scholarly journals Mutant p63 affects epidermal cell identity through rewiring the enhancer landscape

2018 ◽  
Author(s):  
Jieqiong Qu ◽  
Sabine Tanis ◽  
Jos P.H. Smits ◽  
Evelyn N. Kouwenhoven ◽  
Martin Oti ◽  
...  

AbstractTranscription factor p63 is a key regulator of epidermal keratinocyte proliferation and differentiation. In humans mutations in p63 cause several developmental disorders with defects of ectoderm-derived structures including the epidermis. The underlying molecular mechanisms of these mutations however remain unclear. Here we characterized the transcriptome and epigenome from EEC syndrome patients carrying mutations in the p63 DNA-binding domain. The transcriptome of p63 mutant keratinocytes deviated from the normal epidermal cell identity. Epigenomic analyses showed that the deregulated gene expression in p63 mutant keratinocytes resulted from an altered enhancer landscape contributed by loss of p63-bound active enhancers and by unexpected gain of enhancers. The gained enhancers in mutant keratinocytes were frequently bound by deregulated transcription factors such as RUNX1. Reversing RUNX1 overexpression partially rescued deregulated gene expression as well as the enhancer distribution. Our findings support the pivotal role of p63 in controlling the enhancer landscape of epidermal keratinocytes and identify a novel mechanism whereby p63 DNA-binding mutations associated with EEC syndrome rewire the enhancer landscape and affect epidermal cell identity.

2021 ◽  
Vol 12 (5) ◽  
Author(s):  
Chenliang Gou ◽  
Wenkai Ni ◽  
Panpan Ma ◽  
Fengbo Zhao ◽  
Zhou Wang ◽  
...  

AbstractPsoriasis is a common chronic skin disease, characterized by abnormal interplay between hyperproliferative epidermal keratinocytes and self-reactive immune cells with not fully addressed molecular mechanism. N4BP1 (NEDD4-binding protein 1) is considered as an immune regulator for a long time but its physiological role is not determined yet. Here, we found that the expression of N4BP1 in skin was highest among all 54 tested tissues, and its expression was further upregulated in psoriatic skin. N4BP1-deficient mice exhibited normal grossly, but developed severe and prolonged IMQ-induced psoriasis-like disease comparing to controls. N4BP1 mainly expressed in keratinocytes and located on nucleus. Up- but not downregulated genes in N4BP1-deficient skin were specifically enriched in keratinocyte proliferation and differentiation. The proliferation of N4BP1-deficient primary keratinocytes was faster compared to that of controls. The upregulated genes upon ablation of N4BP1 were highly enriched in targets of AP-1 transcription factor. Knocking out N4BP1 resulted in upregulation of JunB and FosB, and conversely, overexpression of N4BP1 greatly reduced their expression. Furthermore, N4BP1 binds with JunB and FosB encoding mRNAs and greatly reduces their stability. In addition, with a high expression in neutrophils, N4BP1 limits survival of neutrophils in blood and infiltration of neutrophils in psoriatic skin by targeting CXCL1, CCL20, and S100A8. These findings demonstrate that N4BP1 controls the proper function of keratinocytes and neutrophils by negatively regulating JunB, FosB, and CXCL1, respectively, and that is critical for psoriasis prevention.


1999 ◽  
Vol 11 (2) ◽  
pp. 71-73
Author(s):  
J.P.H. Burbach ◽  
P. Cazorla ◽  
M.P. Smidt

Several psychiatric diseases are considered to be neuro-developmental disorders. Amongst these are schizophrenia and autism, in which genetic and environmental components have been indicated. In these disorders intrinsic molecular mechanisms of brain development may be deranged due to genetic predispositions, or modified by external influences. Brain development is a delicate process of well-tuned cellular proliferation and differentiation of multipotent neural progenitor cells driven by spatiotemporal cues. One of the fundamental mechanisms is the interaction between external signals, e.g. growth factors, and internal regulators, e.g. transcription factors. An important transmitter system involved in behavioural and affective functions relevant for psychiatric disorders is the mesencephalic dopamine (DA) system. The mesencephalic DA system is organized in two anatomically and functionally different systems. DA neurons in the ventral tegmental area project to the mesolimbic system and are mostly related to control of behaviour. It has been implicated in drug addiction and affective disorders like dipolar disorder and schizophrenia. The dopamine system of the substantia nigra (nigro-striatal pathway) is implicated in movement control. Degeneration of this system, as in Parkinson's disease, or altered function in tardive dyskinesia have highlighted its importance in human disease. Recent findings in molecular neurobiology have provided the first clues to molecular mechanisms involved in developing and mature DA neurons. These may have clinical implications in novel therapeutic strategies.


