Epigenetic Control Mechanisms In Somatic Cells Mediated By Dna Methyltransferase 1

DNA methylation regulates gene expression through a complex network of protein/protein and protein/DNA interactions in chromatin. The maintenance methylase, DNA methyltransferase 1 (DNMT1), is a prominent enzyme in the process that is linked to DNA replication and drives the heritable nature of epigenetic modifications in somatic cells. The mechanistic details that explain how DNMT1 catalytic action is directed in a chromatin setting are not well understood. We hypothesize that post translational modifications and a variety of protein-protein interactions processes are key regulatory elements that set the methylation of CpG elements essential for normal growth behavior in somatic cells. These fundamental processes can be disrupted by DNA damage leading to inappropriate gene silencing and loss of growth control in somatic cells. First, we show that DNMT1 is post-translationally modified by sumoylation and we have mapped these sumoylation sites by defined mutations. Sumoylated DNMT1 is catalytically active on genomic DNA in vivo and substantially increases the enzymatic activity of DNMT1 both in vitro and in chromatin. These data establish that sumoylation modulates the endogenous activity of a prominent epigenetic maintenance pathway in cells. Second, we investigated novel mechanisms whereby somatic cells can erase then reset DNA methylation events in somatic cells. In this study, the relationship between DNA damage and gene silencing was explored. To this end, we generated a HeLa cell line containing a specialized GFP reporter cassette (DRGFP) containing two mutated GFP genes and a unique ISceI restriction endonuclease site. These cells do not express GFP. A unique double strand break is then delivered by transfecting in the gene for I-SceI. About 4% of the cells produced a functional GFP by gene conversion and homologous recombination (HR); however roughly half iv of the GFP recombinants expressed the gene poorly and this was attributed to gene silencing. Silencing of the GFP expressing cell clones was due to DNA methylation and could be reversed using a drug that inhibits global methylation (5-aza-2\u27-deoxycytidine). Approximately half of the repaired genes were heavily methylated, and half were hypomethylated. That is, a key intermediate methylation state after HR repair is hemimethylated DNA, defined as methylation limited to one strand. Evidence is given that DNMT1 is acting as a de novo methylase at the HR repair patches in cells. Moreover, the DNA damage inducible protein, GADD45, interacts specifically with the catalytic domain of DNMT1 and GADD45 binds with extremely high affinity to hemimethylated DNA sites. Thus, GADD45 is a key regulatory element in silencing of HR repaired DNA segments and appears to inhibit the activity of DNMT1. Consistent with these results, we found that GADD45 increased the expression of recombinant GFP following HR repair, further suggesting its role in orchestrating strand specific DNA methylation by DNMT1. Since these experiments were performed in live cells, there is strong physiological relevance. We propose that DS DNA damage and the resulting HR process involves precise, strand selected DNA methylation mediated by the prominent methylase enzyme, DNMT1. Moreover, DS DNA break repair through HR and gene conversion, may potentially erase and reset DNA methylation patterns and therefore alter the expression of repaired genes. The overall process is tightly regulated by the DNA damage inducible protein GADD45, which may coordinate strand specific methylation by recruiting DNMT1 to HR repair templates. The ability of GADD45 to modulate DNMT1 catalytic activity may explain its role as a passive mediator of demethylation that has been reported by other groups. The overall process of silencing post DNA repair is a strong evolutionary force that may predispose cells to malignant transformatio

GADD45 alpha inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair

In this work, we examine regulation of DNA methyltransferase 1 (DNMT1) by the DNA damage inducible protein, GADD45 alpha. We used a system to induce homologous recombination (HR) at a unique double-strand DNA break in a GFP reporter in mammalian cells. After HR, the repaired DNA is hypermethylated in recombinant clones showing low GFP expression (HR-L expressor class), while in high expressor recombinants (HR-H clones) previous methylation patterns are erased. GADD45 alpha, which is transiently induced by double-strand breaks, binds to chromatin undergoing HR repair. Ectopic overexpression of GADD45 alpha during repair increases the HR-H fraction of cells (hypomethylated repaired DNA), without altering the recombination frequency. Conversely, silencing of GADD45 alpha increases methylation of the recombined segment and amplifies the HR-L expressor (hypermethylated) population. GADD45 alpha specifically interacts with the catalytic site of DNMT1 and inhibits methylation activity in vitro. We propose that double-strand DNA damage and the resulting HR process involves precise, strand selected DNA methylation by DNMT1 that is regulated by GADD45 alpha. Since GADD45 alpha binds with high avidity to hemimethylated DNA intermediates, it may also provide a barrier to spreading of methylation during or after HR repair

