The latest EMBO workshop was held in ICVS in Braga on October 22-25th and focused on the state-of-the-art and novel opportunities in epigenetic neurosciences. Particular interest was on the parallel of epigenetic and nervous system plasticity as epigenetic marks not only dynamically change during physiological brain development, but also in the context of brain disorders. Leading experts and young-researchers crossed together from the bottom to the top of Waddington’s landscape in an ‘epigenetic Yamanaka’ style and went back downhill using iPSCs to bridge (epi)genotype and neuro-phenotype.
Below you find some summaries to let you enjoy the evolutions in the field.
Novel Chromatin Pathways to Induce Totipotency
Maria-Elena Torres-Padilla, IGBMC, Strasbourg, France
Following fertilization, terminally differentiated gametes undergo epigenetic reprogramming in order to create a totipotent zygote. The zygote first undergoes a series of divisions without significant increase in cell volume, resulting in the formation of the blastocyst. By this point, the first differentiation event has already occurred, segregating the outer trophectoderm, which is developmentally restricted to extra-embryonic tissues, from the inner cell mass, which comprises pluripotent embryonic cells that will develop into the embryo.
How embryonic cells adopt their fate after fertilization and whether the chromatin conformation within each cell gradually promotes its identity throughout development remains unknown. Maria-Elena Torres-Padilla points at these questions, central for our understanding of cell plasticity, development and reprogramming and postulates that individual cells in the early embryo develop a chromatin configuration that is permissive for cell fate allocation by operating at both a local and global level.
The composition of the embryonic chromatin is markedly atypical, characterized by the incorporation of several histone variants and a lack of most of the histone post-translational modifications that are normally found associated with constitutive heterochromatin. Moreover, there is now evidence of the global open chromatin configuration in individual cells of the early embryo, particularly in cells that are destined to become pluripotent inner cell mass cells (Burton, Torres-Padilla, Nature 2014).
Programming and Reprogramming of Trophoblast Lineage
Myriam Hemberger, Babraham Institute, Cambridge, United Kingdom
Myriam Hemberger underscores that the first cell fate decision is the most incisive in development. Three distinct cell lineages arise at the blastocyst stage: the throphectoderm that gives rise to the placenta, the epiblast that will form the proper embryo and the primitive endoderm that will form the major components of the yolk sac. Four different stem cell types recapitulate the developmental capacity of the cell lineages.
Using genome-wide DNA analyses, The group of Myriam Hemberger characterized distinct lineage-specific DNA methylation profiles for these stem cell types: the embryonic (ES) and epiblast (EpiSC) stem cells that are pluripotent and committed to an embryonic lineage fate and the trophoblast (TS) and extraembryonic endoderm (XEN) stem cells that contribute predominantly to tissues of the placenta and yolk sac, respectively. Despite these established lineage barriers, ES cells can seemingly acquire TS-like characteristics upon manipulation of transcription factors or signalling cascades.
The progression of ES-to-TS reprogramming was interrogated and although trans differentiation into TS-like cells was initiated, lineage conversion remained incomplete in all models. These data reveal that an epigenetic memory of the first cell fate decision prevents complete reprogramming even of ground state pluripotent ES cells into trophoblast. The epigenetic barriers between the first cell lineages seem to be extremely stable, underscoring the importance of the first cell fate decision in development, health and disease.
Disease Avatars: Modelling Epigenetic Dysfunction in Neurodevelopmental Disorders
Giuseppe Testa, European Institute of Oncology, Italy
After the “crisis” in molecular biology in the years 1960-80, a decade after the detection of the DNA code, Giuseppe Testa states that we are nowadays in the middle of the molecular biomedicine crisis struggling to bridge (epi)genotype to phenotype. Cell reprogramming promises to transform the study of the functional impact of human genetic variation on health and disease in developmentally relevant human settings and Giuseppe Testa applied iPSCs to chart for the basis of neurodevelopmental disorders.
He especially investigates two disorders caused by a symmetrical copy number variations of 7q11.23 and displaying a striking combination of shared as well as symmetrically opposite phenotypes: Williams Beuren syndrome and 7q11.23 microduplication syndrome associated with Autism Spectrum Disorder. This pair of syndromes entails respectively the loss or gain of 26-28 genes, including several transcription factors and chromatin remodelers. Can the pluripotent state a meaningful stage for the study of 7q11.23 dosage imbalances?
