The ability of cells to respond to external stimuli is one of the characteristics of life as we know it. Multicellular organisms have developed a huge machinery that interprets the cellular environment and instigates an appropriate cellular response by changing gene expression, metabolism, proliferation state and motility. Decades of research have studied the pathways transmitting the various signals within the cell. However, whilst we know most of the players, we know surprisingly little about the mechanistic details of how extrinsic signals are interpreted and integrated within the genome. In this article we revisit the long-standing debate of whether factors regulating cellular growth (cytokines) act in an instructive or permissive fashion on cell fate decisions. We touch upon this topic by highlighting the paradigm of AP-1 as one of the most important signaling-responsive transcription factor family and summarize our work and that of others to explain what is known about cytokine responsive cis-regulatory elements driving differential gene expression. We propose that cytokines and, by extension, multiple types of external signals are the main drivers of cell differentiation and act via inducible transcription factors that transmit signaling processes to the genome and are essential for changing gene expression to drive transitions between gene regulatory networks. Importantly, inducible transcription factors cooperate with cell type specific factors within a pre-existing chromatin landscape and integrate multiple signaling pathways at specific enhancer elements, to both maintain and alter cellular identities. We also propose that signaling processes and signaling responsive transcription factors are at the heart of tumor development.
The covalent modification of specific DNA nucleotides by addition of a methyl group, termed DNA methylation, was observed in bacteria in 1925 and in mammals in 1948. Yet, the function of this modification was uncertain for many years, particularly its roles in mammalian cells. During the past five decades, work from Howard Cedar and his lab has provided fundamental and groundbreaking insight into the role DNA methylation plays in regulating gene expression in health and disease. Using simple yet elegant experiments, Cedar and his team provided unequivocal evidence for the direct role of DNA methylation in transcription regulation, and demonstrated that DNA methylation serves as a stable heritable epigenetic mark. Building on these foundational discoveries, Howard Cedar and his team have further illuminated the critical role of DNA methylation in organismal development and cellular function, as well as the contribution of altered DNA methylation to cancer. Further, Cedar and his lab also demonstrated that the developmentally regulated removal of DNA methylation is pre-programmed in the genome via sequence motifs that recruit trans-acting factors at specific developmental phases. Howard Cedar's pioneering scientific contributions have resulted in paradigm shifts in the study of transcription as well as DNA replication and set up the groundwork for fields of research that continue to thrive and expand into areas such as diagnostics, modeling of aging and targeted treatments.
Aging is associated with a decline in visual function and increased prevalence of ocular disease, correlating with changes in the transcriptome and epigenome of cells in the eye. Here, we sought to identify the transcriptional mechanisms that are necessary to maintain photoreceptor viability and function during aging. To do this, we performed a targeted photoreceptor-specific RNAi screen in Drosophila to identify transcriptional regulators whose knockdown results in premature, age-dependent retinal degeneration. From an initial set of 155 RNAi lines each targeting a unique gene and spanning a diverse set of transcription factors, chromatin remodelers, and histone modifiers, we identified 18 high-confidence target genes whose decreased expression in adult photoreceptors leads to premature and progressive retinal degeneration. These 18 target genes were enriched for factors involved in the regulation of transcription initiation, pausing, and elongation, suggesting that these processes are essential for maintaining the health of aging photoreceptors. To identify the genes regulated by these factors, we profiled the photoreceptor transcriptome in a subset of lines. Strikingly, two of the 18 target genes, Spt5 and domino, show similar changes in gene expression to those observed in photoreceptors with advanced age. Together, our data suggest that dysregulation of factors involved in transcription initiation and elongation plays a key role in shaping the transcriptome of aging photoreceptors. Further, our findings indicate that the age-dependent changes in gene expression not only correlate but might also contribute to an increased risk of retinal degeneration.