2010 ◽  
Vol 48 ◽  
pp. 187-200 ◽  
Author(s):  
Ryutaro Hirasawa ◽  
Robert Feil

In many epigenetic phenomena, covalent modifications on DNA and chromatin mediate somatically heritable patterns of gene expression. Genomic imprinting is a classical example of epigenetic regulation in mammals. To date, more than 100 imprinted genes have been identified in humans and mice. Many of these are involved in foetal growth and deve lopment, others control behaviour. Mono-allelic expression of imprinted genes depends on whether the gene is inherited from the mother or the father. This remarkable pattern of expression is controlled by specialized sequence elements called ICRs (imprinting control regions). ICRs are marked by DNA methylation on one of the two parental alleles. These allelic marks originate from either the maternal or the paternal germ line. Perturbation of the allelic DNA methylation at ICRs is causally involved in several human diseases, including the Beckwith–Wiedemann and Silver–Russell syndromes, associated with aberrant foetal growth. Perturbed imprinted gene expression is also implicated in the neuro-developmental disorders Prader–Willi syndrome and Angelman syndrome. Embryo culture and human-assisted reproduction procedures can increase the occurrence of imprinting-related disorders. Recent research shows that, besides DNA methylation, covalent histone modifications and non-histone proteins also contribute to imprinting regulation. The involvement of imprinting in specific human pathologies (and in cancer) emphasizes the need to further explore the underlying molecular mechanisms.


2019 ◽  
Author(s):  
Catarina S. Silva ◽  
Aditya Nayak ◽  
Xuelei Lai ◽  
Veronique Hugouvieux ◽  
Jae-Hoon Jung ◽  
...  

AbstractThe Evening Complex (EC), composed of the DNA-binding protein LUX ARRHYTHMO (LUX) and two additional proteins, EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and light entrainment and regulates important clock output genes such asPHYTOCHROME INTERACTING FACTOR 4(PIF4), a key transcription factor involved in temperature dependent plant growth. These properties make the EC an attractive target for altering plant development through targeted mutations to the complex. However, the molecular basis for EC function was not known. Here we show that binding of the EC requires all three proteins and that ELF3 decreases the ability of LUX to bind DNA whereas the presence of ELF4 restores interaction with DNA. To be able to manipulate this complex, we solved the structure of the DNA-binding domain of LUX bound to DNA. Using structure-based design, a LUX variant was constructed that showed decreasedin vitrobinding affinity but retained specificity for its cognate sequences. This designed LUX allele modulates hypocotyl elongation and flowering. These results demonstrate that modifying the DNA-binding affinity of LUX can be used to titrate the repressive activity of the entire EC, tuning growth and development in a predictable manner.Significance StatementCircadian gene expression oscillates over a 24 hr. period and regulates many genes critical for growth and development. In plants, the Evening Complex (EC), a three-protein repressive complex made up of LUX ARRYTHMO, EARLY FLOWERING 3 and EARLY FLOWERING 4, acts as a key component of the circadian clock and is a regulator of thermomorphogenic growth. However, the molecular mechanisms of complex formation and DNA-binding have not been identified. Here we determine the roles of each protein in the complex and present the structure of the LUX DNA-binding domain in complex with DNA. Based on these data, we used structure-based protein engineering to produce a version of the EC with alteredin vitroandin vivoactivity. These results demonstrate that the EC can be modified to alter plant growth and development at different temperatures in a predictable manner.


