Final Report Summary - NCRNAX (Regulation and function of non-coding RNAs in epigenetic processes: the paradigm of X-chromosome inactivation)
Non-coding RNAs are now recognized as essential players in many biological processes, but our understanding of their functional repertoire is still limited. The main goal of our project was to gain insights into the regulation and function of non-coding RNAs and their contribution to the control of gene regulation both in mouse and in humans, using X-chromosome inactivation as a paradigm. X-inactivation, which is the transcriptional silencing of one of the X chromosomes in female mammals, is indeed controlled by the interplay of several non-coding RNAs, at the center of which is Xist. Xist is the master regulator of the process, its RNA accumulates on the chromosome from which it is expressed and triggers its silencing.
The first part of our project thus focuses on the mechanisms controlling Xist, as this is essential to understand how X-inactivation is regulated. We have identified mechanisms involved both in the repression and in the activation of Xist. We have contributed to identify the core pluripotency factors (i.e. the factors that control the pluripotent state of cells) as being directly involved in the developmental control of X-inactivation through the repression of Xist on the one hand and the activation of Xist repressors on the other. These results were the first to provide the molecular basis linking X-chromosome inactivation and cell differentiation/development. We have also demonstrated that the transcription factor YY1 has a prominent and conserved role in the transcriptional activation of Xist.
Xist is not the only non-coding RNA involved in X-chromosome inactivation and indeed, the region around Xist (termed the X-inactivation center) has the particularity of harboring several long non-coding genes, several of which were shown to participate to the X-inactivation process. Ftx is one non-coding gene of the region whose function was still unknown. To probe for a function of Ftx in X-inactivation, we have generated several cellular and animal models. We have shown that Ftx contributes to the regulation of Xist and its exact role in X-inactivation is now being addressed. The mutant Ftx mice that we have generated moreover represents one of the rare animal models for non-coding RNA, allowing to explore its function in vivo.
X-inactivation has been mostly studied so far in the mouse model, and although the process is achieved in all eutherians, differences have been noted between rodents and other species. To investigate these differences further, especially in humans, we have decided to focus on human embryonic stem (ES) cells as this is the only ex vivo system that allows to study the initiation of the process and the key regulatory steps involved. Unlike their murine counterpart, human ES cells display variable X-inactivation status, which are moreover unstable in culture. We have shown that YY1 is likely involved in the unstable expression of XIST in human ES cells. We have moreover discovered a novel non-coding RNA, XACT, which appears to be specific to the humans. No ortholog was found in mouse and in other species. Striking, XACT RNA accumulates on the active X chromosome, in embryonic cells only. This offers a mirror image to that of XIST, which accumulates on the inactive X. We propose that XACT is important for the proper dynamics of X-chromosome inactivation during early human development.
The first part of our project thus focuses on the mechanisms controlling Xist, as this is essential to understand how X-inactivation is regulated. We have identified mechanisms involved both in the repression and in the activation of Xist. We have contributed to identify the core pluripotency factors (i.e. the factors that control the pluripotent state of cells) as being directly involved in the developmental control of X-inactivation through the repression of Xist on the one hand and the activation of Xist repressors on the other. These results were the first to provide the molecular basis linking X-chromosome inactivation and cell differentiation/development. We have also demonstrated that the transcription factor YY1 has a prominent and conserved role in the transcriptional activation of Xist.
Xist is not the only non-coding RNA involved in X-chromosome inactivation and indeed, the region around Xist (termed the X-inactivation center) has the particularity of harboring several long non-coding genes, several of which were shown to participate to the X-inactivation process. Ftx is one non-coding gene of the region whose function was still unknown. To probe for a function of Ftx in X-inactivation, we have generated several cellular and animal models. We have shown that Ftx contributes to the regulation of Xist and its exact role in X-inactivation is now being addressed. The mutant Ftx mice that we have generated moreover represents one of the rare animal models for non-coding RNA, allowing to explore its function in vivo.
X-inactivation has been mostly studied so far in the mouse model, and although the process is achieved in all eutherians, differences have been noted between rodents and other species. To investigate these differences further, especially in humans, we have decided to focus on human embryonic stem (ES) cells as this is the only ex vivo system that allows to study the initiation of the process and the key regulatory steps involved. Unlike their murine counterpart, human ES cells display variable X-inactivation status, which are moreover unstable in culture. We have shown that YY1 is likely involved in the unstable expression of XIST in human ES cells. We have moreover discovered a novel non-coding RNA, XACT, which appears to be specific to the humans. No ortholog was found in mouse and in other species. Striking, XACT RNA accumulates on the active X chromosome, in embryonic cells only. This offers a mirror image to that of XIST, which accumulates on the inactive X. We propose that XACT is important for the proper dynamics of X-chromosome inactivation during early human development.