The crosstalk between metabolism and epigenetics is an emerging field that is gaining importance in different areas such as cancer and aging, where changes in metabolism significantly impacts the cellular epigenome, in turn dictating changes in chromatin as an adaptive mechanism to bring back metabolic homeostasis. A key metabolic pathway influencing an organism's epigenetic state is one-carbon metabolism (OCM), which includes the folate and methionine cycles. Together, these cycles generate S-adenosylmethionine (SAM), the universal methyl donor essential for DNA and histone methylation. SAM serves as the sole methyl group donor for DNA and histone methyltransferases, making it a crucial metabolite for chromatin modifications. In this review, we will discuss how SAM and its byproduct, S-adenosylhomocysteine (SAH), along with the enzymes and cofactors involved in OCM, may function in the different cellular compartments, particularly in the nucleus, to directly regulate the epigenome in aging and cancer.
Circadian rhythms play an essential role in the regulation of intestinal absorption and barrier function. Tight junctions, including claudins, are fundamental components of the intestinal epithelial barrier. However, the regulatory mechanisms governing their diurnal expression remain poorly understood. Furthermore, the impact of circadian rhythms on intestinal permeability through claudin modulation has yet to be fully explored. Here we investigated the expression and the diurnal rhythms of claudin transcripts in the intestinal epithelium. We identified histone deacetylase 3 (HDAC3) as an epigenetic regulator that represses claudin expression and drives the diurnal rhythms via histone deacetylation. Loss of HDAC3 leads to increased intestinal permeability and dampened its diurnal rhythm. We further revealed that HDAC3 affects the basolateral localization of claudin-3. Together, our findings give insights into epigenetic modification in regulating tight junction and its diurnal rhythms, providing targets for therapeutic mediations in gastrointestinal disorders.
The attachment of mono-ubiquitin to histones as a post-translational modification plays important roles in regulating chromatin structure and function. Like other epigenetic modifications, the site of ubiquitin attachment is critically important in determining its functional outcome. Depending on the type of histone and the specific lysine residue that is modified, ubiquitination acts in diverse pathways including DNA damage repair, transcription elongation, and transcription repression. Specific reader, writer and eraser activities have evolved to distinguish nucleosomes by ubiquitination of different sites. To facilitate biochemical studies of ubiquitinated nucleosomes, we have developed an efficient strategy to chemically ligate intact ubiquitin and histone proteins at specific sites to generate near-native ubiquitin-histone conjugates. Because these chemically-ligated ubiquitin conjugates are hydrolysable, they enabled us to characterize in vitro the specificities of several histone deubiquitinases. To gain insight into the mechanisms that contribute to the specificities of these deubiquitinases, we used a free Ub sensor-based real-time assay to determine their Michaelis-Menten kinetics. Our results confirmed previously reported specificities of BAP1 and USP22, but also revealed specificities of other histone deubiquitinases that have been less well defined in the literature.
Interactions between epigenetics and metabolites play critical roles in regulating the pluripotency and differentiation of embryonic stem cells. Proper glucose metabolism and DNA methylation are essential for orchestrating accurate lineage specification and the normal functions of embryonic stem cells. However, the impact of Ten-eleven Translocation (TET)-mediated DNA methylation modifications on the metabolism of mouse embryonic stem cells (mESCs) remains less well defined. In this study, we investigated the consequences of Tet triple knockout (Tet-TKO) in mESCs and observed notable alterations in glucose metabolism. These changes were marked by enhanced glucose uptake and glycolysis, likely owing to the upregulation of genes critical for glucose metabolism. Furthermore, Tet-TKO mESCs exhibited defects in glucose-dependent differentiation, suggesting that cells with epigenetic defects might display metabolic vulnerability when exposed to external nutritional cues. Collectively, our findings establish the pivotal role of the TET family of dioxygenases in maintaining proper glucose metabolism and safeguarding stem cell lineage specification, thus enhancing our understanding of the intricate interplay between epigenetic modifications and cellular metabolism in stem cells.
