Francisco Antequera

Functional organization of the eukaryotic genome

All eukaryotic genomes, regardless of their size, are greatly compressed inside the cell nucleus. The first level of compaction depends on the nucleosomes -the basic units of chromatin- which are made up of 147 base pairs of DNA wrapped around a histone octamer. Each human diploid nucleus contains 2 meters of DNA and around 30 million nucleosomes. The genome of a haploid yeast spans 5 mm and is packed by 80000 nucleosomes, approximately.

In addition to their structural function, nucleosomes control genome processes by modulating the access of regulatory proteins to DNA or through the epigenetic modification of histones. This regulatory function depends on the precise positioning of nucleosomes relative to the DNA sequence. Nucleosome positioning is regulated by chromatin remodelling complexes, the binding of transcription factors and the DNA sequence itself.

In our laboratory, we are studying how the DNA sequence specifies the position of nucleosomes in the genome. We use species of the yeasts Schizosaccharomyces and Saccharomyces as model systems, and biochemical, genetic, genomic and bioinformatic experimental approaches. In recent years, we have reported that the 147 nucleotides of mononucleosomal DNA adopt a well-defined distribution pattern that we have called nucleosomal signatures. Despite the high degree of phylogenetic conservation of histones, nucleosomal signatures differ even among species of the same genus (Quintales et al. 2015) (Figure 1A), which raises questions regarding their biological significance.

Through genomic and bioinformatic approaches, we have shown that nucleosomal signatures contain information that directs the positioning of nucleosomes in chromosomes in vivo. By using this information, we have designed synthetic DNA molecules capable of positioning nucleosomes with the same periodicity as the host genome where they integrate. It is equally possible to remaster genes of an organism through the incorporation of the nucleosomal signature of a different host genome by selecting synonymous codons such that the ectopic gene adopts the nucleosomal organization of the recipient genome while maintaining the expression of the original protein (González et al. 2016) (Figure 1B).

The design of DNA molecules capable of driving their own nucleosomal organization opens the possibility of modifying specific chromatin regions to study the impact on transcriptional regulation, genome stability and the landscape of epigenetic modifications. These approaches are also relevant to the fields of synthetic biology and genome design and could be used to optimize genes and expression vectors of interest in biotechnology. We are currently exploring these possibilities in our laboratory.

Nucleosomal signatures and nucleosomal organization

A) Nucleosomal signatures of the four nucleotides (adenine, green; thymine, red; citosine, blue; guanine, black) along mononucleosomal DNA of Schizosaccharomyces pombe, S. octosporus, S.s japonicus and Saccharomyces cerevisiae. Y-axis indicates the composition of each nucleotide and the X-axis indicates the distance in nucleotides from the central position of mononucleosomal DNA (0). Ellipses represent nucleosomes.

B) Nucleosomal signatures in orthologous genes of two different species. The diagram shows the transcription initiation (white arrows), nucleosome positioning and the proteins encoded by each gene. When the gene of Species 2 is introduced in the genome of Species 1, nucleosomes adopt an irregular pattern (non-positioned nucleosomes). Incorporating information from the nucleosomal signature of Species 1 into the gene of Species 2 through the use of synonymous codons, nucleosomes adopt the organization of Species 1, but continue to express the original protein of Species 2.

Group members
Francisco Antequera Research Professor (CSIC)
Laura Durán Postdoctoral
Alicia García Postdoctoral
Loreto Megido Predoctoral
Laura Rodríguez Postgraduate
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
Genome regulation through nucleosomal positioning
MINECO: BFU2017-89622-P
S. pombe Genomic Browsers
Differential gene expression under oxidative stress

Replication origins and recombination hotspots

Nucleosomal organization and transcription

NUCwave