Author(s):  
Caojie Liu ◽  
Ning Kang ◽  
Yuchen Guo ◽  
Ping Gong

Background: Regulation of gene expression is critical for stem cell differentiation, tissue development, and human health maintenance. Recently, epigenetic modifications of histone and chromatin remodeling have been verified as key controllers of gene expression and human diseases.Objective: In this study, we review the role of chromodomain helicase DNA-binding (CHD) proteins in stem cell differentiation, cell fate decision, and several known human developmental disorders and cancers.Conclusion: CHD proteins play a crucial role in stem cell differentiation and human diseases.


2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Luca Fagnocchi ◽  
Stefania Mazzoleni ◽  
Alessio Zippo

Stem cells balance their self-renewal and differentiation potential by integrating environmental signals with the transcriptional regulatory network. The maintenance of cell identity and/or cell lineage commitment relies on the interplay of multiple factors including signaling pathways, transcription factors, and the epigenetic machinery. These regulatory modules are strongly interconnected and they influence the pattern of gene expression of stem cells, thus guiding their cellular fate. Embryonic stem cells (ESCs) represent an invaluable tool to study this interplay, being able to indefinitely self-renew and to differentiate towards all three embryonic germ layers in response to developmental cues. In this review, we highlight those mechanisms of signaling to chromatin, which regulate chromatin modifying enzymes, histone modifications, and nucleosome occupancy. In addition, we report the molecular mechanisms through which signaling pathways affect both the epigenetic and the transcriptional state of ESCs, thereby influencing their cell identity. We propose that the dynamic nature of oscillating signaling and the different regulatory network topologies through which those signals are encoded determine specific gene expression programs, leading to the fluctuation of ESCs among multiple pluripotent states or to the establishment of the necessary conditions to exit pluripotency.


2021 ◽  
Vol 22 (22) ◽  
pp. 12426
Author(s):  
Christelle Gross ◽  
Gaëtan Le-Bel ◽  
Pascale Desjardins ◽  
Manel Benhassine ◽  
Lucie Germain ◽  
...  

In order to reduce the need for donor corneas, understanding of corneal wound healing and development of an entirely tissue-engineered human cornea (hTECs) is of prime importance. In this study, we exploited the hTEC to determine how deep wound healing affects the transcriptional pattern of corneal epithelial cells through microarray analyses. We demonstrated that the gene encoding clusterin (CLU) has its expression dramatically repressed during closure of hTEC wounds. Western blot analyses confirmed a strong reduction in the expression of the clusterin isoforms after corneal damage and suggest that repression of CLU gene expression might be a prerequisite to hTEC wound closure. Transfection with segments from the human CLU gene promoter revealed the presence of three regulatory regions: a basal promoter and two more distal negative regulatory regions. The basal promoter bears DNA binding sites for very potent transcription factors (TFs): Activator Protein-1 (AP-1) and Specificity protein-1 and 3 (Sp1/Sp3). By exploiting electrophoretic mobility shift assays (EMSA), we demonstrated that AP-1 and Sp1/Sp3 have their DNA binding site overlapping with one another in the basal promoter of the CLU gene in hCECs. Interestingly, expression of both these TFs is reduced (at the protein level) during hTEC wound healing, thereby contributing to the extinction of CLU gene expression during that process. The results of this study contribute to a better understanding of the molecular mechanisms accounting for the repression of CLU gene expression during corneal wound healing.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1171-1171
Author(s):  
Zhi-Jian Liu ◽  
Ioana Nitulescu ◽  
Henry Pelish ◽  
Matthew Shair ◽  
Martha Sola-Visner

