Active canonical Wnt signaling results in recruitment of β‐catenin to DNA by TCF/LEF family members, leading to transcriptional activation of TCF target genes. However, additional transcription ...factors have been suggested to recruit β‐catenin and tether it to DNA. Here, we describe the genome‐wide pattern of β‐catenin DNA binding in murine intestinal epithelium, Wnt‐responsive colorectal cancer (CRC) cells and HEK293 embryonic kidney cells. We identify two classes of β‐catenin binding sites. The first class represents the majority of the DNA‐bound β‐catenin and co‐localizes with TCF4, the prominent TCF/LEF family member in these cells. The second class consists of β‐catenin binding sites that co‐localize with a minimal amount of TCF4. The latter consists of lower affinity β‐catenin binding events, does not drive transcription and often does not contain a consensus TCF binding motif. Surprisingly, a dominant‐negative form of TCF4 abrogates the β‐catenin/DNA interaction of both classes of binding sites, implying that the second class comprises low affinity TCF‐DNA complexes. Our results indicate that β‐catenin is tethered to chromatin overwhelmingly through the TCF/LEF transcription factors in these three systems.
Synopsis
Integrated genome‐wide ChIP‐seq data in multiple cell types reveals that Tcf4 globally determines Wnt/beta‐catenin transcriptional programs.
β‐catenin‐bound elements can be divided in two classes according to TCF4 co‐occupancy.
However, all β‐catenin was displaced by a dominant negative form of TCF4.
These data show that β‐catenin recruitment is overwhelmingly mediated by TCF/LEF.
Integrated genome‐wide ChIP‐seq data in multiple cell types reveals that Tcf4 globally determines Wnt/beta‐catenin transcriptional programs.
The Wnt signaling pathway controls stem cell identity in the intestinal epithelium and in many other adult organs. The transcription factor Ascl2 (a Wnt target gene) is a master regulator of ...intestinal stem cell identity. It is unclear how the continuous Wnt gradient along the crypt axis is translated into discrete expression of Ascl2 and discrete specification of stem cells at crypt bottoms. We show that (1) Ascl2 is regulated in a direct autoactivatory loop, leading to a distinct on/off expression pattern, and (2) Wnt/R-spondin can activate this regulatory loop. This mechanism interprets the Wnt levels in the intestinal crypt and translates the continuous Wnt signal into a discrete Ascl2 “on” or “off” decision. In turn, Ascl2, together with β-catenin/Tcf, activates the genes fundamental to the stem cell state. In this manner, Ascl2 forms a transcriptional switch that is both Wnt responsive and Wnt dependent to define stem cell identity.
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•Wnt and Ascl2 activate a gene signature fundamental to the intestinal stem cell state•β-catenin/Tcf4 and Ascl2 co-occupy DNA and synergistically activate transcription•Ascl2 forms an autoactivating loop that leads to an on/off expression pattern•This loop translates the Wnt gradient into a discrete transcriptional decision
The Wnt signaling pathway controls stem cell identity in the intestinal epithelium, but it has remained unclear how the continuous Wnt gradient is translated into discrete cell type specification. Schuijers et al. show that the transcription factor Ascl2 forms a bimodal switch that interprets Wnt levels and specifies stem cells.
Abstract SMYD3 is a member of the SET and MYND-domain family of methyl-transferases, the increased expression of which correlates with poor prognosis in various types of cancer. In liver and colon ...tumors, SMYD3 is localized in the nucleus, where it interacts with RNA Pol II and H3K4me3 and functions as a selective transcriptional amplifier of oncogenes and genes that control cell proliferation and metastatic spread. Smyd3 expression has a high discriminative power for the characterization of liver tumors and positively correlates with poor prognosis. In lung and pancreatic cancer, SMYD3 acts in the cytoplasm, potentiating oncogenic Ras/ERK signaling through the methylation of the MAP3K2 kinase and the subsequent release from its inhibitor. A clinico-pathological analysis of lung cancer patients uncovers prognostic significance of SMYD3 only for first progression survival. However, stratification of patients according to their smoking history significantly expands the prognostic value of SMYD3 to overall survival and other features, suggesting that smoking-related effects saturate the clinical analysis and mask the function of SMYD3 as an oncogenic potentiator.
Innate T cells, including invariant natural killer T (iNKT) and mucosal-associated innate T (MAIT) cells, are a heterogeneous T lymphocyte population with effector properties preprogrammed during ...their thymic differentiation. How this program is initiated is currently unclear. Here, we show that the transcription factor BCL-6 was transiently expressed in iNKT cells upon exit from positive selection and was required for their proper development beyond stage 0. Notably, development of MAIT cells was also impaired in the absence of Bcl6. BCL-6-deficient iNKT cells had reduced expression of genes that were associated with the innate T cell lineage, including Zbtb16, which encodes PLZF, and PLZF-targeted genes. BCL-6 contributed to a chromatin accessibility landscape that was permissive for the expression of development-related genes and inhibitory for genes associated with naive T cell programs. Our results revealed new functions for BCL-6 and illuminated how this transcription factor controls early iNKT cell development.
The small intestinal epithelium is the most rapidly self-renewing tissue of mammals. Proliferative cells are confined to crypts, while differentiated cell types predominantly occupy the villi. We ...recently demonstrated the existence of a long-lived pool of cycling stem cells defined by
Lgr5 expression and intermingled with post-mitotic Paneth cells at crypt bottoms. We have now determined a gene signature for these Lgr5 stem cells. One of the genes within this stem cell signature is the Wnt target
Achaete scute-like 2 (
Ascl2). Transgenic expression of the Ascl2 transcription factor throughout the intestinal epithelium induces crypt hyperplasia and ectopic crypts on villi. Induced deletion of the
Ascl2 gene in adult small intestine leads to disappearance of the Lgr5 stem cells within days. The combined results from these gain- and loss-of-function experiments imply that Ascl2 controls intestinal stem cell fate.