An efficient iterative CBCT reconstruction approach using gradient projection sparse reconstruction algorithm

The purpose of this study is to develop a fast and convergence proofed CBCT reconstruction framework based on the compressed sensing theory which not only lowers the imaging dose but also is computationally practicable in the busy clinic. We simplified the original mathematical formulation of gradient projection for sparse reconstruction (GPSR) to minimize the number of forward and backward projections for line search processes at each iteration. GPSR based algorithms generally showed improved image quality over the FDK algorithm especially when only a small number of projection data were available. When there were only 40 projections from 360 degree fan beam geometry, the quality of GPSR based algorithms surpassed FDK algorithm within 10 iterations in terms of the mean squared relative error. Our proposed GPSR algorithm converged as fast as the conventional GPSR with a reasonably low computational complexity. The outcomes demonstrate that the proposed GPSR algorithm is attractive for use in real time applications such as on-line IGRT

NUMERICAL SIMULATIONS OF ADDED RESISTANCE IN REGULAR HEAD WAVES ON A CONTAINER SHIP

Although shipping was not included in the final text of the Paris Agreement in 2015, IMO (International Maritime Organization) adopted the EEDI (Energy Efficiency Design Index) and the EEOI (Energy Efficiency Operational Indicator) to control climate change and also to reduce gas emission from ships. Accurate prediction of added resistance in waves is essential to evaluate the minimum fuel consumption of a ship in a real sea state. In this paper, the added resistance and motions of a KCS (KRISO Container Ship) with rudder were calculated using a commercial CFD program, STAR-CCM+. Wave forcing was used to generate the waves in the numerical domain, in which no extra wave generation and damping zones were produced. DFBI (Dynamic Fluid Body Interaction) was used for the motions of the KCS with rudder. In this study, five (5) regular head waves from a short wavelength to a long wavelength based on the LPP were considered. Finally, added resistance and the heave and pitch motions of the simulation were compared with experimental data. Simulation and experimental data were in qualitatively and quantitatively good agreement

The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules

Molecular mechanisms by which long noncoding RNA (lncRNA) molecules may influence cancerous condition are poorly understood. The aberrant expression of SPRIGHTLY lncRNA, encoded within the drosophila gene homolog Sprouty-4 intron, is correlated with a variety of cancers, including human melanomas. We demonstrate by SHAPE-seq and dChIRP that SPRIGHTLY RNA secondary structure has a core pseudoknotted domain. This lncRNA interacts with the intronic regions of six pre-mRNAs: SOX5, SMYD3, SND1, MEOX2, DCTN6, and RASAL2, all of which have cancer-related functions. Hemizygous knockout of SPRIGHTLY by CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 in melanoma cells significantly decreases SPRIGHTLY lncRNA levels, simultaneously decreases the levels of its interacting pre-mRNA molecules, and decreases anchorage-independent growth rate of cells and the rate of in vivo tumor growth in mouse xenografts. These results provide the first demonstration of an lncRNA’s three-dimensional coordinating role in facilitating cancer-related gene expression in human melanomas

DNA Damage, Homology-Directed Repair, and DNA Methylation

To explore the link between DNA damage and gene silencing, we induced a DNA double-strand break in the genome of Hela or mouse embryonic stem (ES) cells using I-SceI restriction endonuclease. The I-SceI site lies within one copy of two inactivated tandem repeated green fluorescent protein (GFP) genes (DR-GFP). A total of 2%–4% of the cells generated a functional GFP by homology-directed repair (HR) and gene conversion. However, ~50% of these recombinants expressed GFP poorly. Silencing was rapid and associated with HR and DNA methylation of the recombinant gene, since it was prevented in Hela cells by 5-aza-2′-deoxycytidine. ES cells deficient in DNA methyl transferase 1 yielded as many recombinants as wild-type cells, but most of these recombinants expressed GFP robustly. Half of the HR DNA molecules were de novo methylated, principally downstream to the double-strand break, and half were undermethylated relative to the uncut DNA. Methylation of the repaired gene was independent of the methylation status of the converting template. The methylation pattern of recombinant molecules derived from pools of cells carrying DR-GFP at different loci, or from an individual clone carrying DR-GFP at a single locus, was comparable. ClustalW analysis of the sequenced GFP molecules in Hela and ES cells distinguished recombinant and nonrecombinant DNA solely on the basis of their methylation profile and indicated that HR superimposed novel methylation profiles on top of the old patterns. Chromatin immunoprecipitation and RNA analysis revealed that DNA methyl transferase 1 was bound specifically to HR GFP DNA and that methylation of the repaired segment contributed to the silencing of GFP expression. Taken together, our data support a mechanistic link between HR and DNA methylation and suggest that DNA methylation in eukaryotes marks homologous recombined segments

