FACER: comprehensive molecular and functional characterization of epigenetic chromatin regulators

Lu, Jianping; Xu, Juan; Li, Junyi; Pan, Tao; Bai, Jing; Wang, Liqiang; Jin, Xiyun; Lin, Xiaoyu; Zhang, Yunpeng; Li, Yongsheng; Sahni, Nidhi; Li, Xia

doi:10.1093/nar/gky679

Cited by 80 publications

(95 citation statements)

References 51 publications

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“…The data sets used to compile the genes encoding the ERs were downloaded in October 2018 from the EpiFactors database (available at http://epifactors.autosome.ru/) [9] and the Functional Atlas of Chromatin Epigenetic Regulators (FACER) (available at http://bio-bigdata.hrbmu.edu.cn/FACER/) [8]. The EpiFactors and FACER databases are manually curated databases providing information about 815 and 870 epigenetic regulators, respectively.…”

Section: Collection Of Epigenetic Regulators (Ers)mentioning

confidence: 99%

“…To investigate the properties of epigenetic regulators (ERs) associated with human disease, we first compiled a comprehensive set of ERs from two high-quality data sources: the EpiFactors database [9] and the Functional Atlas of Chromatin Epigenetic Regulators (FACER) [8]. In addition to these well-curated gene lists, annotated human proteins under the related GO terms were also retrieved from the GO database (see Materials and Methods).…”

Section: Identification Of Er Genes Associated With Various Human Dismentioning

confidence: 99%

“…Over the past decade, extensive researches have been directed towards understanding epigenetic regulatory mechanisms, including various individual components in the regulatory machinery. These components, referred to as epigenetic regulators (ERs) [7], are usually classified into three categories according to their regulatory roles in epigenetics: DNA modifiers, histone modifiers, and chromatin remodelers [8,9]. While DNA modifiers methylate and demethylate the cytosine bases of DNA molecules, histone modifiers covalently modify amino acid residues of histone molecules.…”

Section: Introductionmentioning

confidence: 99%

“…While DNA modifiers methylate and demethylate the cytosine bases of DNA molecules, histone modifiers covalently modify amino acid residues of histone molecules. In contrast, chromatin remodelers are a different type of ER that decouple the association between nucleosomes and DNA, and replace or move nucleosomes in the chromatin [3,8,10]. Mutation and deregulation of these ERs are observed in many complex human diseases, including cancers, neurodegenerative diseases, and developmental disorders [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

“…Recently, many ER genes have been demonstrated to be very intolerant to loss-of-function variation, even when compared to the dosage-sensitive transcription factors, underscoring the important roles of ERs in various diseases [14]. By integrating numerous studies and curated databases, more than several hundred ERs and their sources have been compiled [8,9]. However, very few studies have systematically investigated the protein-protein interaction (PPI) networks as well as the evolutionary properties of ERs that may link to human disease, and to our knowledge there are no prior studies looking at co-expression modules associated with ERs in the developmental transcriptome.…”

Section: Introductionmentioning

confidence: 99%

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Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations

Ohsawa

Umemura

Terada

et al. 2020

Genes

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We carried out a system-level analysis of epigenetic regulators (ERs) and detailed the protein–protein interaction (PPI) network characteristics of disease-associated ERs. We found that most diseases associated with ERs can be clustered into two large groups, cancer diseases and developmental diseases. ER genes formed a highly interconnected PPI subnetwork, indicating a high tendency to interact and agglomerate with one another. We used the disease module detection (DIAMOnD) algorithm to expand the PPI subnetworks into a comprehensive cancer disease ER network (CDEN) and developmental disease ER network (DDEN). Using the transcriptome from early mouse developmental stages, we identified the gene co-expression modules significantly enriched for the CDEN and DDEN gene sets, which indicated the stage-dependent roles of ER-related disease genes during early embryonic development. The evolutionary rate and phylogenetic age distribution analysis indicated that the evolution of CDEN and DDEN genes was mostly constrained, and these genes exhibited older evolutionary age. Our analysis of human polymorphism data revealed that genes belonging to DDEN and Seed-DDEN were more likely to show signs of recent positive selection in human history. This finding suggests a potential association between positive selection of ERs and risk of developmental diseases through the mechanism of antagonistic pleiotropy.

