ArticleBMC genomics2019
Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- CASCADES, a novel SOX2 super-enhancer-associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma.Molecular oncology · 2025Article
- Super-enhancer omics in stem cell.Molecular cancer · 2024Review
- Crosstalk betweenInternational journal of molecular sciences · 2023Review
- SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells.Bioinformatics (Oxford, England) · 2022Article
- Enhancer RNA (eRNA) in Human Diseases.International journal of molecular sciences · 2022Review
- Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells.eLife · 2022Article
- Transcriptional Landscape of Enhancer RNAs in Peripheral Blood Mononuclear Cells from Patients with Systemic Lupus Erythematosus.Journal of inflammation research · 2022Article
- Targeting phase separation on enhancers induced by transcription factor complex formations as a new strategy for treating drug-resistant cancers.Frontiers in oncology · 2022Review
- Identification of cell states using super-enhancer RNA.BMC genomics · 2021Article
- LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency.Journal of molecular cell biology · 2021Article
- Noncoding RNAs in Glioblastoma: Emerging Biological Concepts and Potential Therapeutic Implications.Cancers · 2021Review
- Observational
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4 authors.
Funding
Abstract
backgroundSuper-enhancer RNAs (seRNAs) are a kind of noncoding RNA transcribed from super-enhancer regions. The regulation mechanism and functional role of seRNAs are still unclear. Although super-enhancers play a critical role in the core transcriptional regulatory circuity of embryonic stem cell (ESC) differentiation, whether seRNAs have similar properties should be further investigated.
resultsWe analyzed cap analysis gene expression sequencing (CAGE-seq) datasets collected during the differentiation of embryonic stem cells (ESCs) to cardiomyocytes to identify the seRNAs. A non-negative matrix factorization algorithm was applied to decompose the seRNA profiles and reveal two hidden stages during the ESC differentiation. We further identified 95 and 78 seRNAs associated with early- and late-stage ESC differentiation, respectively. We found that the binding sites of master regulators of ESC differentiation, including NANOG, FOXA2, and MYC, were significantly observed in the loci of the stage-specific seRNAs. Based on the investigation of genes coexpressed with seRNA, these stage-specific seRNAs might be involved in cardiac-related functions such as myofibril assembly and heart development and act in trans to regulate the co-expressed genes.
conclusionsIn this study, we used a computational approach to demonstrate the possible role of seRNAs during ESC differentiation.
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