Abstract Several recent studies have demonstrated substantial biological differences between cord blood (CB)- and adult peripheral blood (PB)-derived megakaryocytes (MKs). Specifically, neonatal (CB) progenitors proliferate at a much higher rate than adult (PB) progenitors, and generate 10-fold more MKs per progenitor when cultured with thrombopoietin (Tpo). The highly proliferative neonatal MKs undergo cytoplasmic maturation without polyploidization, which ultimately generates large numbers of small, low ploidy, but fully mature MKs. Adult MKs, in contrast, undergo successive rounds of endomitosis to reach much higher ploidy levels, and maturation is coupled with polyploidization, so that MKs with the highest ploidy levels are also the most mature. The molecular mechanisms underlying these developmental differences are just beginning to be elucidated. Here, we investigated the effects of cortistatin A (CA), a highly specific small molecule inhibitor of cyclin-dependent kinase 8 (CDK8) and its paralog CDK19, on megakaryopoiesis. CDK8 and CDK19, together with CCNC (Cyclin C), MED12/MED12L and MED13/MED13L, form "CDK modules" which can associate with Mediator, a 26-subunit complex that acts as a bridge between transcription factors and the transcriptional machinery to coordinate gene expression. The Mediator complex has been implicated in developmental disorders and cancer. CB-derived MK progenitors treated with CA from day 7 to day 14 of culture exhibited a dose-dependent reduction in proliferation (6.2±1.7 vs. 24.9±2.2 fold expansion in treated vs. control cultures; p=0.003), accompanied by an increase in ploidy levels to those comparable to adult PB-derived MKs (34±6% vs. 8.9±0.9% MKs with ploidy ≥8N in treated vs. control cultures; p=0.014). MK maturation, evaluated by CD42b surface expression level, also increased with advancing ploidy in CA-treated MKs, in a manner similar to that observed in adult MKs, and CA-treated mature MKs were capable of pro-platelet formation in vitro. These changes were not observed when undifferentiated CB-derived CD34+ or CD41-negative cells were treated, indicating that the effect was specific to committed MK progenitors. CA treatment induced the expected decrease in STAT-1 phosphorylation at Serine 727, a specific site of CDK8-mediated phosphorylation, confirming effective CDK8 inhibition in treated MKs. Next, we used microarray to evaluate the gene expression profile of CB-derived MKs following CA treatment for 4 and 8 hours vs. untreated cells. These studies revealed significant CA-induced changes in the MK gene expression profile. By Gene Set Enrichment Analysis (GSEA), CA treatment significantly upregulated genes that were downregulated in CB- vs. PB-derived MKs. Furthermore, genes upregulated by CA in CB-derived MKs were also upregulated in the megakaryoblastic cell line SET2 (Pelish, Liau et al., Nature, in press), suggesting that the gene expression program affected in SET2 cells is likely the same one affected in neonatal MKs. At the protein level, we observed time- and dose-dependent increases in RUNX-1 in CA-treated vs. control MKs. In summary, this study demonstrated that treatment with CA induced a phenotypic switch from neonatal to adult-like megakaryopoiesis, accompanied by changes in the MK gene expression profile. These findings indicate a novel role for Mediator kinases in the regulation of megakaryopoiesis, and potentially on the developmental differences between neonatal and adult MKs. These studies open the door to a better understanding of and to potential novel therapies for a number of developmental stage-specific megakaryocyte and platelet disorders, which exclusively or more severely affect neonates and infants, including the thrombocytopenia/absent radius (TAR) syndrome and the transient myeloproliferative disorder associated with trisomy 21 and GATA1s mutations. Disclosures No relevant conflicts of interest to declare.


2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Benjamin Frempah ◽  
Lerin R. Luckett-Chastain ◽  
Randle M. Gallucci

Irritant Contact Dermatitis (ICD) is characterized by epidermal hyperplasia and inflammatory cytokine release. IL-6 has been shown to be involved in the pathogenesis of ICD; however, the involvement of the IL-22/IL-22Rα axis and its relation to IL-6 in the inflammatory response following irritant exposure are unknown. Using a chemical model of ICD, it was observed that mice with a keratinocyte-specific knockout of IL-6Rα (IL-6RαΔker) presented with increased inflammation and IL-22Rα and IL-22 protein expression relative to WT following irritant exposure, indicating that IL-6Rα deficiency in epidermal keratinocytes leads to the upregulation of IL-22Rα and its ligand during ICD. Furthermore, it was shown that IL-6 negatively regulates the expression of IL-22Rα on epidermal keratinocytes. This effect is functional as the effects of IL-22 on keratinocyte proliferation and differentiation were markedly reduced when keratinocytes were pretreated with IL-6 prior to IL-22 treatment. These results show that IL-6 modulates the IL-22/IL-22Rα axis in the skin and suggest that this occurrence may be associated with the increased epidermal hyperplasia and exacerbated inflammatory response observed in IL-6RαΔker mice during ICD.


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