The development of multicellular organisms occurs through a series of cell state transitions controlled by gene regulatory networks. Central to these networks are transcription factors (TFs) which bind enhancers and activate the expression of other genes, some of which are also TFs. Gene regulatory networks (GRN) connect TFs and enhancers in a nonlinear circuit capable of producing complex behavior such as bifurcations between stable cell states. Our dynamic network modelling of the Embryonic Stem Cell (ESC) to Definitive Endoderm (DE) transition requires an as yet unknown negative feedback mechanism for stability. Here, we show that cell state specific microRNAs (miRNAs) can provide this negative feedback by inactivating other cell lineage determining TFs (ESC or DE) during the transition. Our model provides a mechanism to maintain stable cell states without requiring a large set of cell-type-specific repressive TFs, of which there are fewer known examples than activators. In support of this model, we use computational models and analyze gene and miRNA expression and chromatin accessibility data from human cell lines to detect enhancers activating the miRNAs consistent with our network model. Our analysis highlights the interplay between TFs and miRNAs during ESC to DE transition and proposes a novel model for gene regulation.
Early-onset preeclampsia (EOPE) is a severe maternal hypertensive disorder of pregnancy, where placental dysfunction is a component of the pathophysiology. Previously, we developed the eoPRED tool, which is a DNA methylation (DNAme)-based method that estimates the likelihood that a placenta came from a pregnancy complicated by EOPE. We hypothesize that this score may reflect maternal vascular malperfusion (MVM), which is the most common placental pathology observed in early-onset preeclampsia (EOPE), but is also associated with preterm birth and fetal growth restriction. To test this we evaluated whether eoPRED score is associated with the severity of MVM pathology in placentas from both preeclamptic and non-preeclamptic pregnancies. We utilized 493 placentas with both Infinium EPICv1.0 DNA methylation data and histopathologic characterization by a placental pathologist. We evaluated associations between eoPRED score and four major classes of placental pathology: maternal vascular malperfusion (MVM), fetal vascular malperfusion (FVM), chronic inflammation (CI), and acute inflammation (AI). eoPRED score was higher in placentas from pregnancies with EOPE (n = 7) than controls without preeclampsia (n = 402, p < 0.001). Independent of EOPE, eoPRED correlated with the grade of MVM (R = 0.34, p < 0.01), but was not associated with any other pathology class. eoPRED score can not only be used to identify cases of likely EOPE but is also associated with placental maternal vascular dysfunction in the absence of preeclampsia. This score may thus be useful in placental DNAme datasets lacking pathology information to identify associations between exposures/and or birth outcomes with placental dysfunction.
Transcription is one of the central dogmas of life. Most genes in eukaryotes are transcribed by RNA polymerase II (Pol II). For Pol II to transcribe along the gene body, it must overcome nucleosomes, which are barriers for Pol II. It is still a mystery how Pol II ejects nucleosomes during transcription elongation. I hypothesize that a group of chromatin remodelers (SWI/SNF, RSC, SWR1, INO80) carry a group of histone acetyltransferases (NuA4, Spt-Ada-Gcn-acetyltransferase, NuA3) to deposit acetyl-groups on histone tails to generate pan-acetylated nucleosomes or fragile nucleosomes along gene bodies for Pol II to transcribe. Specifically, for the first round of transcription, the RSC complex works with NuA4 to acetylate histone tails of H2A and H4; the SWI/SNF complex carries SAGA to add acetyl-groups to histone tails of H2B and H3. For the second and subsequent rounds, SWR1 pairs with a piccolo NuA4 to acetylate the histone tails of H2A and H4 of newly inserted nucleosomes, while INO80 pairs with NuA3 to acetylate the histone tails of H2B and H3 within newly inserted nucleosomes along the gene body. After the mission is accomplished, ISW1b couples with Rpd3s to remove acetyl groups on H2A and H4, while CHD1 carries HDA1 along the gene body to remove acetyl groups on H2B and H3.