scholarly journals De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Roza H. Ali Masalmeh ◽  
Francesca Taglini ◽  
Cristina Rubio-Ramon ◽  
Kamila I. Musialik ◽  
Jonathan Higham ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Methylation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Cpg Islands ◽  
Dna Methyltransferases ◽  
Transcriptional Elongation ◽  
Methyltransferase Activity ◽  
Methylation Activity ◽  
Colorectal Tumours

AbstractThe aberrant gain of DNA methylation at CpG islands is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CpG islands are targeted by de novo DNA methyltransferases in a sequence-specific manner, but this has not been tested. Using ectopically integrated CpG islands, here we find that aberrantly methylated CpG islands are subject to low levels of de novo DNA methylation activity in colorectal cancer cells. By delineating DNA methyltransferase targets, we find that instead de novo DNA methylation activity is targeted primarily to CpG islands marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CpG islands are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNA methyltransferase activity at CpG islands in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.

scholarly journals De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands

2019 ◽  
Author(s):  
Roza H. Ali Masalmeh ◽  
Cristina Rubio-Ramon ◽  
Francesca Taglini ◽  
Jonathan Higham ◽  
Hazel Davidson-Smith ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Cpg Islands ◽  
Dna Methyltransferases ◽  
Transcriptional Elongation ◽  
Normal Tissues ◽  
Colorectal Cancer Cells ◽  
Low Levels ◽  
Colorectal Tumours

AbstractThe aberrant gain of DNA methylation at CpG islands (CGIs) is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CGIs are targeted by de novo DNA methyltransferases (DNMTs) in a sequence-specific manner but this has not been tested. Using ectopically integrated CGIs, we find that aberrantly methylated CGIs are subject to low levels of de novo DNMT activity in colorectal cancer cells. By delineating DNMT targets, we find that instead de novo DNMT activity is targeted primarily to CGIs marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CGIs are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNMT activity at CGIs in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.

scholarly journals Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B

2020 ◽  
Vol 48 (7) ◽  
pp. 3949-3961 ◽  
Author(s):  
Chien-Chu Lin ◽  
Yi-Ping Chen ◽  
Wei-Zen Yang ◽  
James C K Shen ◽  
Hanna S Yuan
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Cytosine Methylation ◽  
Catalytic Domain ◽  
De Novo ◽  
Water Channel ◽  
Dna Methyltransferases ◽  
Structural Basis ◽  
Cpg Sites ◽  
Methylation Patterns

Abstract DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B–3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.

scholarly journals Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jean S. Fain ◽  
Axelle Loriot ◽  
Anna Diacofotaki ◽  
Aurélie Van Tongelen ◽  
Charles De Smet
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Tumor Development ◽  
Transcriptional Elongation ◽  
Dna Hypomethylation ◽  
Dna Hypermethylation ◽  
Bioinformatics Analyses ◽  
Genomic Regions ◽  
Methylation Patterns

AbstractTumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark deposited during transcriptional elongation and known to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of regional DNA hypermethylation. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo/hypermethylation, and some of these included tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.

scholarly journals Kaiso regulates DNA methylation homeostasis

2020 ◽  
Author(s):  
D Kaplun ◽  
G Filonova ◽  
Y. Lobanova ◽  
A Mazur ◽  
S Zhenilo
Keyword(s):  
Dna Methylation ◽  
Complex Formation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Main Idea ◽  
Dna Methyltransferases ◽  
The Other ◽  
Dna Hypermethylation ◽  
Mouse Embryonic Fibroblasts ◽  
Embryonic Fibroblasts

ABSTRACTGain and loss of DNA methylation in cells is a dynamic process that tends to achieve an equilibrium. Many factors are involved in maintaining the balance between DNA methylation and demethylation. Previously, it was shown that methyl-DNA protein Kaiso may attract NcoR, SMRT repressive complexes affecting histone modifications. On the other hand, the deficiency of Kaiso resulted in slightly reduced methylation of ICR in H19/Igf2 locus and Oct4 promoter in mouse embryonic fibroblasts. However, nothing is known whether Kaiso may attract DNA methyltransferase to influence DNA methylation level. The main idea of this work is that Kaiso may lead to DNA hypermethylation attracting de novo DNA methyltransferases. We demonstrated that Kaiso regulates TRIM25 promoter methylation. It can form a complex with DNMT3b. BTB/POZ domain of Kaiso and ADD domain of DNA methyltransferase are essential for complex formation. Thus, Kaiso can affect DNA methylation.

