Mammalian Developmental Epigenetics

With each generation, the precise spatio-temporal unfolding of embryonic development requires a tight orchestration of dynamic changes in chromatin states and corresponding transcriptional programs. While development is often approached as simply hardwired in the genome, there is a growing appreciation that the environment provides key inputs into the bookmarking and activation of the genome during ontogeny, but such inputs remain very poorly understood at the mechanistic level. Our lab is interested in understanding the genome-environment interactions that shape mammalian development and reproduction. Of particular interest are pluripotent cells that exist in the mammalian embryo and give rise to all cell types of the body. Recent work from our lab highlights that such foundational aspects as genome organization, transcription and environmental input are regulated in unique and novel ways in pluripotent cells of the early embryo and the germline. Our research is organized around 3 principal avenues of inquiry, each of which has several points of synergy with the other avenues.

 
 
 
 

Stem cell hypertranscription

 

Hypertranscription, the global amplification of a large part of the genome, is pervasive in stem/progenitor cells but has remained largely undetected until recently (read our recent review on this topic). We are investigating the molecular mechanisms by which factors such as the chromatin remodeler Chd1 promote hypertranscription in stem cells (Percharde et alGuzman-Ayala et alKoh et al).  In parallel, we are interested in exploring the occurrence and function of hypertranscription in other stem/progenitor cells, such as in the brain, intestine or skin, and in regeneration contexts.

 Stem cell hypertranscription

Stem cell hypertranscription

We are also dissecting the regulation of open chromatin and hypertranscription in a systematic manner, using genome-wide screens in ES cells. The results of one such screen, recently published, reveal that  the permissive chromatin state and hypertranscription of pluripotent stem cells is acutely tuned to their translational capacity, itself dependent on nutrient availability. This work led to the discovery of a paused pluripotent state in mouse ES cells and blastocysts, induced by mTor inhibition (Bulut-Karslioglu et al).  The ability to reversibly suspend development of a mammal in the laboratory, and to mimic such developmental pausing in ES cells, offers a tractable model to dissect a number of fascinating questions. The relationship between open chromatin of pluripotent stem cells, growth pathways and developmental timing will continue to be a fruitful area of inquiry in our lab.  

 
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Roles of transposons in development

 Roles of transposons in development

Roles of transposons in development

Unique protein coding genes occupy only a minor fraction (~1.5%) of our genome. About half of the mouse and human genomes is comprised of Transposable Elements (TEs), which are sequences capable of moving to different locations in the genome. Interestingly, the TEs of the LINE1 and ERVs families are highly expressed in mouse and human pre-implantation embryos and ES cells (Yan et alGöke et alFadloun et al). ERVL has a sharp peak of expression at the 2-cell (2C) state in mouse embryos and marks a rare cell population in ES cells (Macfarlan et al). This ERVL-marked 2C state is thought to correspond to totipotent cells that, unlike ES cells, are still capable of giving rise to trophectoderm (Macfarlan et al). LINE1 is also expressed in neural progenitor cells, where it has been proposed to promote neuronal diversity (Muotri et al).

Our lab has long been fascinated with investigating the function of TEs in pluripotent stem cells. We very recently reported that RNA from the retrotransposon LINE1 orchestrates the progression of totipotent cells at the 2-cell stage towards pluripotent cells of the blastocyst by partnering with the protein Nucleolin to regulate the expression of ribosomal RNA, the transcription factor Dux and the ERVL-associated 2C program. Via this mechanism, LINE1/Nucleolin are required for early development and for self-renewal of ES cells (Percharde et al). These results cast a fundamentally novel light on our understanding of early embryogenesis and pluripotency, with TEs as key orchestrators. We are exploring approaches in human ES cells and mouse models to uncover novel essential roles for TEs in multiple stem/progenitor cells during normal development, degeneration and regeneration. 

 
 
 

Environment-epigenome interactions

 Environment-epigenome interactions

Environment-epigenome interactions

Developmental and stem cell biologists often assume that development is a process hardwired in the genome and insulated from environmental influence. However, a growing body of evidence shows that deficiencies in maternal diet or exposure to environmental toxins during gestation may affect developmental trajectories and program postnatal disease propensity in the progeny(Gluckman et alBoekelheide et alBygren). The mechanisms that underlie the environmental modulation of developmental and stem cell biology remain largely unknown.

We discovered that the essential nutrient Vitamin C impacts the transcriptional and epigenetic state of ES cells in remarkable ways by acting as a specific co-factor for Tet enzymes and greatly enhancing DNA demethylation (Blaschke et al ). We are now using mouse models of Vitamin C deficiency to determine the effect of windows of withdrawal during gestation on epigenetic states in the embryo. Our results raise the possibility that dietary Vitamin C regulates the epigenetic state and function of the germline in vivo, potentially with transgenerational consequences. Our findings have implications in other stem cell systems where Tet enzymes are active, including the hematopoietic system and the brain. In addition, deficiencies in the activity of Tets have been causally linked to several types of cancer (e.g. Lian et al, Shih et al). This work highlights how sensitive the epigenetic state of pluripotent stem cells is to environmental factors, be it nutrition in vivo or media composition in vitro.

Moving forward on this avenue, our lab will explore how environmental stresses are sensed by pluripotent stem cells, and in particularly whether they induce the mutagenic activity of TEs. A conserved response to a variety of cellular stresses across living organisms is the de-repression of TEs (Fedoroff). Such stress response may be a mechanism for evolvability, by ensuring that novel genomic variants generated by TEs can undergo selection under a challenging environment. However, the downside of evolvability conferred by TEs at a species level may be genetic developmental programming of disease at the individual level. In particular, stresses during gestation may activate TEs that mutagenize the genome, creating mosaic individuals that are sensitized for adult-onset disease and may transmit new variants to the next generations. We are interested in using tools such as functional genomics and single-cell genome sequencing to understand the impact of stress-induced TEs on cellular heterogeneity during pluripotent stem cell differentiation and development.

 
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