Review of Progress in Predicting Protein Methylation Sites

Ao, Chunyan; Jin, Shunshan; Lin, Yandan; Zou, Quan

doi:10.2174/1385272823666190723141347

Cited by 10 publications

(4 citation statements)

References 105 publications

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“…This has meant that the stable and critical epigenetic modification style, methylation, has become most viable candidate for colon cancer biomarker research (Cheng et al, 2018;Hong, 2018;Tang et al, 2018;Wang et al, 2019). The abnormal DNA methylation pattern associated with colon cancer has been verified (Simmer et al, 2012;Ao et al, 2019;Zuo et al, 2020). High and low methylated CpG sites have been identified using the data of Illumina Human Methylation 450K (Naumov et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Colon Cancer-Related Genes Identification and Function Study Based on Single-Cell Multi-Omics Integration

Sun

Guo

Zhao

et al. 2021

Front. Cell Dev. Biol.

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Transcriptomes and DNA methylation of colon cancer at the single-cell level are used to identify marker genes and improve diagnoses and therapies. Seven colon cancer subtypes are recognized based on the single-cell RNA sequence, and the differentially expressed genes regulated by dysregulated methylation are identified as marker genes for different types of colon cancer. Compared with normal colon cells, marker genes of different types show very obvious specificity, especially upregulated genes in tumors. Functional enrichment analysis for marker genes indicates a possible relation between colon cancer and nervous system disease, moreover, the weak immune system is verified in colon cancer. The heightened expression of markers and the reduction of methylation in colon cancer promote tumor development in an extensive mechanism so that there is no biological process that can be enriched in different types.

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Section: Introductionmentioning

confidence: 99%

Colon Cancer-Related Genes Identification and Function Study Based on Single-Cell Multi-Omics Integration

Sun

Guo

Zhao

et al. 2021

Front. Cell Dev. Biol.

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“…DNA methylation regulates temporal and spatial gene expression and condition-dependent phenotypic traits, including changing flower symmetry [ 9 ] or phenotypic plasticity [ 10 ] in different biological processes [ 11 ]. Histone methylation, as a vital and reversible post-translational modification (PTM), is one of the most important modifications on histone lysine (K) and arginine (R) residues and regulates many crucial biological processes [ 12 ]. RNA methylation is an important modification in plant development and the abiotic stress response.…”

Section: Introductionmentioning

confidence: 99%

Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator?

Shi,

Wang,

Wang

et al. 2023

Horticulture Research

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Recognized as a pivotal developmental transition, flowering marks the continuation of a plant’s life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.

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“…Numerous studies have shown that 5hmC, 6mA, and 4mC, and others are widely present in the genome, and significant progress has been made ( Wu et al, 2016 ; Ao et al, 2019 ; Hu et al, 2019 ; Zhu et al, 2019 ; Zou et al, 2019 ; Cai et al, 2020 ; Fu et al, 2020 ; Hong et al, 2020 ). However, methylation-related technologies-the short-read sequencing and long-read have major disadvantages.…”

Section: Introductionmentioning

confidence: 99%

iDNA-MT: Identification DNA Modification Sites in Multiple Species by Using Multi-Task Learning Based a Neural Network Tool

Yang

et al. 2021

Front. Genet.

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MotivationDNA N4-methylcytosine (4mC) and N6-methyladenine (6mA) are two important DNA modifications and play crucial roles in a variety of biological processes. Accurate identification of the modifications is essential to better understand their biological functions and mechanisms. However, existing methods to identify 4mA or 6mC sites are all single tasks, which demonstrates that they can identify only a certain modification in one species. Therefore, it is desirable to develop a novel computational method to identify the modification sites in multiple species simultaneously.ResultsIn this study, we proposed a computational method, called iDNA-MT, to identify 4mC sites and 6mA sites in multiple species, respectively. The proposed iDNA-MT mainly employed multi-task learning coupled with the bidirectional gated recurrent units (BGRU) to capture the sharing information among different species directly from DNA primary sequences. Experimental comparative results on two benchmark datasets, containing different species respectively, show that either for identifying 4mA or for 6mC site in multiple species, the proposed iDNA-MT outperforms other state-of-the-art single-task methods. The promising results have demonstrated that iDNA-MT has great potential to be a powerful and practically useful tool to accurately identify DNA modifications.

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Review of Progress in Predicting Protein Methylation Sites

Cited by 10 publications

References 105 publications

Colon Cancer-Related Genes Identification and Function Study Based on Single-Cell Multi-Omics Integration

Colon Cancer-Related Genes Identification and Function Study Based on Single-Cell Multi-Omics Integration

Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator?

iDNA-MT: Identification DNA Modification Sites in Multiple Species by Using Multi-Task Learning Based a Neural Network Tool

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