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Section: Collection Of Epigenetic Regulators (Ers)mentioning

confidence: 99%

Section: Identification Of Er Genes Associated With Various Human Dismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations

Ohsawa

Umemura

Terada

et al. 2020

Genes

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A novel model incorporating chromatin regulatory factors for risk stratification, prognosis prediction, and characterization of the microenvironment in Wilms tumor

Zhao

Chu

Song

et al. 2023

The Journal of Gene Medicine

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BackgroundWilms tumor, also known as nephroblastoma, a pediatric most‐frequent malignant‐kidney tumor, may be regulated and influenced by transcriptional and epigenetic mechanisms. Chromatin regulatory factors (CRs) play key roles in epigenetic regulation. The present study aimed to explore the involvement of CRs in the development of nephroblastoma.MethodsRNA‐sequencing and clinical information of nephroblastoma samples were obtained by downloading data from the TARGET database. The Limma package was utilized to perform differential expression analysis of genes (DEGs) between the tumor group and the control group. A Venn map was used for intersection of differential genes and CRs and to perform Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs using the clusterProfiler package. LASSO and Cox analyses were used to construct CR‐related risk models and were evaluated based on clinical parameters. A receiver operating characteristic curve was employed to assess the diagnostic performance of risk model. Furthermore, we used a single‐sample gene set enrichment analysis algorithm for immune cell infiltration analysis. Finally, to confirm the transcriptome expression of pivotal genes in human nephroblastoma cell lines, a quantitative real‐time PCR was employed.ResultsFifteen key CRs were obtained through analysis in nephroblastoma and then the risk model based on 13 important CRs was constructed using the transcriptome data of nephroblastoma. Using the risk model, pediatric nephroblastoma patients were stratified into high‐ and low‐risk groups based on their individual risk scores. The risk score of CRs can predict adverse outcomes in pediatric nephroblastoma, and this gene cluster is closely related to various immunity characteristics of nephroblastoma. Moreover, the nephroblastoma cell line exhibited higher expression levels of prognostic genes (VRK1, ARNTL, RIT1, PRDM6, and TSPY1) compared to the HEK293 T cell line.ConclusionsThe risk characteristics derived from CRs have tremendous significance in predicting prognosis and guiding clinical classification and intervention strategies for pediatric nephroblastoma.

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Cancer stem cells in brain tumors: From origin to clinical implications

Lin,

Li,

2023

MedComm

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Malignant brain tumors are highly heterogeneous tumors with a poor prognosis and a high morbidity and mortality rate in both children and adults. The cancer stem cell (CSC, also named tumor‐initiating cell) model states that tumor growth is driven by a subset of CSCs. This model explains some of the clinical observations of brain tumors, including the almost unavoidable tumor recurrence after initial successful chemotherapy and/or radiotherapy and treatment resistance. Over the past two decades, strategies for the identification and characterization of brain CSCs have improved significantly, supporting the design of new diagnostic and therapeutic strategies for brain tumors. Relevant studies have unveiled novel characteristics of CSCs in the brain, including their heterogeneity and distinctive immunobiology, which have provided opportunities for new research directions and potential therapeutic approaches. In this review, we summarize the current knowledge of CSCs markers and stemness regulators in brain tumors. We also comprehensively describe the influence of the CSCs niche and tumor microenvironment on brain tumor stemness, including interactions between CSCs and the immune system, and discuss the potential application of CSCs in brain‐based therapies for the treatment of brain tumors.

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FACER: comprehensive molecular and functional characterization of epigenetic chromatin regulators

Cited by 80 publications

References 51 publications

Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations

Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations

A novel model incorporating chromatin regulatory factors for risk stratification, prognosis prediction, and characterization of the microenvironment in Wilms tumor

Cancer stem cells in brain tumors: From origin to clinical implications

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