Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.BS-Seq | epigenetic profiling | DNA methylation | gene body methylation | UHRF1C ytosine DNA methylation is an epigenetic mark important in many gene regulatory systems, including genomic imprinting, X-chromosome inactivation, silencing of transposons and other repetitive DNA sequences, as well as expression of endogenous genes. Methylation is conserved in most major eukaryotic groups, including many plants, animals, and fungi, although it has been lost from certain model organisms such as the budding yeast Saccharomyces cerevisiae and nematode worm Caenorhabditis elegans (1-3). DNA methylation can be categorized into three types according to the sequence context of the cytosines, namely CG, CHG, and CHH (H = A, C, or T). CG methylation is maintained by conserved Dnmt1 DNA methyltransferase enzymes. CHH methylation, and, to some extent CHG methylation, is generally maintained by the activity of the conserved Dnmt3 methyltransferases, whereas high levels of CHG methylation seen in the model plant Arabidopsis are maintained by the plant-specific methyltransferase CMT3 (2, 3). Generally speaking, DNA methylation is thought to occur "globally" in vertebrates, with CG sites being heavily methylated genome-wide except for those in CpG islands, whereas invertebrates, plants, and fungi have "mosaic" methylation, characterized by interspersed methylated and unmethylated domains (4). These differences are an interesting starting point for studying divergence in methylation pathways and regulatory mechanisms; however, determining precise genomescale methylation patterns has been a challenge for complex genomes until the recent development of high-throughput sequencing technology. In this paper, we generated shotgun bisulfite sequencing data to profile DNA methylation in eight eukaryotic organisms. These organisms display wide variations in methylati...

LGR4/5 receptors and their cognate RSPO ligands potentiate Wnt/β-catenin signalling and promote proliferation and tissue homeostasis in epithelial stem cell compartments. In the liver, metabolic zonation requires a Wnt/β-catenin signalling gradient, but the instructive mechanism controlling its spatiotemporal regulation is not known. We have now identified the RSPO-LGR4/5-ZNRF3/RNF43 module as a master regulator of Wnt/β-catenin-mediated metabolic liver zonation. Liver-specific LGR4/5 loss of function (LOF) or RSPO blockade disrupted hepatic Wnt/β-catenin signalling and zonation. Conversely, pathway activation in ZNRF3/RNF43 LOF mice or with recombinant RSPO1 protein expanded the hepatic Wnt/β-catenin signalling gradient in a reversible and LGR4/5-dependent manner. Recombinant RSPO1 protein increased liver size and improved liver regeneration, whereas LGR4/5 LOF caused the opposite effects, resulting in hypoplastic livers. Furthermore, we show that LGR4(+) hepatocytes throughout the lobule contribute to liver homeostasis without zonal dominance. Taken together, our results indicate that the RSPO-LGR4/5-ZNRF3/RNF43 module controls metabolic liver zonation and is a hepatic growth/size rheostat during development, homeostasis and regeneration.

SUMMARY UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Here, we use transgenic zebrafish, cultured cells and human tumors to demonstrate that UHRF1 is an oncogene. UHRF1 overexpression in zebrafish hepatocytes destabilizes and delocalizes DNMT1, causes DNA hypomethylation and Tp53-mediated senescence. Hepatocellular carcinoma (HCC) emerges when senescence is bypassed. tp53 mutation both alleviates senescence and accelerates tumor onset. Human HCCs recapitulate this paradigm, as UHRF1 overexpression defines a subclass of aggressive HCCs characterized by genomic instability, TP53 mutation and abrogation of the TP53-mediated senescence program. We propose that UHRF1 overexpression is a mechanism underlying DNA hypomethylation in cancer cells and that senescence is a primary means of restricting tumorigenesis due to epigenetic disruption.

The MCM2-7 helicase complex is loaded on DNA replication origins during the G1 phase of the cell cycle to license the origins for replication in S phase. How the initiator primase-polymerase complex, DNA polymerase ␣ (pol ␣), is brought to the origins is still unclear. We show that And-1/Ctf4 (Chromosome transmission fidelity 4) interacts with Mcm10, which associates with MCM2-7, and with the p180 subunit of DNA pol ␣. And-1 is essential for DNA synthesis and the stability of p180 in mammalian cells. In Xenopus egg extracts And-1 is loaded on the chromatin after Mcm10, concurrently with DNA pol ␣, and is required for efficient DNA synthesis. Mcm10 is required for chromatin loading of And-1 and an antibody that disrupts the Mcm10-And-1 interaction interferes with the loading of And-1 and of pol ␣, inhibiting DNA synthesis. And-1/Ctf4 is therefore a new replication initiation factor that brings together the MCM2-7 helicase and the DNA pol ␣-primase complex, analogous to the linker between helicase and primase or helicase and polymerase that is seen in the bacterial replication machinery. The discovery also adds to the connection between replication initiation and sister chromatid cohesion.[Keywords: And-1/CTF4; DNA replication; genome stability; cell cycle; DNA polymerase] Supplemental material is available at http://www.genesdev.org.

