Our research

In eukaryotic cells, nuclear DNA is packed into chromatin, an intricate nucleoprotein complex. Hereby, the chromatin fiber sustains most of the nuclear functions, including transcription, DNA repair, replication or recombination events. Chromatin structure and dynamics are very tightly regulated, specifically by epigenetic mechanisms which modify chromatin structure and affect gene regulation without altering the DNA sequence. The epigenome consists of a wide array of chemical modifications on chromatin, including

DNA methylation and histone posttranslational marks. Generally, the epigenome contributes to define chromatin structure and compaction at specific genomic loci, determining transcriptional outcomes in time and space. However, misfunction of the epigenome can happen for example in response to damaging environmental cues such as drugs, pollution, endocrine disruptors, stress, malnutrition etc., leading to misregulation of gene expression programs, which in turn promote a number of diseases. We are particularly interested in identifying mechanisms of chromatin and epigenetic regulation within these environmental contexts. To do so, we embrace multidisciplinary research by employing a diverse set of experimental approaches, including molecular and cell biology, transgenic mice, advanced microscopy, functional genomics and bioinformatic analyses.

Currently, we are developing the following research lines:

  • Deciphering epigenetic mechanisms regulating circadian gene expression.


Circadian rhythms orchestrate crucial physiological functions and behavioral aspects around a day in almost all living forms. The circadian clock is a time tracking system that permits organisms to predict and anticipate periodic environmental fluctuations. A master pacemaker in the hypothalamus synchronizes subsidiary clocks in the rest of the tissues. Adequate synchrony between clocks in the organism potentiates a healthy state. Conversely, circadian misalignment leads to metabolic diseases, psychiatric disorders, or cancer. Remarkably, the molecular machinery directing circadian rhythms consists of an intricate network of feedback loops in transcription and translation which impose 24-h cycles in gene expression across all tissues. Interestingly, the molecular clock needs to coordinate its function with many epigenetic remodelers to fine tune transcriptional rhythms.

Hence, the circadian clock provides an ideal framework to study how exposure to environmental signals impacts chromatin dynamics and epigenetic regulation to drive transcriptional programs in a time-specific manner. We have previously described that the histone methyltransferase MLL1 interacts with the NAD+-dependent histone deacetylase SIRT1 in a time-of-day specific manner to deliver either activating or repressive epigenetic marks to clock-controlled gene promoters, hereby imposing transcriptional cycles. Metabolic cues fine tunes this balance in cultured cells (Aguilar-Arnal et al. Nature Structural & Molecular Biology 2015). We are now interested in providing additional insights to into this molecular mechanism and uncovering its physiological implications for example in healthy state and under metabolic imbalance. Additionally, we have found evidence of novel histone methyltransferases implicated in sustaining transcriptional oscillations in cooperation with the molecular clock. 

  • Describing the role of the molecular components of the circadian clock, mostly consisting of transcription factors, in complex diseases.

Disruption of circadian rhythms has been extensively associated with cancer and metabolic diseases, yet the molecular mechanisms involved remain largely unknown. The molecular clock machinery consists of a set of transcriptional activators (CLOCK and BMAL1 proteins, ROR nuclear receptors) and repressors (PER1-3 and CRY1-2 proteins, Rev-Erb nuclear receptors) which rhythmically bind to chromatin, hence imposing rhythms in chromatin transitions and gene expression in a tisssue-specific manner. Using a combination of techniques designed for genome-wide analyses, such as ChIP-seq, ATAC-seq or RNA-seq, with mouse models, we want to investigate the dynamics of specific core clock components in metabolic syndrome and breast cancer diseases. Additionally, we are using transgenic mice bearing mutant forms of the molecular clock to address how the core clock sustains metabolic fitness.

  • Investigating molecular interactions between nuclear architecture and cellular metabolism.

We have previously described a role for the molecular clock in driving circadian chromatin long-range interactions in cultured cells (Aguilar-Arnal et al. Nature Structural & Molecular Biology 2013). 3D chromatin folding is becoming increasingly recognized as an important epigenetic regulatory layer, and differential chromatin conformations are apparent at day and night times. As a result of specific enhancer-promoter interactions occurring at distinct circadian times, transcriptional oscillations are sustained in time and space. We are investigating to which extent cellular metabolism shapes the circadian interactome. Also,we want to gain insights into the molecular drivers of differential long-range chromatin interactions in response to metabolic cues. To do so, we have already set up chromatin conformation capture techniques (4C-seq) and adequate bioinformatics analyses to generate and process the genomic data in the lab.

  • Identifying molecular connections between metabolic transitions and epigenetic reprogramming during stem cell differentiation.

Small molecule metabolites play much underappreciated roles in cell differentiation and homeostasis by controlling the activity of a number of epigenetic remodelers. Previous studies generally determine metabolic states from whole cell lysates, but lack to identify subcellular compartmentalization of metabolites. Yet, local concentrations of certain metabolites could alter enzymatic properties in discrete subnuclear microenvironments. Our recent research describe subnuclear compartments of NADH metabolism which could have futher implications in the local control of gene expression (Aguilar-Arnal et al, PNAS 2016). It is known that a redox switch from glycolytic to oxidative metabolism and a wide epigenetic reprogramming are hallmarks for stem cell activation and lineage commitment. However, the molecular links between these major processes during differentiation remain largely unknown. In the lab, we have set up neural differentiation protocols from human embryonic stem cells (hESC) which combined with CRISP-Cas9 -based genome editing technologies, are allowing us to explore how specific proteins known as metabolic sensors shape the dynamic epigenome during differentiation. Additionally, we are working on human mesenchymal stromal/stem cells (hMSC) to address the role of energy metabolism in the transcriptional control during adipogenesis.

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