The new voyage of the “Argonautes”

A new publication from our group describes a new function for a protein mostly characterized for its role in directing small non-coding RNAs to their targets.

Small RNA molecules, which include the so called micro-RNAs (miRNAs), provide a powerful mechanism to regulate gene expression in the cell cytoplasm either by triggering degradation of the messenger RNAs molecules (mRNA) or by inhibiting their translation into proteins. This mechanism, known as post-transcriptional gene silencing, takes place in the cell cytoplasm and has important implications for understanding developmental and disease processes. The miRNAs are guided to their targets by a molecular complex that is made of a group of proteins called Argonautes. These proteins are essential to direct the miRNAs to their mRNA targets, and their structure and role in the post-transcriptional gene silencing has been thoroughly described up to date.

In this work, we report that Argonaute proteins also play an important role in gene regulation in the cell nucleus. The published work describes how Argonaute proteins, besides their role in post-transcriptional regulation, can also affect gene expression during transcription, the cell process that makes mRNA from DNA. In particular, this work shows evidence that Argonaute can bind to specific locations of the genome. These locations are transcriptional enhancers, regions in the DNA that control of the expression of one or multiple genes by governing when these genes must be turned on or off. Enhancers are usually placed far from the genes they regulate, but they can also occur inside a gene. The activation of enhancers takes place through binding of specific factors, as well as by the acquisition of multiple chemical modifications by the chromatin, the structural packing of DNA in the cell that makes possible to hold the long DNA chains from chromosomes into small volumes in the cell nucleus. Each cell type has a specific subset of enhancers that are activated by generic biochemical modifications of the chromatin and by specific protein factors that control gene expression in that cell, and which ultimately determines the cell identity. The aberrant activation or silencing of enhancers can impact cell function and lead to cell transformation, like cancer.

AGO1_figure

This article describes how the Argonaute protein AGO1 can bind to enhancer regions inside genes when they are activated, and thereby directly affect how the RNA molecule transcribed from that gene locus is processed (see Image). In particular, using high-throughput sequencing techniques to describe the regions of the chromatin that have specific biochemical modifications, and which ones interact with Argonatue proteins, we have discovered that the Argonaute protein, specifically the member AGO1 from the Argonaute protein family, binds preferentially to active transcriptional enhancers and that this association is mediated by the RNA molecules that are produced from the active enhancers, also known as enhancer RNAs (eRNAs). Moreover, the interaction of AGO1 with enhancers occurs mostly inside genic regions and appears to affect the splicing of the host gene rather than its transcription. In summary, this work suggests that AGO1 has a function in the nucleus that is related to the activation of transcriptional enhancers, and from these sites is capable to modulate the processing of the RNA from the same locus. These results contribute to the understanding of the complex regulation of gene expression in eukaryotic cells. This work proposes that Argonautes can perform yet another voyage to the nucleus to control how genes are processed, proving to be important and versatile players in determining cell function.

This work has been funded by the Sandra Ibarra Foundation for cancer and by the European Network on alternative splicing EURASNET.

Alló M, Agirre E, Bessonovc S, Bertucci P, Gómez-Acuña L, Buggiano V, Bellora N, Singh B, Petrillo E, Blaustein M, Miñana B, Dujardin G, Pozzi B, Pelisch F, Bechara E, Agafonov D, Srebrow A, Lührmann R, Valcárcel J, Eyras E*, Kornblihtt AR*. Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells. PNAS doi:10.1073/pnas.1416858111 http://www.pnas.org/content/early/2014/10/08/1416858111

Regulatory Genomics Group

Research in the Computational Gene Regulation group within the Research Unit on Biomedical Informatics focuses on the development of computational methods to study the mechanisms of regulation of alternative pre-mRNA splicing and their role in cancer.

Current Projects

Chromatin and Splicing

There is currently increasing evidence for a relation between the state of chromatin and pre-mRNA splicing. Chromatin structure and histone modifications have been shown to affect both constitutive and alternative splicing, either by recruitment of splicing factors or by modulating Pol II elongation. Along with these basal level controls, identification of specific histone markers could also explain the different splicing patterns between in specific conditions and cell types. Using high-throughput sequencing data, we study the role of various chromatin regulators in the regulation of alternative splicing.

Small RNAs and Splicing

Recent reports suggest that new classes of small RNAs can be produced from longer RNAs. We study the biogenesis and activity of these new RNA classes and their potential effect in the regulation of pre-mRNA splicing, and how these mechanisms can play a role in cancer.

Cancer and Splicing

Many of the hallmarks of cancer, such as evasion of cell-death and tissue invasiveness, are profoundly influenced by alterations in splicing. AS alterations in cancer are generally related to the production of protein variants with opposing functions, e.g. pro- and anti- apoptotic; or simply to the activation of proto-oncogenes or the inactivation of tumor-suppressor genes.  We aim to describe the landscape of splicing alterations in cancer  through a pan-cancer data analysis using TCGA data.