensen, Eds. Article ID: 349832. Springer.


Stroud, H.+, Otero, S. +, Desvoyes, B., Ramirez-Parra, E., Jacobsen, S.E., Gutierrez, C. Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 109, 5370-5375 (2012). + Co-first authors

Sanchez, M.P. +, Costas, C. +, Sequeira-Mendes, J. +, Gutierrez, C. DNA replication control in plants. (2012) Cold Spring Harb. Perspect. Biol. 4:a01014+ Co-first authors

Manzano, C., Ramirez-Parra, E., Casimiro, I., Otero, S., Desvoyes, B., De Rybel, B., Beeckman, T., Casero, P., Gutierrez, C., del Pozo, J.C. Auxin and epigenetic regulation of SKP2B, an F-box that represses lateral root formation. Plant Physiol. 160, 749-762 (2012).

Caro, E., Desvoyes, B., Gutierrez, C. (2012) GTL1 keeps cell growth and nuclear ploidy under control. EMBO J. 31, 4483-4485 (2012).


Costas, C.+, Sanchez, M.P.+, Stroud, H.+, Yu, Y., Oliveros, J.C., Feng, S., Benguria, A., López-Vidriero, I., Zhang, X., Solano, R., Jacobsen, S.E., Gutierrez, C. (2011) Genome-wide mapping of Arabidopsis origins of DNA replication and their associated epigenetic marks. Nat. Struct. Mol. Biol. 18, 395-400.   + Co-first authors

Lario, L., Ramirez-Parra, E., Gutierrez, C., Casati, P., Spampinato, C. (2011) Regulation of plant MSH2 and MSH6 genes in the UV-B induced DNA damage response. J. Exp. Bot. 62, 2925-2937.

Costas, C. +, Desvoyes, B. +, Gutierrez, C. (2011) A chromatin perspective of cell cycle progression. Biochim. Biophys. Acta 1809, 379-387. + Co-first authors

Costas, C. +, Sanchez, M.P. +, Sequeira-Mendes, J. +, Gutierrez, C. (2011) Progress in understanding DNA replication control. Plant Sci. 181, 203-209. + Co-first authors

Sanmartin, M., Sauer, M., Muñoz, A., Zouhar, J., Ordoñez, A., van de Ven, W.T.G., Caro, E., Sanchez, M.P., Raikhel, N., Gutierrez, C., Sanchez-Serrano, J.J., Rojo, E. (2011) A molecular switch for initiating cell differentiation in Arabidopsis. Curr. Biol. 21, 999-1008.


Desvoyes, B., Sanchez, M.P., Ramirez-Parra, E., Gutierrez, C. (2010) Impact of nucleosome dynamics and histone modifications on cell proliferation during Arabidopsis development. Heredity 105, 80-91.

Jacob, Y.*, Stroud, H.*, LeBlanc, C., Feng, S., Zhou, L., Caro, E., Hassel, C., Gutierrez, C., Michaels, S.D., Jacobsen, S.E. (2010) Two histone H3 lysine methyltransferases, ATXR5 and ATXR6, regulate DNA replication in heterochromatin. Nature 466, 987-991.