scholarly journals Atlas of Age- and Tissue-specific DNA Methylation during Early Development of Barley (Hordeum vulgare)

2018 ◽  
Author(s):  
Moumouni Konate ◽  
Michael J. Wilkinson ◽  
Banjamin Mayne ◽  
Eileen Scott ◽  
Bettina Berger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Hordeum Vulgare ◽  
Organ Function ◽  
Tissue Specific ◽  
Organ Differentiation ◽  
Differentiated Cells ◽  
Differentially Methylated Genes ◽  
Organ Specific ◽  
Development And Differentiation ◽  
Methylation Patterns

The barley (Hordeum vulgare) genome comprises over 32,000 genes, with differentiated cells expressing only a subset of genes; the remainder being silent. Mechanisms by which tissue-specific genes are regulated are not entirely understood, although DNA methylation is likely to be involved. DNA methylation patterns are not static during plant development, but it is still unclear whether different organs possess distinct methylation profiles. Methylation-sensitive GBS was used to generate DNA methylation profiles for roots, leaf-blades and leaf-sheaths from five barley varieties, using seedlings at the three-leaf stage. Differentially Methylated Markers (DMMs) were characterised by pairwise comparisons of roots, leaf-blades and leaf-sheaths of three different ages. While very many DMMs were found between roots and leaf parts, only a few existed between leaf-blades and leaf-sheaths, with differences decreasing with leaf rank. Organ-specific DMMs appeared to target mainly repeat regions, implying that organ differentiation partially relies on the spreading of DNA methylation from repeats to promoters of adjacent genes. Furthermore, the biological functions of differentially methylated genes in the different organs correlated with functional specialisation. Our results indicate that different organs do possess diagnostic methylation profiles and suggest that DNA methylation is important for both tissue development and differentiation and organ function.

Stage-differentiated modelling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression

2021 ◽  
Author(s):  
Sangeetha Muthamilselvan ◽  
Abirami Raghavendran ◽  
Ashok Palaniappan
Keyword(s):  
Colorectal Cancer ◽  
Dna Methylation ◽  
Cpg Island ◽  
Early Stage ◽  
P Value ◽  
Consensus Analysis ◽  
One Stage ◽  
Differentially Methylated Genes ◽  
Methylation Patterns ◽  
The Impact

Abstract Background: Aberrant DNA methylation acts epigenetically to skew the gene transcription rate up or down, with causative roles in the etiology of cancers. However research on the role of DNA methylation in driving the progression of cancers is limited. In this study, we have developed a comprehensive computational framework for the stage-differentiated modelling of DNA methylation landscapes in colorectal cancer (CRC), and unravelled significant stagewise signposts of CRC progression. Methods: The methylation β - matrix was derived from the public-domain TCGA data, converted into M-value matrix, annotated with AJCC stages, and analysed for stage-salient genes using multiple approaches involving stage-differentiated linear modelling of methylation patterns and/or expression patterns. Differentially methylated genes (DMGs) were identified using a contrast against controls (adjusted p-value <0.001 and |log fold-change of M-value| >2). These results were filtered using a series of all possible pairwise stage contrasts (p-value <0.05) to obtain stage-salient DMGs. These were then subjected to a consensus analysis, followed by Kaplan–Meier survival analysis to evaluate the impact of methylation patterns of consensus stage-salient biomarkers on disease prognosis.Results: We found significant genome-wide changes in methylation patterns in cancer cases relative to controls agnostic of stage. Our stage-differentiated analysis yielded the following stage-salient genes: one stage-I gene (FBN1), one stage-II gene (FOXG1), one stage-III gene (HCN1) and four stage-IV genes (NELL1, ZNF135, FAM123A, LAMA1). All the biomarkers were hypermethylated, indicating down-regulation and signifying a CpG island Methylator Phenotype (CIMP) manifestation. A significant prognostic signature consisting of FBN1 and FOXG1 survived all the steps of our analysis pipeline, and represents a novel early-stage biomarker. Conclusions: We have designed a workflow for stage-differentiated consensus analysis, and identified stage-salient diagnostic biomarkers and an early-stage prognostic biomarker panel. Our studies further yield a novel CIMP-like signature of potential clinical import underlying CRC progression.

scholarly journals Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage

2010 ◽  
Vol 21 (12) ◽  
pp. 2066-2077 ◽  
Author(s):  
Anita L. Sørensen ◽  
Bente Marie Jacobsen ◽  
Andrew H. Reiner ◽  
Ingrid S. Andersen ◽  
Philippe Collas
Keyword(s):  
Dna Methylation ◽  
Cell Types ◽  
Molecular Evidence ◽  
Mesenchymal Progenitors ◽  
H3k27 Methylation ◽  
Differentiated Cells ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
A Minor ◽  
Methylation Patterns

Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and developmental functions, whereas genes hypermethylated only in MSCs are associated with early development functions. We find that most lineage-specification promoters are DNA hypomethylated and harbor a combination of trimethylated H3K4 and H3K27, whereas early developmental genes are DNA hypermethylated with or without H3K27 methylation. Promoter DNA methylation patterns of differentiated cells are largely established at the progenitor stage; yet, differentiation segregates a minor fraction of the commonly hypermethylated promoters, generating greater epigenetic divergence between differentiated cell types than between their undifferentiated counterparts. We also show an effect of promoter CpG content on methylation dynamics upon differentiation and distinct methylation profiles on transcriptionally active and inactive promoters. We infer that methylation state of lineage-specific promoters in MSCs is not a primary determinant of differentiation capacity. Our results support the view of a common origin of mesenchymal progenitors.