In contrast to the deregulated hepatocellular division that is a feature of many hepatic diseases and malignancies, physiologic liver growth during embryonic development and after partial hepatectomy (PH) in adults is characterized by tightly controlled cell proliferation. We used forward genetic screening in zebrafish to test the hypothesis that a similar genetic program governs physiologic liver growth during hepatogenesis and regeneration after PH. We identified the uhrf1 gene, a cell cycle regulator and transcriptional activator of top2a expression, as required for hepatic outgrowth and embryonic survival. By developing a methodology to perform PH on adult zebrafish, we found that liver regeneration in uhrf1 ؉/؊ adult animals is impaired. uhrf1 transcript levels dramatically increase after PH in both mice, and zebrafish and top2a is not up-regulated in uhrf1 ؉/؊ livers after PH. This indicates that uhrf1 is required for physiologic liver growth in both embryos and adults and illustrates that zebrafish livers regenerate.hepatic outgrowth ͉ hepatogenesis ͉ partial hepatectomy T he liver's capacity to regenerate after acute injury allows for the full restoration of liver mass and function. In the most reliable model to study liver regeneration in rodents, Ϸ70% of the liver mass is removed with partial hepatectomy (PH), resulting in the reentry of the normally quiescent hepatocytes into the cell cycle (1). Within a week of this procedure, the presurgical liver mass is restored (2). Whereas pathologic liver growth is characterized by uncontrolled cell division, physiologic liver growth during PH-induced liver regeneration is a tightly regulated process. Hepatic outgrowth, the final stage of liver development during which the liver bud expands, is another example of physiologic liver growth. There is very little known regarding the process that controls hepatic outgrowth in the embryo, and with decades of research on liver regeneration, the genetic requirements of physiologic liver growth remains an active area of scientific inquiry.Studies with knockout mice have identified a few genes that are essential for both hepatic outgrowth and regeneration; of these, none are liver-specific. For example, a liver specific knockout of c-jun results in defective liver regeneration (3), whereas homozygous c-jun deletion results in embryonic lethality and hypoplastic livers (4, 5). Similar studies have shown that the hepatocyte growth factor/c-met (6-8), ␤-catenin (9), and TNF␣ (10-12) pathways also regulate physiologic liver growth in embryos and adults. Comparison of the gene expression profiles in regenerating and embryonic livers has identified a handful of genes that are coregulated during both processes (13, 14); however, the functional significance of these findings has not yet been addressed.Zebrafish present an excellent system for such genetic studies. The robust regenerative potential of adult zebrafish is well established (15), and PH-induced liver regeneration has been reported in trout (16), suggesting similar st...

Reactivation of resolved hepatitis B virus (HBV) infection has been reported in allogeneic hematopoetic stem cell transplantation (HSCT) recipients, but its epidemiology is not well characterized. We performed a retrospective assessment of the timing and risk factors of HBV reactivation among patients with resolved HBV infection undergoing allogeneic HSCT between January 2000 and March 2008. HBV reactivation was defined as development of positive hepatitis B surface antigen after transplant. Among the 61 patients with resolved HBV infection before transplant (hepatitis B core antibody-positive, hepatitis B surface antigen-negative), 12 (19.7%) developed HBV reactivation. The cumulative probability of HBV reactivation 1, 2, and 4 years after transplant was 9.0%, 21.7%, and 42.9%, respectively. In a time-dependent Cox model, the adjusted hazard ratio (HR) of HBV reactivation for patients with pretransplant hepatitis B surface antibody levels <10 milli-international units per milliliter (mIU/mL) was 4.56 (95% confidence interval [CI] 1.23-16.9) compared to those with levels > or =10 mIU/mL; the adjusted HR among patients who developed extensive chronic graft-versus-host disease (cGVHD) was 7.21 (95% CI 1.25-41.5) compared to those who did not. HBV reactivation is a common late complication among allogeneic HSCT recipients with pretransplant resolved infection. Screening for HBV reactivation should be considered for at-risk HSCT recipients. In this cohort, HBV reactivation often developed in patients with cGVHD. Liver biopsy was useful in those patients with both to delineate the contribution of each to liver dysfunction.

The Fontan procedure has undergone many modifications since first being performed on a patient with tricuspid valve atresia in 1968. It is now the procedure of choice for individuals born with single-ventricle physiology or for those in whom a biventricular repair is not feasible. Forty years of experience with the Fontan procedure have gradually revealed the shortfalls of such a circulatory arrangement. Sequelae related to the underlying congenital anomaly or to the altered physiology of passive, nonpulsatile flow through the pulmonary arterial bed can result in failure of the Fontan circulation over time. Liver abnormalities including abnormalities in the clotting cascade have been well documented in Fontan patients. The clinical significance of these findings, however, has remained poorly understood. As Fontan survivors have increased in age and number, we have begun to better recognize subclinical hepatic dysfunction and the contribution of liver disease to adverse outcomes in this population. The purpose of this review is to summarize the existing data pertaining to liver disease in the Fontan population and to identify some questions that have yet to be answered.

SYNOPSIS Ubiquitin-like protein, containing PHD and RING finger domains-1 (UHRF1) is required for cell cycle progression and epigenetic regulation. In this study, we show that depleting cancer cells of UHRF1 causes activation of the DNA damage response pathway, cell cycle arrest in G2/M and apoptosis dependent on caspase-8. The DNA damage response in cells depleted of UHRF1 is illustrated by: phosphorylation of histone H2AX on serine 139, phosphorylation of CHK2 on threonine 68, phosphorylation of CDC25 on serine 216 and phosphorylation of CDK1 on tyrosine 15. Moreover, we find that UHRF1 accumulates at sites of DNA damage suggesting that the cell cycle block in UHRF1 depleted cells is due to an important role in damage repair. The consequence of UHRF1 depletion is apoptosis: cells undergo activation of caspases 8 and 3 and depletion of caspase-8 prevents cell death induced by UHRF1 knock-down. Interestingly, the cell cycle block and apoptosis occurs in p53 containing and deficient cells. From these studies we conclude that UHRF1 links epigenetic regulation with DNA replication.