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

Expression of the long noncoding RNA (lncRNA) SPRY4-IT1 is low in normal human melanocytes but high in melanoma cells. siRNA knockdown of SPRY4-IT1 blocks melanoma cell invasion and proliferation, and increases apoptosis. To investigate its function further, we affinity purified SPRY4-IT1 from melanoma cells and used mass spectrometry to identify the protein lipin 2, an enzyme that converts phosphatidate to diacylglycerol (DAG), as a major binding partner. SPRY4-IT1 knockdown increases the accumulation of lipin2 protein and upregulate the expression of diacylglycerol O-acyltransferase 2 (DGAT2) an enzyme involved in the conversion of DAG to triacylglycerol (TAG). When SPRY4-IT1 knockdown and control melanoma cells were subjected to shotgun lipidomics, an MS-based assay that permits the quantification of changes in the cellular lipid profile, we found that SPRY4-IT1 knockdown induced significant changes in a number of lipid species, including increased acyl carnitine, fatty acyl chains, and triacylglycerol (TAG). Together, these results suggest the possibility that SPRY4-IT1 knockdown may induce apoptosis via lipin 2-mediated alterations in lipid metabolism leading to cellular lipotoxicity

GADD45α inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair

In this work, we examine regulation of DNA methyltransferase 1 (DNMT1) by the DNA damage inducible protein, GADD45α. We used a system to induce homologous recombination (HR) at a unique double-strand DNA break in a GFP reporter in mammalian cells. After HR, the repaired DNA is hypermethylated in recombinant clones showing low GFP expression (HR-L expressor class), while in high expressor recombinants (HR-H clones) previous methylation patterns are erased. GADD45α, which is transiently induced by double-strand breaks, binds to chromatin undergoing HR repair. Ectopic overexpression of GADD45α during repair increases the HR-H fraction of cells (hypomethylated repaired DNA), without altering the recombination frequency. Conversely, silencing of GADD45α increases methylation of the recombined segment and amplifies the HR-L expressor (hypermethylated) population. GADD45α specifically interacts with the catalytic site of DNMT1 and inhibits methylation activity in vitro. We propose that double-strand DNA damage and the resulting HR process involves precise, strand selected DNA methylation by DNMT1 that is regulated by GADD45α. Since GADD45α binds with high avidity to hemimethylated DNA intermediates, it may also provide a barrier to spreading of methylation during or after HR repair

Exosome-mediated MIR211 modulates tumor microenvironment via the DUSP6-ERK5 axis and contributes to BRAFV600E inhibitor resistance in melanoma

The microRNA MIR211 is an important regulator of melanoma tumor cell behavior. Previous studies suggested that in certain tumors, MIR211 acted as a tumor suppressor while in others it behaved as an oncogenic regulator. When MIR211 is expressed in BRAFV600E-mutant A375 melanoma cells in mouse xenografts, it promotes aggressive tumor growth accompanied by increased cellular proliferation and angiogenesis. We demonstrate that MIR211 is transferred to adjacent cells in the tumor micro-environment via exosomes. Cross-species genome-wide transcriptomic analysis showed that human tumor-derived MIR211 interacts with the mouse transcriptome in the tumor microenvironment, and activates ERK5 signaling in human tumor cells via the modulation of a feedback loop. Human miR211 directly inhibits human DUSP6 protein phosphatase at the post-transcriptional level. We provide support for the hypothesis that DUSP6 inhibition conferred resistance of the human tumor cells to the BRAF inhibitor vemurafenib and to the MEK inhibitor cobimetinib, with associated increases in ERK5 phosphorylation. These findings are consistent with a model in which MIR211 regulates melanoma tumor proliferation and BRAF inhibitor resistance by inducing ERK5 signaling within the complex tumor microenvironment. We propose that the MIR211-ERK5 axis represents an important and sensitive regulatory arm in melanoma with potential theranostic applications