Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Lizio, Marina; Abugessaisa, Imad; Noguchi, Shuhei; Kondo, Atsushi; Hasegawa, Akira; Hon, Chung-Chau; Hoon, Michiel de; Severin, Jessica; Oki, Shinya; Hayashizaki, Yoshihide; Carninci, Piero; Kasukawa, Takeya; Kawaji, Hideya

doi:10.1093/nar/gky1099

Cited by 192 publications

(204 citation statements)

References 37 publications

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“…Some methods used to accomplish this are RNA immunoprecipitation (RIP) [168,169], RNA antisense purification coupled with mass spectrometry (RAP-MS) [120,170], variations of ChIP-seq [78,79], and several other RNA-protein interaction techniques, as discussed in a recent review [171]. Additionally, there are several valuable databases, such as FANTOM [172,173] and ENCODE [10,59], that contain annotated enhancers using datasets generated by several of these approaches.…”

Section: Common Methods Used For Detecting Ernasmentioning

confidence: 99%

Transcriptional control by enhancers and enhancer RNAs

2019

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The regulation of gene expression is a fundamental cellular process and its misregulation is a key component of disease. Enhancers are one of the most salient regulatory elements in the genome and help orchestrate proper spatiotemporal gene expression during development, in homeostasis, and in response to signaling. Notably, molecular aberrations at enhancers, such as translocations and single nucleotide polymorphisms, are emerging as an important source of human variation and susceptibility to disease. Herein we discuss emerging paradigms addressing how genes are regulated by enhancers, common features of active enhancers, and how non-coding enhancer RNAs (eRNAs) can direct gene expression programs that underlie cellular phenotypes. We survey the current evidence, which suggests that eRNAs can bind to transcription factors, mediate enhancer-promoter interactions, influence RNA Pol II elongation, and act as decoys for repressive cofactors. Furthermore, we discuss current methodologies for the identification of eRNAs and novel approaches to elucidate their functions.

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Section: Common Methods Used For Detecting Ernasmentioning

confidence: 99%

Transcriptional control by enhancers and enhancer RNAs

2019

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“…The gene expression level of NLRs can be estimated from the average transcript per million (TPM) value annotated for individual samples obtained from a particular human tissue or cell type. In this case, a consensus dataset generated after application of a normalization pipeline to three transcriptomic repositories (i.e., Human Protein Atlas, HPA [ 48 ]; genome-based tissue expression, GTEx [ 49 ]; and functional annotation of the mammalian genome project, FANTOM5 [ 50 ]). A gene is associated with enhanced expression for a given tissue when a significantly higher mRNA level is identified in a particular tissue compared to the average level in all other tissues combined.…”

Section: The Nlr Inflammasomesmentioning

confidence: 99%

ATP-Binding and Hydrolysis in Inflammasome Activation

2020

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The prototypical model for NOD-like receptor (NLR) inflammasome assembly includesnucleotide-dependent activation of the NLR downstream of pathogen- or danger-associatedmolecular pattern (PAMP or DAMP) recognition, followed by nucleation of hetero-oligomericplatforms that lie upstream of inflammatory responses associated with innate immunity. Asmembers of the STAND ATPases, the NLRs are generally thought to share a similar model of ATPdependentactivation and effect. However, recent observations have challenged this paradigm toreveal novel and complex biochemical processes to discern NLRs from other STAND proteins. Inthis review, we highlight past findings that identify the regulatory importance of conserved ATPbindingand hydrolysis motifs within the nucleotide-binding NACHT domain of NLRs and explorerecent breakthroughs that generate connections between NLR protein structure and function.Indeed, newly deposited NLR structures for NLRC4 and NLRP3 have provided unique perspectiveson the ATP-dependency of inflammasome activation. Novel molecular dynamic simulations ofNLRP3 examined the active site of ADP- and ATP-bound models. The findings support distinctionsin nucleotide-binding domain topology with occupancy of ATP or ADP that are in turndisseminated on to the global protein structure. Ultimately, studies continue to reveal how the ATPbindingand hydrolysis properties of NACHT domains in different NLRs integrate with signalingmodules and binding partners to control innate immune responses at the molecular level.

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“…The transcription start site (TSS) data of DEmiRs were extracted from the FANTOM5 database, and 100 bp upstream and downstream were considered to be promoter regions of DEmiRs [27]. The identified differentially methylated miRNA promoter regions from the MBD-seq data were defined as differentially methylated promoters (DMPs).…”

Section: Methylation Analysis Of Promoter Region Of Mirna Associated mentioning

confidence: 99%

Identification of Epigenetic Interactions between MicroRNA and DNA Methylation Associated with Polycystic Ovarian Syndrome

Mao¹,

Li²,

Zhao³

et al. 2019

Preprint

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Aberration in microRNA (miRNA) expression or DNA methylation is a causal factor for polycystic ovarian syndrome (PCOS), a common endocrine disorder and leading cause of infertility. However, the epigenetic interactions between miRNA and DNA methylation remain unexplored in PCOS. In this study, we conducted an integrated analysis of RNA-seq, miRNA-seq and MBD-seq on ovarian granulosa cells of PCOS and control groups to reveal the epigenetic interactions involved in the pathogenesis of PCOS. Firstly, we identified 830 genes and 30 miRNAs that were expressed differently in PCOS, and seven miRNAs were found to negatively regulate targeted mRNA expression. Next, in total, 130 miRNAs were found to be significantly differently methylated in promoter regions, while 13 were found to be associated with miRNA expression. Furthermore, the promoter hypermethylation of miR-429, miR-141-3p, and miR-126-3p was proven to suppress miRNA expression and therefore upregulate their corresponding genes, including XIAP, BRD3, MAPK14 and SLC7A5. Our results demonstrate that DNA methylation regulates miRNA expression and therefore controls its corresponding gene expression. The reactivation of the transcription of epigenetically silenced genes may be one of the key elements in PCOS pathogenesis. Meanwhile, the epigenetic mechanisms underlying the regulation of miRNA expression can provide a potential therapeutic target for PCOS in the future.

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Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Cited by 192 publications

References 37 publications

Transcriptional control by enhancers and enhancer RNAs

Transcriptional control by enhancers and enhancer RNAs

ATP-Binding and Hydrolysis in Inflammasome Activation

Identification of Epigenetic Interactions between MicroRNA and DNA Methylation Associated with Polycystic Ovarian Syndrome

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