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Dr Sandra Cortijo

Dr Sandra Cortijo

Visiting Researcher

Sainsbury Laboratory
University of Cambridge
Bateman Street

Cambridge CB2 1LR

Research Interests

I am interested in understanding how genes are regulated in response to environmental changes. This response is often noisy rather than uniform with different individuals showing variable gene expression behaviours. Such transcriptional variability can be beneficial when environmental conditions are unpredictable. Up to now, most studies on transcriptional variability have been performed in unicellular organisms or in cell cultures and little is known about transcriptional variability in a multicellular organism. My research project focuses on understanding transcriptional variability between cells and between individuals using the plant model Arabidopsis thaliana, combining transcriptomic and microscopy approaches. Plants are a wonderful system to understand better transcriptional variability in response to environment as they cannot move and thus have to continually sense and respond to environmental changes.


AraNoisy is a web-based tool for accessing inter-individual transcriptional variability in Arabidopsis thaliana, throughout a 24-hour diurnal cycle. Gene expression variability for individual genes of interest can be viewed here.

Previous work

I worked in Vincent Colot’s group for my PhD (Ecole Normale Supérieure, Paris, France) to understand the role of DNA methylation on development in plants. Toward the end of my PhD, I became interested in the potential role of chromatin in modulating plant development in response to the environment and joined in 2012 the Phil Wigge’s group at the Sainsbury laboratory at Cambridge University (SLCU). While I was conducting my PhD and Postdoctoral studies, I persistently felt I was missing an important aspect in the transcriptional regulation: transcriptional variability. To explore the importance of transcriptional variability in the response to environment I joined the group of James Locke in 2016.

Key Publications

Cortijo S, Aydin Z, Ahnert S, Locke J. Widespread inter-individual gene expression variability in Arabidopsis thaliana. Accepted in Molecular Systems Biology 11 Dec 2018.


*Cortijo S, *Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA: Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. Mol Plant 2017, 10:1258-1273. (* authors contributed equally to the work).


Ezer D, Jung JH, Lan H, Biswas S, Gregoire L, Box MS, Charoensawan V, Cortijo S, Lai X, Stockle D, Zubieta C, Jaeger KE, Wigge PA. The evening complex coordinates environmental and endogenous signals in Arabidopsis. Nature plants. 2017 3: 17087


Jung JH, Domijan M, Klose C, Biswas S, Ezer D, Gao M, Khattak AK, Box MS, Charoensawan V, Cortijo S, Kumar M, Grant A, Locke JC, Schafer E, Jaeger KE, Wigge PA. Phytochromes function as thermosensors in Arabidopsis. Science. 2016 354: 886-889


Ito T, Tarutani Y, To TK, Kassam M, Duvernois-Berthet E, Cortijo S, Takashima K, Saze H, Toyoda A, Fujiyama A, Colot V, Kakutani T. Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis. PLoS Genet. 2015 Apr 22;11(4):e1005154. doi: 10.1371/journal.pgen.1005154.


Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F. Mapping the epigenetic basis of complex traits. Science. 2014 Mar 7;343(6175):1145-8. doi: 10.1126/science.1248127. (CS, WR and CTM contributed equally to the work)


Cortijo S, Wardenaar R, Colomé-Tatché M, Johannes F, Colot V. Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. Methods Mol Biol. 2014;1112:125-49. doi: 10.1007/978-1-62703-773-0_9. (CS and WR contributed equally to the work)


Silveira AB, Trontin C, Cortijo S, Barau J, Del Bem LE, Loudet O, Colot V, Vincentz M. Extensive natural epigenetic variation at a de novo originated gene. PLoS Genet. 2013 Apr;9(4):e1003437. doi: 10.1371/journal.pgen.1003437.


Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V. MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics. 2012 Nov 15;28(22):2930-9. doi: 10.1093/bioinformatics/bts562.


Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F. Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16240-5. doi: 10.1073/pnas.1212955109. (CTM and CS contributed equally to the work)


Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Després B, Drevensek S, Barneche F, Dèrozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 2011 May 18;30(10):1928-38. doi: 10.1038/emboj.2011.103.

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