Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

Gao, Fei; Liu, Xiaolei; Wu, Xiuping; Wang, Xuelin; Gong, Desheng; Lu, Hanlin; Xia, Yudong; Song, Yong; Wang, Junwen; Du, Jing; Liu, Siyang; Han, Xu; Tang, Yizhi; Yang, Huanming; Jin, Qi; Zhang, Xiuqing; Liu, Mingyuan

doi:10.1186/gb-2012-13-10-r100

Cited by 92 publications

(97 citation statements)

References 41 publications

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“…DNMT activity was measured using the DNMT Activity/Inhibition Assay Ultra kit (Epigentek), as described previously (30,31). Briefly, 5-g nuclear extracts for each assay were used as the start material, and the procedure was according to the manufacturer's instructions.…”

Section: Rnamentioning

confidence: 99%

Ras-induced Epigenetic Inactivation of the RRAD (Ras-related Associated with Diabetes) Gene Promotes Glucose Uptake in a Human Ovarian Cancer Model

Mao

et al. 2014

Journal of Biological Chemistry

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Section: Rnamentioning

confidence: 99%

Ras-induced Epigenetic Inactivation of the RRAD (Ras-related Associated with Diabetes) Gene Promotes Glucose Uptake in a Human Ovarian Cancer Model

Mao

et al. 2014

Journal of Biological Chemistry

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“…Furthermore, MeDIP-qPCR analysis revealed that a small amount of methylated DNA might be present in different developmental stages of D. melanogaster (Table 3). The presence of mosaic DNA methylation patterns has been described in different developmental stages of invertebrates 5,[40][41][42][43][44] . DNA methylation increased drastically during developmental stages, and adults exhibited the highest observed DNA methylation level in Trichinella spiralis 43 .…”

Section: Discussionmentioning

confidence: 99%

“…The presence of mosaic DNA methylation patterns has been described in different developmental stages of invertebrates 5,[40][41][42][43][44] . DNA methylation increased drastically during developmental stages, and adults exhibited the highest observed DNA methylation level in Trichinella spiralis 43 . It has been demonstrated that DNMT1a is essential during early embryogenesis of Nasonia vitripennis and lowering of maternal DNMT1a mRNA resulted in embryonic lethality during the onset of gastrulation 44 .…”

Section: Discussionmentioning

confidence: 99%

DNA Methylation Changes in a Gene-Specific Manner in Different Developmental Stages of <i>Drosophila melanogaster</i>

Panikar¹,

Paingankar²,

Deshmukh³

et al. 2017

Current Science

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Although genomic DNA of Drosophila melanogaster has been shown to contain little cytosine methylation, the distribution of this genome-wide methylation patterns in different life stages remains to be elucidated. We have developed an immunochemical method using cDNA microarray to assess methylation. In the present work, this methylation microarray method was employed to identify DNA methylation in and around the genes in different life stages of D. melanogaster. This led to the identification of methylated genes in three stages of D. melanogaster, viz. embryo, pupa and adult. It is noteworthy that there was differential methylation in genes in different life cycle stages. Remarkably, a few functional annotation clusters showed negative correlation between transcription of a particular gene and its methylation status. In this analysis, some of the genes attributed to characteristic biological processes of particular life stage in D. melanogaster were found to be methylated in other life stages. Our analysis while providing a methylation map also suggests that gene-specific DNA methylation is altered during the life cycle stages of D. melanogaster. Keywords:Developmental regulation, DNA methylation, Drosophila development, epigenetics, gene-specific methylation, 5 methyl cytosine.DNA methylation is involved in the regulation of several molecular processes in an eukaryotic system. Methylation plays an important role in gene silencing 1,2 , chromatin remodelling 3 and repression of transposon activity 4 . In vertebrates, X chromosome inactivation and genomic imprinting are influenced by DNA methylation, wherein these phenomena are essential for the normal development of an organism. Invertebrates such as insects show significantly distinct life stages and developmental stagespecific regulation of gene expression which plays a crucial role in the transitions between differentiated lifehistory stages. Many research groups have emphasized the presence of DNA methylation in invertebrates and have advocated that DNA methylation might be the mechanism for developmental gene regulation involved in life cycle transition [5][6][7][8][9][10] . The genome-wide DNA methylation maps of insects like Drosophila melanogaster 9 , Bombyx mori 11 , Solenopsis invicta 12 and Apis mellifera 13,14 have been generated using whole genome bisulphite sequencing. Therefore it is important to study whether these methylation signatures play an important role in life cycle processes in invertebrates.Though Drosophila lacks the canonical DNMT1, DNMT3A and DNMT3B, the presence of very low levels of DNA methylation has been reported in D. melanogaster [15][16][17][18][19][20][21][22] . Presence of methylated DNA has been a controversial issue since few reports suggest that D. melanogaster lacks DNA methylation and DNMT2 is indeed an RNA methyltransferase that uses a DNA methyltransferase type of mechanism [23][24][25] . Capuano et al. 19 employed a sensitive LC-MS/MS method to report the presence of 0.034% cytosine DNA methylation in D. melanogaster...

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“…In recent years, the methylation ascertainment method applied by Lister et al [9], which is widely used in the methylation analysis software such as Bismark [22] and Bisulfighter [23], has been employed to determine the methylcytosines from BS-seq data [5], [24] and has been shown to have a much lower false positive rate than the simple filtering method [25], [26]. We termed the method as “Lister” hereafter.…”

Section: Introductionmentioning

confidence: 99%

A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data

et al. 2014

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High-throughput bisulfite sequencing technologies have provided a comprehensive and well-fitted way to investigate DNA methylation at single-base resolution. However, there are substantial bioinformatic challenges to distinguish precisely methylcytosines from unconverted cytosines based on bisulfite sequencing data. The challenges arise, at least in part, from cell heterozygosis caused by multicellular sequencing and the still limited number of statistical methods that are available for methylcytosine calling based on bisulfite sequencing data. Here, we present an algorithm, termed Bycom, a new Bayesian model that can perform methylcytosine calling with high accuracy. Bycom considers cell heterozygosis along with sequencing errors and bisulfite conversion efficiency to improve calling accuracy. Bycom performance was compared with the performance of Lister, the method most widely used to identify methylcytosines from bisulfite sequencing data. The results showed that the performance of Bycom was better than that of Lister for data with high methylation levels. Bycom also showed higher sensitivity and specificity for low methylation level samples (<1%) than Lister. A validation experiment based on reduced representation bisulfite sequencing data suggested that Bycom had a false positive rate of about 4% while maintaining an accuracy of close to 94%. This study demonstrated that Bycom had a low false calling rate at any methylation level and accurate methylcytosine calling at high methylation levels. Bycom will contribute significantly to studies aimed at recalibrating the methylation level of genomic regions based on the presence of methylcytosines.

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Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

Cited by 92 publications

References 41 publications

Ras-induced Epigenetic Inactivation of the RRAD (Ras-related Associated with Diabetes) Gene Promotes Glucose Uptake in a Human Ovarian Cancer Model

Ras-induced Epigenetic Inactivation of the RRAD (Ras-related Associated with Diabetes) Gene Promotes Glucose Uptake in a Human Ovarian Cancer Model

DNA Methylation Changes in a Gene-Specific Manner in Different Developmental Stages of <i>Drosophila melanogaster</i>

A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data

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