Recent studies have demonstrated an increasingly significant role of epigenetic mechanisms for regulation of critical developmental programs important for establishing and maintaining cell lineage fates.
7,44,45 The first cell fate decision during development generates two primary lineages of the blastocyst, the trophoectoderm that differentiates into the trophoblast subtypes of the placenta and the inner cell mass that forms the embryo.
19,27 The main mechanisms of trophoblast epigenetic regulation include DNA methylation, histone modifications and X-chromosome inactivation.
46,47In contrast to pluripotent embryonic stem cells responsible for the formation of the embryo, DNA of the trophoblast epigenome is hypomethylated. This hypomethylation is critical for implantation and trophoblast differentiation. As trophoblasts differentiate into a more invasive subtype, occurring simultaneously with the progression of EMT, the trophoblast epigenome is continually demethylated. Reduced DNA methylation promotes activation of genetic information critical to trophoblast lineage commitment.
47–51 Despite global hypomethylation of the trophoblast lineage, DNA methylation is indispensable for extraembryonic development. For example, the DNA methyltransferase regulatory factor DNMT3L is highly expressed in the epithelial trophoectoderm and DNMT3L-deficient mice exhibit multiple trophoblast defects, including failure to form syncytiotrophoblasts of the placenta.
52–54 Furthermore, recent genome-wide sequencing studies have demonstrated that DNA hypomethylation is located primarily in intergenic regions, which raises the question of the importance of DNA methylation for the direct control of genetic information.
Histone modifications comprise the second layer of trophoblast epigenetic regulation. Gene expression levels are controlled by the degree of chromatin compaction, which is mediated by wrapping DNA around an octamer of four core histones H2A, H2B, H3 and H4. The charged tails of histones are often modified by acetylation and methylation marks, which generally contribute to the respective activation or repression of genetic information. The repressive histone modification H3K27me3 conferred by the multi-subunit Polycomb complex has been extensively studied for control of gene expression during differentiation of embryonic lineages. Immunohistochemistry of the mouse blastocyst reveals reduced levels of H3K27me3 in the trophectoderm compared with the inner cell mass.
47,55–58 Furthermore, genome-wide sequencing studies demonstrate that few promoters in TS cells are marked by this modification.
59 These findings contrast with post-implantation stage extraembryonic tissues, where high gene-specific levels of H3K27me3 are detected. These results suggest that an alternative repressive modification is dominant in TS cells and that the repressive H3K27me3 modification becomes important only after implantation, likely driving later lineage commitment decisions critical to the formation of the placenta. This could explain why mutants of Polycomb complex members, such as EZH2, SUZ12 and EED, demonstrate defects later during development of extraembryonic tissues while not directly affecting TS cells.
55,56 Specifically, EED mutants exhibit trophoblast differentiation defects demonstrated by failure to produce secondary invasive trophoblast giant cells, suggesting that H3K27me3 modifications might be important during activation of a specific transcriptional program.
57,60 For example, invading trophoblast giant cells play important roles during the EMT events of placentation. Furthermore, the activating H3K4me3 and the repressive H3K9me3 modifications demonstrate importance in TS cell maintenance, but the biological connections to EMT are unclear.
47 Further studies with these histone methylation marks could provide insight into the importance of these modifications in specific transcriptional and EMT programs.
Histone acetylation is associated with active gene transcription due to its ability to decondense and open chromatin.
61,62 Recent work from our lab has demonstrated that global loss of histone acetylation is a dominant mechanism for the activation of TS cell differentiation programs. As TS cells are differentiated by FGF4 withdrawal, acetylation of all four core histones H2A, H2B, H3 and H4 is globally reduced over a 5-day time-course of differentiation. Occurring in parallel with trophoblast differentiation programs, the induction of trophoblast EMT is also epigenetically regulated by histone acetylation patterns.
7 The discovery that trophoblast EMT programs are regulated by epigenetic mechanisms of histone acetylation stemmed from the observation of overlapping phenotypes between KI4 mice and mice deficient for the histone acetyltransferase CBP.
33,63,64 KI4 and CBP knockout mice both display skeletal, neural tube and craniofacial defects combined with growth retardation and embryonic lethality. Biochemical assays, including kinase and histone acetylation assays, demonstrate that regulation of CBP acetyltransferase activity is controlled by MAP3K4/JNK-dependent phosphorylation of CBP. Loss of MAP3K4 activity results in diminished CBP histone acetyltransferase activity. Furthermore, loss of CBP activity through either loss of MAP3K4 activity in TS
KI4 cells or by shRNA knockdown of CBP in TS
shCBP cells results in the selective loss of H2A and H2B acetylation and the induction of a mesenchymal phenotype. Similar to TS
KI4 cells, TS
shCBP cells exhibit loss of apical-basal polarity and increased expression of mesenchymal markers and invasiveness, while maintaining the expression of stemness genes (). Examination of self-renewing TS
KI4 and TS
SNAI1 cells with properties of stemness and EMT reveals selective loss of acetylation from histones H2A and H2B, suggesting a specific role for H2A and H2B acetylation in regulation of TS cell EMT (). In support of this conclusion, three separate models of TS cell EMT (TS
KI4, TS
SNAI1 and TS
shCBP cells) exhibit selective inhibition of H2A and H2B acetylation (). For TS
KI4 cells, this selective loss of H2A and H2B acetylation occurs independently of changes in H3K4 and H3K9 histone methylation patterns, indicating that changes in histone acetylation but not methylation are responsible for the induction of EMT in TS cells. In addition to the examination of histone acetylation patterns, genome-wide H2BK5Ac ChIP-seq studies coupled with gene expression analysis revealed that genes both significantly downregulated and hypoacetylated in TS
KI4 cells clustered into pathways critical for maintenance of the actin cytoskeleton, focal adhesions and the extracellular matrix.
7 These results highlight the importance of H2B acetylation for maintenance of the trophoblast epithelial phenotype. To our knowledge, this is the first analysis directly connecting selective histone acetylation marks to the transcriptional activation of the trophoblast EMT program. We hypothesize that loss of H2A and H2B acetylation is an epigenetic signature critical to the induction of EMT metastability. Although this intermediate EMT phenotype is usually transient in nature, TS
KI4 and TS
shCBP cells are uniquely paused in the metastable EMT state due to perturbation of the upstream modifier CBP and subsequent incomplete modulation of the epigenetic landscape.