Francisco Antequera

Functional organization of the eukaryotic genome

Our laboratory is interested in the organization and structure of the eukaryotic genome. Specifically, we are studying how the DNA sequence, the epigenetic modifications and the organization of nucleosomes specify the sites where replication, transcription and recombination initiate. We use the yeast Schizosaccharomyces pombe and human and mouse cells as model systems and our experimental approaches include genetics, molecular biology and computational genomics.

In the mammalian genome many replication origins colocalize with CpG islands, which are associated with 70% of all human gene promoters. These regions are non-methylated, are approximately 1 kb long, have a high G+C content, and their nucleosomes show specific epigenetic modifications. We have reported that replication initiation is associated with the re-replication of a nucleosome-free region that also colocalizes with the transcription start site of many genes in the human genome (Gómez and Antequera, 2008).

In S. pombe, the only sequence requirement to specify functional replication origins is a high A+T content since exogenous A+T-rich DNA fragments without homology with the S. pombe genome can drive replication initiation in the chromosomes as efficiently as endogenous origins (Cotobal et al. 2010). More recently, we have studied how the coordination of the polarity of replication and transcription is determinant to maintaining the epigenetic modifications of centromeric DNA through the RNAi machinery (Zaratiegui et al. 2011). We have also studied how access to the DNA molecule through nucleosome-free regions at gene promoters is an essential factor that regulates meiotic recombination (de Castro et al. 2012).

We are currently generating genome-wide high-resolution sequencing maps of nucleosomes and of their epigenetic modifications (Soriano et al. 2013). The example in the Figure shows that chromatin remodelling during meiosis is limited to specific nucleosomes at the promoters of some genes, while the rest of the genome remains invariable. Based on these observations, we are studying the functional link between the DNA sequence, nucleosome positioning and the epigenetic modifications. We are interested in how these factors regulate the expression, stability and evolution of the genome.

Nucleosome dynamics and differential transcription

The nucleosomal profile was generated by next-generation sequencing of mononucleosomal DNA from exponential mitotic cells or from synchronous meiotic cells. The data are from a sample five hours after the initiation of meiosis. The only detectable difference in the region shown is a nucleosome that is absent in the bidirectional promoter between the mcm2 and mlo2 genes when they are expressed during mitosis. The nucleosome is present in meiotic cells, when both genes are downregulated. Green lines represent transcription on both DNA strands as detected by tiling genomic microarrays.

Group members
Francisco Antequera Research Professor (CSIC)
Laura Durán Postdoctoral
Alicia García Postdoctoral
Sara González PhD Student
Luis Quintales Full Professor (USAL)
Mar Sánchez Postdoctoral
Rodrigo Santamaría Tenured Professor (USAL)
Recent publications
González S, García A, Vázquez E, Serrano R, Sánchez M, Quintales L and Antequera F (2016)
Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome
Genome Research 26: 1532-1543 (doi: 10.1101/gr.207241.116)
Quintales L, Soriano I, Vázquez E, Segurado M and Antequera F (2015)
A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins
Open Biology 5: 140218 (doi: 10.1098/rsob.140218)
Materne P, Anandhakumar J, Migeot V, Soriano I, Yague-Sanz C, Hidalgo E, Mignion C, Quintales L, Antequera F and Hermand D (2015)
Promoter nucleosome dynamics regulated by signaling through the CTD code
eLIFE 4: e09008 (doi: 10.7554/eLife.09008)
Vázquez E and Antequera F (2015)
Replication dynamics in fission and budding yeasts via DNA polymerase tracking
BioEssays 37: 1067-1073 (doi: 10.1002/bies.201500072)
Castel E, Ren J, Bhattacharjee S, Chang A, Sánchez M, Valbuena A, Antequera F & Martienssen R (2014)
Dicer promotes transcription termination at sites of replication stress to maintain genome stability
Cell 159: 572-583 (doi: 10.1016/j.cell.2014.09.031)
Research grants
Determinants of nucleosome positioning and chromatin engineering
MINECO: BFU2014-52143-P
S. pombe Genomic Browsers
Differential gene expression under oxidative stress

Replication origins and recombination hotspots

Nucleosomal organization and transcription