What are the transcriptional consequences? What is the extent to which the molecular switches can be probed into patient-specific induced pluripotent stem cells (iPSC) and their differentiated neural derivatives? Strikingly, 7q11.23 CNV disrupt transcriptional circuits already at the pluripotent state. Transcriptional dysregulation is caused by dosage imbalances in GTF2I, a critical transcription factor, associated to a major chromatin repressive complex with a well-established function in neuronal development.
Adult Neurogenesis and Epigenetic DNA Modifications
Hongjun Song, Institute for Cell Engineering, Johns Hopkins University, United States
Emerging evidence suggests important roles for epigenetic regulation in activity-dependent brain functions, including synaptic plasticity, learning and memory, circadian rhythm, drug addiction, and adult neurogenesis. Hongjun Song found that DNA (de)methylation plays a very important role in neurons, as this changes global synaptic transmission.
Neuronal stimulation induces DNA demethylation at specific promoters of brain-derived neurotrophic facto and fibroblast growth factor 1 in a Gadd45b- and TET1-dependent fashion in the adult mouse dentate gyrus. More recently the group of Hongjun Song discovered by single-base methylome analysis significant non-CpG methylation in these neurons. Neuronal CpH (H = A/C/T) methylation is conserved in human brains, enriched in regions of low CpG density, depleted at protein-DNA interaction sites and anti-correlated with gene expression.
Both methylated CpGs and CpHs can respress transcription in vitro and are recognized and maintained by MECP2 and DNMT3A respectively. This study implicates novel modification of the neuronal DNA methylome as a previously under-appreciated mechanism for activity-dependent epigenetic regulation in the adult nervous system.
Transgenerational Inheritance of Ancestral Olfactory Experience
Brian Dias, Emory University, Atlanta, United States
Exposure of populations to traumatic events like wars, famines and terrorist attacks can influence descendant generations. Perhaps, one of the more striking examples of this comes from the observation that exposure of pregnant women to the 9/11 terrorist attacks profoundly affected the physiology of their gestating babies. Brian Dias shows how a parental traumatic olfactory experience influences behaviour and neural structure in subsequent generations.
They subjected male F0 mice to odor (acetophenone) fear conditioning before conception and found that subsequently conceived F1 and F2 generations had an increased behavioural sensitivity to the F0-conditioned acetophenone, but not to other odors. Interestingly, as acetophenone activates a known odorant receptor (Olfr151), the behavioural sensitivity of the F1 and F2 generations to acetophenone was complemented by an enhanced neuroanatomical representation of the Olfr151 pathway.
Bisulfite sequencing of sperma DNA from conditioned F0 males and F1 naïve offspring revealed CpG hypomethylation in the Olfr151 gene. In addition, in vitro fertilization, F2 inheritance and cross fostering revealed that these transgenerational effects are inherited via parental gametes. These findings provide a framework for addressing how environmental information may be inherited transgenerationally at behavioural, neuroanatomical and epigenetic levels.
Snapshots: Quick Reviews
Many short talks gave the ideal opportunity for young researchers to present their work, and to the audience to enjoy all the interesting evolutions in the field.
- Emilie Bonnaud (INSERM, Toulouse, France) investigated the dysregulation of signalling pathways that regulate epigenetics in the pathogenesis of neurological disorders. Using an interesting Bornavirus model, she demonstrated that Bornavirus infection decreases H2B and H4 acetylation levels on selected lysine residues, through inhibition of histone acetyl-transferase activities. Moreover she found that the viral phophoprotein is responsible for this perturbation and further investigates how BDV-P acetylation influences gene expression upon neural activation.
- Antonio Mateus-Pinheiro (ICVS, Braga, Portugal) explored methylation and hydroxymethylation landscapes and demonstrated that stress exposure compromises different neuroplastic processes in the healthy and stressed brain.
- As cellular metabolite pools are proposed to directly alter the epigenome in relation to changing environment and altered metabolic state, Philipp Mews (University of Pennsylvania, United States) linked the intermediary metabolism to chromatin remodelling. He characterized acetyl-CoA synthetase 1 (AceCS1) as a particularly important player for histone acetylation in neuronal cells. He speculates that AceCS1 not only mediates the re-activation of extracellular acetate that fluctuates with diet and metabolism, but also of acetate that derives from nuclear HDAC activities.
**EpiGenie sends out a great big thanks to Anne Rochtus, who is a PhD student in the Center for Molecular and Vascular Biology at KU Leuven in Belgium, for providing this conference coverage.