112 EXPRESSION OF DNA METHYLTRANSFERASES (DNMT) IN PLACENTAL TISSUES DURING EARLY PREGNANCY IN SHEEP

2011 ◽  
Vol 23 (1) ◽  
pp. 161
Author(s):  
A. T. Grazul-Bilska ◽  
M. L. Johnson ◽  
P. P. Borowicz ◽  
D. A. Redmer ◽  
L. P. Reynolds
Keyword(s):  
Dna Methylation ◽  
Regression Analysis ◽  
Embryonic Development ◽  
Mrna Expression ◽  
Early Pregnancy ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Fetal Loss ◽  
Dna Methyltransferases ◽  
Placental Development

Normal placental development is critical for placental function and thus for normal embryonic and fetal growth and development. Many factors, including those from the environment or from the application of assisted reproductive techniques, are known to affect embryonic development. Additionally, altered DNA methylation was reported for fetal and/or maternal placenta from compromised pregnancies, and this may contribute to high embryonic/fetal loss. DNA methylation regulated by DNA methyltransferase (DNMT) plays an important role during embryonic development. However, little is known about the expression of DNMT in placental tissues during early pregnancy in any species. To determine the mRNA expression of DNMT 3a and 3b (developmentally-regulated DNMT) in normal placenta, caruncular (CAR, maternal placenta) tissue and fetal membranes (FM, chorioallantois or fetal placenta) were collected on Days 14, 16, 18, 20, 22, 24, 26, 28, and 30 after natural mating (n = 5–8 ewes day–1) and on Day 9–11 after oestrus (n = 7; non-pregnant [NP] controls, CAR only), snap-frozen, and then used for quantitative real time RT-PCR. For each tissue, data were analysed statistically by ANOVA with the day of pregnancy as the main effect. In CAR and FM, mRNA expression of DNMT3A and 3b was affected (P < 0.01–0.02) by day of pregnancy. In CAR, expression of DNMT3A was similar in NP controls and on days 14, 16, 18, and 30, was decreased (P < 0.01) ∼2-fold on day 20, and then gradually increased to day 30 of pregnancy. In CAR, expression of DNMT3b was similar in NP controls and on days 14, 16, 18, 24, 26, and 28, but was greater (P < 0.02) by ∼2-fold on days 22 and 30 than in NP controls or on days 24 and 26 of pregnancy. For CAR, regression analysis of DNMT3a mRNA expression demonstrated a cubic pattern (R2 = 0.253; P = 0.01) of expression during early pregnancy. In FM, DNMT3a increased (P < 0.01) ∼2-fold from day 16 to 24–30, but DNMT3b gradually decreased (∼0.5–5-fold; P < 0.01) from day 16 to day 30 of pregnancy. For FM, regression analysis of mRNA expression for DNMT3a demonstrated a linear increase (R2 = 0.301; P < 0.01), but for DNMT3b a cubic pattern (R2 = 0.624; P < 0.01) of expression during early pregnancy. These data indicate that DNMT3a and 3b mRNA are differentially expressed in CAR and FM, and the temporal pattern of expression of DNMT3a and 3b differs between maternal and fetal placental tissues during early pregnancy in sheep. Thus, significant changes in mRNA expression of DNMT3a and 3b in CAR and FM indicate that de novo methylation is present in the placenta during early pregnancy in sheep and may be regulated in part by the level of DNMT expression. These data provide a foundation for determining the basis for altered DNA methylation of placental and embryonic tissues in compromised pregnancies. Supported by USDA grant 2007-01215 to LPR and ATGB, and NIH grant HL64141 to LPR and DAR.

scholarly journals Mechanisms of DNA Methyltransferase Recruitment in Mammals

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 617 ◽  
Author(s):  
Marthe Laisné ◽  
Nikhil Gupta ◽  
Olivier Kirsh ◽  
Sriharsa Pradhan ◽  
Pierre-Antoine Defossez
Keyword(s):  
Dna Methylation ◽  
Transcription Factors ◽  
Functional Role ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Dna Methyltransferases ◽  
Future Research ◽  
Epigenetic Mark ◽  
Epigenetic Events ◽  
Chromatin Modifiers

DNA methylation is an essential epigenetic mark in mammals. The proper distribution of this mark depends on accurate deposition and maintenance mechanisms, and underpins its functional role. This, in turn, depends on the precise recruitment and activation of de novo and maintenance DNA methyltransferases (DNMTs). In this review, we discuss mechanisms of recruitment of DNMTs by transcription factors and chromatin modifiers—and by RNA—and place these mechanisms in the context of biologically meaningful epigenetic events. We present hypotheses and speculations for future research, and underline the fundamental and practical benefits of better understanding the mechanisms that govern the recruitment of DNMTs.

