Characterization of Epigenetic and Transcriptional Landscape in Infantile Hemangiomas with ATAC-Seq and RNA-Seq

Li, Xueqing; Chen, Yuanzheng; Fu, Cong; Li, Hongwen; Yang, Kun; Bi, Jianhai; Huo, Ran

doi:10.2217/epi-2020-0060

Cited by 13 publications

(7 citation statements)

References 41 publications

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“…Further, SASH1 was reported as direct target of microRNAs 102,103 . Inhibition of these microRNAs lead to lower cell proliferation and higher apoptotic rates as well as an increase in the protein expression of SASH1 in several cell lines, as shown recently 104,105 …”

Section: Sash1/sly3mentioning

confidence: 80%

The emerging and diverse roles of the SLy/SASH1‐protein family in health and disease—Overview of three multifunctional proteins

et al. 2021

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Section: Sash1/sly3mentioning

confidence: 80%

The emerging and diverse roles of the SLy/SASH1‐protein family in health and disease—Overview of three multifunctional proteins

et al. 2021

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“…In addition, MALAT1 was shown to be upregulated in IHs and knockdown resulted in inhibition of IH growth 23 . Other genes identified include SPDEF and SOX 4, 24 and also FABP4 , which is pro‐angiogenic and regulated by VEGF and mTOR 25 . In a study of familial IHs, FGFR4 , PDGFRB and FLT4 were found to be candidate genes 26 .…”

Section: Pathogenesismentioning

confidence: 99%

News on infantile haemangioma. Part 1: clinical course and pathomechanism

2020

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Summary Currently, there is no doubt that the first choice of treatment for alarming infantile haemangiomas (IHs) is oral beta‐blockers. However, research in this field remains active, as the pathogenesis of IH is still not completely elucidated. Furthermore, there are different approaches to the management of IHs with beta‐blockers. In Part 1 of this review we will discuss the state‐of‐the‐art evidence for IH with regard to (i) the definition, epidemiology, course, risk factors and sequelae, and (ii) the pathogenesis, focusing on genetic studies. This review will update the reader on the latest developments in the pathogenesis of IH. Furthermore, we hope this review will give more insight into risk factors and sequelae of IH, thereby contributing to better decisions in the clinical management of patients with IH. The therapy and evaluation of IHs will be discussed in Part 2 of this review.

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“…The relationship between chromatin accessibility and transcription is complicated. Previous studies show little overlap between corresponding differences in chromatin and transcription [10][11][12], which highlights the complex interactions between the chromatin state and downstream gene expression. Furthermore, few studies have analyzed if changes in open chromatin induced by an intervention occur in transcriptional enhancers that can be coupled to heterologous minimal promoters to engineer intervention-inducible reporter constructs.…”

mentioning

confidence: 90%

Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs

Merrill

Montgomery

Pabon

et al. 2021

Preprint

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Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for epigenomic investigations. Integrating epigenomic and transcriptomic data has the potential to reveal the chromatin-mediated mechanisms regulating transcription. However, integrating these two data types remains challenging. We used the insulin signaling pathway as a model to investigate chromatin regions and gene expression changes using ATAC- and RNA-seq in insulin-treated Drosophila S2 cells. We show that insulin causes widespread changes in chromatin accessibility and gene expression. Then, we attempted to integrate ATAC- and RNA-seq data to predict functionally-relevant chromatin regions that control the transcriptional response to insulin. We show that using differential chromatin accessibility can predict functionally-relevant genome regions, but that stratifying differentially-accessible chromatin regions by annotated feature type provides a better prediction of whether a chromatin region regulates gene expression. In particular, our data demonstrate a strong correlation between chromatin regions annotated to distal promoters (1-2 kb from the transcription start site). To test this prediction, we cloned candidate distal promoter regions upstream of luciferase and validated the functional relevance of these chromatin regions. Our data show that distal promoter regions selected by correlations with RNA-seq are more likely to control gene expression. Thus, correlating ATAC- and RNA-seq data can home in on functionally-relevant chromatin regions.

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Characterization of Epigenetic and Transcriptional Landscape in Infantile Hemangiomas with ATAC-Seq and RNA-Seq

Cited by 13 publications

References 41 publications

The emerging and diverse roles of the SLy/SASH1‐protein family in health and disease—Overview of three multifunctional proteins

The emerging and diverse roles of the SLy/SASH1‐protein family in health and disease—Overview of three multifunctional proteins

News on infantile haemangioma. Part 1: clinical course and pathomechanism

Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs

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