Most studies on TCF7L2 SNP variants in the pathogenesis of type 2 diabetes (T2D) focus on a role of the encoded transcription factor TCF4 in β cells. Here, a mouse genetics approach shows that ...removal of TCF4 from β cells does not affect their function, whereas manipulating TCF4 levels in the liver has major effects on metabolism. In Tcf7l2−/− mice, the immediate postnatal surge in liver metabolism does not occur. Consequently, pups die due to hypoglycemia. By combining chromatin immunoprecipitation with gene expression profiling, we identify a TCF4-controlled metabolic gene program that is acutely activated in the postnatal liver. In concordance, adult liver-specific Tcf7l2 knockout mice show reduced hepatic glucose production during fasting and display improved glucose homeostasis when maintained on high-fat diet. Furthermore, liver-specific TCF4 overexpression increases hepatic glucose production. These observations imply that TCF4 directly activates metabolic genes and that inhibition of Wnt signaling may be beneficial in metabolic disease.
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► Wnt/TCF4 regulates metabolic genes in postnatal and adult liver directly ► TCF4-dependend metabolic program is activated under situations of metabolic demand ► Among other metabolic processes, TCF4 regulates hepatic glucose production
SNPs in TCF7L2, encoding the Wnt effector TCF4, are the strongest genetic risk factors for type 2 diabetes, but surprisingly, the metabolic functions of this protein, as determined in mice, take place in the liver, not in the pancreas.
The molecular events that drive hepatitis B virus (HBV)-mediated transformation and tumorigenesis have remained largely unclear, due to the absence of a relevant primary model system. Here we propose ...the use of human liver organoids as a platform for modeling HBV infection and related tumorigenesis. We first describe a primary ex vivo HBV-infection model derived from healthy donor liver organoids after challenge with recombinant virus or HBV-infected patient serum. HBV-infected organoids produced covalently closed circular DNA (cccDNA) and HBV early antigen (HBeAg), expressed intracellular HBV RNA and proteins, and produced infectious HBV. This ex vivo HBV-infected primary differentiated hepatocyte organoid platform was amenable to drug screening for both anti-HBV activity and drug-induced toxicity. We also studied HBV replication in transgenically modified organoids; liver organoids exogenously overexpressing the HBV receptor sodium taurocholate co-transporting polypeptide (NTCP) after lentiviral transduction were not more susceptible to HBV, suggesting the necessity for additional host factors for efficient infection. We also generated transgenic organoids harboring integrated HBV, representing a long-term culture system also suitable for viral production and the study of HBV transcription. Finally, we generated HBV-infected patient-derived liver organoids from non-tumor cirrhotic tissue of explants from liver transplant patients. Interestingly, transcriptomic analysis of patient-derived liver organoids indicated the presence of an aberrant early cancer gene signature, which clustered with the hepatocellular carcinoma (HCC) cohort on The Cancer Genome Atlas Liver Hepatocellular Carcinoma dataset and away from healthy liver tissue, and may provide invaluable novel biomarkers for the development of HCC and surveillance in HBV-infected patients.
The WNT/β-catenin signaling pathway controls a plethora of biological processes throughout animal development and adult life. Because of its fundamental role during animal lifespan, the WNT pathway ...is subject to strict positive and negative multi-layered regulation, while its aberrant activity causes a wide range of pathologies, including cancer. At present, despite the inroads into the molecules involved in WNT-mediated transcriptional responses, the fine-tuning of WNT pathway activity and the totality of its target genes have not been fully elucidated. Over the past few years, long non-coding RNAs (lncRNAs), RNA transcripts longer that 200nt that do not code for proteins, have emerged as significant transcriptional regulators. Recent studies show that lncRNAs can modulate WNT pathway outcome by affecting gene expression through diversified mechanisms, from the transcriptional to post-translational level. In this review, we selectively discuss those lncRNA-mediated mechanisms we believe the most important to WNT pathway modulation.
Cross-regulatory cascades between hepatic transcription factors have been implicated in the determination of the hepatic phenotype. Analysis of recruitments to regulatory regions and the temporal and ...spatial expression pattern of the main hepatic regulators during liver development revealed a gradual increase in complexity of autoregulatory and cross-regulatory circuits. Within these circuits we identified a core group of six transcription factors, which regulate the expression of each other and the expression of other downstream hepatic regulators. Changes in the promoter occupancy patterns during development included new recruitments, release, and exchange of specific factors. We also identified promoter and developmental stage-specific dual regulatory functions of certain factors as an important feature of the network. Inactivation of HNF-4alpha in embryonic, but not in adult, liver resulted in the diminished expression of most hepatic factors, demonstrating that the stability of the network correlates with its complexity. The results illustrate the remarkable flexibility of a self-sustaining transcription factor network, built up by complex dominant and redundant regulatory motifs in developing hepatocytes.
We analyzed the order of recruitment of factors to the HNF-4α regulatory regions upon the initial activation of the gene during enterocyte differentiation. An initially independent assembly of ...regulatory complexes at the proximal promoter and the upstream enhancer regions was followed by the tracking of the entire DNA-protein complex formed on the enhancer along the intervening DNA until it encountered the proximal promoter. This movement correlated with a unidirectional spreading of histone hyperacetylation. Transcription initiation coincided with the formation of a stable enhancer-promoter complex and remodeling of the nucleosome situated at the transcription start site. The results provide experimental evidence for the involvement of a dynamic process culminating in enhancer-promoter communication during long-distance gene activation.
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