Dissecting molecular mechanisms of epigenetic silencing

Collaborators: Howard Chang & Edith Heard


Epigenetic silencing: X-chromosome inactivation as a model

Every cell in the body contains the exact same DNA, but a number of proteins and RNAs modify DNA to activates or repress a distinct set of genes that are essential the cells specific function.  Understanding the molecular underpinnings of such gene regulation is critical for our understanding of embryonic development, as well as disease.  The most dramatic case of developmental gene regulation is X chromosome inactivation (XCI), the process by which female mammals inactivate one of the two X chromosomes in every cell.  This process of silencing genes, condensing chromatin, and relegating the chromosome to the periphery of the nucleus is orchestrated by a host of molecular players.  It begins with expression of the long noncoding RNA (lncRNA) Xist, which spreads out to coat the chromatin, and recruits protein cofactors to silence gene expression and induce heterochromatin formation.

Together, the Chang and Heard labs are studying the molecular mechanisms that underlie XCI, including: the evolution and activation of Xist, the recruitment of repressive proteins, and the resulting condensation of the inactivated X chromosome.  Combining the Chang Lab’s expertise in lncRNA biology and epigenomic tool development, with the Heard Lab’s extensive knowledge of XCI and developmental genomics, has significantly contributed to our understanding of XCI and the broader mapping and understanding of epigenetic processes.


Dissecting molecular mechanisms of epigenetic silencing: X chromosome inactivation as a model paradigm

Through their collaboration, the Chang and Heard labs aim to dissect XCI at every level.  They aim to develop novel technologies for studying lncRNA-mediated epigenomic processes and extend their findings to broader processes in development and disease.  In their first collaborative project, the Chang and Heard labs were amongst the first to identify the Xist-associated proteome - the set of protein binding partners that carry out gene silencing and heterochromatin formation after Xist activation (Chu et al., 2015). The labs are now working to uncover the detailed mechanism by which a central protein carries out its XCI function.  The Chang lab is performing genome-wide and evolutionary analysis, while the Heard lab seeks a full mechanistic view of the protein by deciphering assembly of the Xist-protein complex and the protein domains required for this assembly.

Following assembly of the Xist RNA-protein complex, a cascade of modifications to the epigenome ultimately results in compaction of the X into the Barr body.  The Chang and Heard labs, together with Job Dekker’s lab, described this process providing the first multi-level map of the inactive X chromosome (Giorgetti et al., 2016).  Together, the labs applied these allele-specific mapping techniques to study monoallelic gene regulation broadly on the autosomes (Xu et al., 2017). Continuing this line of research, their aim is to understand the molecular actors that orchestrate X chromosome inactivation as well as the resulting changes to gene regulation, not only to shed light on this remarkable female-specific process, but also on developmental epigenetic processes more broadly. 

Spatio-temporal investigation of X-inactivation mechanisms in vivo

Bridging Excellence Fellowship for Joyce Man

In mammals, males and females differ genetically in their sex chromosomes – XX in females and XY in males. This leads to a potential imbalance, as more than a thousand genes on the X chromosome would be expressed in a double dose in females compared to males. To avoid this imbalance, that would lead to early embryonic lethality, female embryos shut down the expression of genes on one of their two X chromosomes. This process of X-chromosome inactivation (XCI) is initiated by the Xist non-coding RNA. Despite its central role in XCI, the exact molecular mechanisms by which Xist coats, spreads across the X chromosome and mediates gene silencing during early development remain elusive. In particular different genes are differentially silenced during XCI. To investigate this dynamic process we will use cutting edge genomic (Heard lab at EMBL) and enzyme-mediated proximity labeling approaches (Chang lab at Stanford) to map the localization of Xist RNA at high resolution and define its RNA and protein interaction networks, in wildtype and mutant mouse embryonic stem cells. This will allow us to track Xist RNA in time and space, capture its targets as well as known and new interaction partners at high temporal resolution as XCI happens. This project will help us answer important questions about gene regulation and epigenetic pathways in general, as well as providing molecular insights into Xist RNA-mediated XCI.

This project is supported by a Bridging Excellence Fellowship, awarded to Joyce Man


Find out more:

Are you interested in finding out more about the X chromosome inactivation project? Would you like to delve into the complex mechanisms of epigenetic silencing?  Get in touch! We would love to hear from you.

Joyce Man, Bridging Excellence Fellow