The determination of tissue-specific DNA methylation patterns in forensic biofluids using bisulfite modification and pyrosequencing

2012 ◽  
Vol 33 (12) ◽  
pp. 1736-1745 ◽  
Author(s):  
Tania Madi ◽  
Kuppareddi Balamurugan ◽  
Robin Bombardi ◽  
George Duncan ◽  
Bruce McCord
Keyword(s):  
Dna Methylation ◽  
Tissue Specific ◽  
Methylation Patterns ◽  
Bisulfite Modification

scholarly journals Dysregulation of DNA Methylation and Epigenetic Clocks in Prostate Cancer among Puerto Rican Men

Biomolecules ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 2
Author(s):  
Anders Berglund ◽  
Jaime Matta ◽  
Jarline Encarnación-Medina ◽  
Carmen Ortiz-Sanchéz ◽  
Julie Dutil ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Dna Methylation ◽  
Stem Cell ◽  
The United States ◽  
Epigenetic Clock ◽  
Normal Tissues ◽  
Differentially Methylated Genes ◽  
Stem Cell Divisions ◽  
Methylation Patterns ◽  
Ancestry Proportions

In 2021, approximately 248,530 new prostate cancer (PCa) cases are estimated in the United States. Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. The objective of this study was to assess DNA methylation patterns between aggressive and indolent PCa along with ancestry proportions in 49 H/L men from Puerto Rico (PR). Prostate tumors were classified as aggressive (n = 17) and indolent (n = 32) based on the Gleason score. Genomic DNA samples were extracted by macro-dissection. DNA methylation patterns were assessed using the Illumina EPIC DNA methylation platform. We used ADMIXTURE to estimate global ancestry proportions. We identified 892 differentially methylated genes in prostate tumor tissues as compared with normal tissues. Based on an epigenetic clock model, we observed that the total number of stem cell divisions (TNSC) and stem cell division rate (SCDR) were significantly higher in tumor than adjacent normal tissues. Regarding PCa aggressiveness, 141 differentially methylated genes were identified. Ancestry proportions of PR men were estimated as African, European, and Indigenous American; these were 24.1%, 64.2%, and 11.7%, respectively. The identification of DNA methylation profiles associated with risk and aggressiveness of PCa in PR H/L men will shed light on potential mechanisms contributing to PCa disparities in PR population.

scholarly journals The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Ming Zhou ◽  
Ceyda Coruh ◽  
Guanghui Xu ◽  
Laura M. Martins ◽  
Clara Bourbousse ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Global Scale ◽  
Epigenetic Landscape ◽  
Specific Expression ◽  
Tissue Specific ◽  
Dna Motif ◽  
Epigenetic Diversity ◽  
Aberrant Dna Methylation ◽  
Open Question ◽  
Methylation Patterns

AbstractDNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As is evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that CLASSY1-4 (CLSY1-4), four locus-specific regulators of DNA methylation, also control tissue-specific methylation patterns, with the most striking pattern observed in ovules where CLSY3 and CLSY4 control DNA methylation at loci with a highly conserved DNA motif. On a more global scale, we demonstrate that specific clsy mutants are sufficient to shift the epigenetic landscape between tissues. Together, these findings reveal substantial epigenetic diversity between tissues and assign these changes to specific CLSY proteins, elucidating how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.

Tissue-specific DNA methylation patterns of the rat glial fibrillary acidic protein gene

1994 ◽  
Vol 39 (6) ◽  
pp. 694-707 ◽  
Author(s):  
D. F. Condorelli ◽  
V. G. Nicoletti ◽  
V. Barresi ◽  
A. Caruso ◽  
S. Conticello ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Glial Fibrillary Acidic Protein ◽  
Protein Gene ◽  
Acidic Protein ◽  
Tissue Specific ◽  
Methylation Patterns

scholarly journals Adaptation of the targeted capture Methyl-Seq platform for the mouse genome identifies novel tissue-specific DNA methylation patterns of genes involved in neurodevelopment

Epigenetics ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. 581-596 ◽  
Author(s):  
Benjamin Hing ◽  
Enrique Ramos ◽  
Patricia Braun ◽  
Melissa McKane ◽  
Dubravka Jancic ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mouse Genome ◽  
Tissue Specific ◽  
Targeted Capture ◽  
Methylation Patterns

scholarly journals DNA methylation patterns and disease activity in a longitudinal cohort of lupus patients

2020 ◽  
Author(s):  
Patrick Coit ◽  
Lourdes Ortiz-Fernandez ◽  
Emily E. Lewis ◽  
W. Joseph McCune ◽  
Kathleen Maksimowicz-McKinnon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
African American ◽  
Disease Activity ◽  
Vital Role ◽  
Interferon Response ◽  
Type I ◽  
Activity Levels ◽  
Differentially Methylated Genes ◽  
Active Lupus Nephritis ◽  
Methylation Patterns

Epigenetic dysregulation is implicated in the pathogenesis of lupus. We performed a longitudinal analysis to assess changes in DNA methylation in lupus granulocytes over 4 years of follow up and across disease activity levels using 229 patient samples. We demonstrate that DNA methylation profiles in lupus are influenced by ancestry-specific genetic variants and are highly stable over time. DNA methylation levels in two CpG sites correlated significantly with changes in lupus disease activity. Progressive demethylation in SNX18 was observed with increasing disease activity in African-American patients. Importantly, demethylation of a CpG site located within GALNT18 was associated with the development of active lupus nephritis. Differentially methylated genes between African-American and European-American lupus patients include type I interferon-response genes such as IRF7 and IFI44, and genes related to the NFkB pathway. TREML4, which plays a vital role in toll-like receptor signaling, was hypomethylated in African-American patients and demonstrated a strong cis-meQTL association.

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