Regulation of telomeric function by DNA methylation differs between humans and mice

2020 ◽  
Vol 29 (19) ◽  
pp. 3197-3210
Author(s):  
Shir Toubiana ◽  
Gal Larom ◽  
Riham Smoom ◽  
Robert J Duszynski ◽  
Lucy A Godley ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Cpg Islands ◽  
Open Chromatin ◽  
Chromatin Modifications ◽  
Embryonic Fibroblasts ◽  
Subtelomeric Heterochromatin ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract The most distal 2 kb region in the majority of human subtelomeres contains CpG-rich promoters for TERRA, a long non-coding RNA. When the function of the de novo DNA methyltransferase DNMT3B is disrupted, as in ICF1 syndrome, subtelomeres are abnormally hypomethylated, subtelomeric heterochromatin acquires open chromatin characteristics, TERRA is highly expressed, and telomeres shorten rapidly. In this study, we explored whether the regulation of subtelomeric epigenetic characteristics by DNMT3B is conserved between humans and mice. Studying the DNA sequence of the distal 30 kb of the majority of murine q-arm subtelomeres indicated that these regions are relatively CpG-poor and do not contain TERRA promoters similar to those present in humans. Despite the lack of human-like TERRA promoters, we clearly detected TERRA expression originating from at least seven q-arm subtelomeres, and at higher levels in mouse pluripotent stem cells in comparison with mouse embryonic fibroblasts (MEFs). However, these differences in TERRA expression could not be explained by differential methylation of CpG islands present in the TERRA-expressing murine subtelomeres. To determine whether Dnmt3b regulates the expression of TERRA in mice, we characterized subtelomeric methylation and associated telomeric functions in cells derived from ICF1 model mice. Littermate-derived WT and ICF1 MEFs demonstrated no significant differences in subtelomeric DNA methylation, chromatin modifications, TERRA expression levels, telomere sister chromatid exchange or telomere length. We conclude that the epigenetic characteristics of murine subtelomeres differ substantially from their human counterparts and that TERRA transcription in mice is regulated by factors others than Dnmt3b.

scholarly journals Prmt5 Negatively Regulates Erythropoiesis By Multiple Mechanisms, Including Controlling DNA Methyltransferase 3A Protein Levels

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1181-1181
Author(s):  
Pierre-Jacques Hamard ◽  
Luisa Luciani ◽  
Fan Liu ◽  
Guoyan Cheng ◽  
Megan A. Hatlen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Tumor Suppressor ◽  
Board Of Directors ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Fetal Liver ◽  
Arginine Methylation ◽  
Dna Methyltransferases ◽  
Dna Demethylation ◽  
Advisory Committees

Abstract The shift in sites of hematopoiesis during embryonic development leads to primitive hematopoiesis within the fetal liver at E12.5, which generates primarily erythrocytes. Definitive hematopoiesis, which occurs within the bone marrow, follows at birth. During the erythroid differentiation of fetal hematopoiesis, progenitor cell maturation is accompanied by global DNA demethylation, a process necessary for fetal liver erythrocyte formation and accompanied by diminishing expression of the de novo DNA methyltransferases, Dnmt3a and Dnmt3b. In our current study of hematopoietic cell specific Prmt5 knockout mice, we have identified Prmt5 as a master regulator of erythropoiesis; the cell-specific deletion of Prmt5 in fetal liver cells is embryonic lethal as Prmt5-null embryos have severe anemia and increased expression of Dnmt3a and Dnmt3b proteins. RNA-seq and pathway analysis studies revealed profound defects in several critical pathways that regulate normal hematopoiesis, including the tumor suppressor p53 pathway. Methyl-seq studies are currently being conducted to determine the effects of the enforced expression of key DNA methyltransferases on global DNA methylation and gene expression in erythroid progenitors and how it leads to a block in erythrocyte maturation. To decipher the extent of Dnmt3a or p53's involvement in the observed phenotypes, we have generated double knockout mouse models that are being analyzed. Mechanistically, p53 has been shown to be directly methylated by Prmt5, a modification that affects its tumor suppressor activity. Here we have found that Dnmt3a is also a substrate of Prmt5 and the effects of the di methylation of Dnmt3a on its function are currently under investigation. Thus, we have uncovered a potential functional interaction between DNA methylation and protein arginine methylation triggered by Prmt5 that regulates primitive erythropoiesis. Disclosures Levine: Foundation Medicine: Consultancy; CTI BioPharma: Membership on an entity's Board of Directors or advisory committees; Loxo Oncology: Membership on an entity's Board of Directors or advisory committees.

scholarly journals Targets and genomic constraints of ectopic Dnmt3b expression

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Yingying Zhang ◽  
Jocelyn Charlton ◽  
Rahul Karnik ◽  
Isabel Beerman ◽  
Zachary D Smith ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Cpg Island ◽  
Cpg Islands ◽  
Cell Types ◽  
Aberrant Methylation ◽  
Genome Wide Data ◽  
Mammalian Genomes ◽  
Different Cell Types

DNA methylation plays an essential role in mammalian genomes and expression of the responsible enzymes is tightly controlled. Deregulation of the de novo DNA methyltransferase DNMT3B is frequently observed across cancer types, yet little is known about its ectopic genomic targets. Here, we used an inducible transgenic mouse model to delineate rules for abnormal DNMT3B targeting, as well as the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpG islands to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually non-overlapping at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation. Our genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a distributive activity of ectopically expressed Dnmt3b that leads to discordant CpG island hypermethylation and provides new insights for interpreting the cancer methylome.

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