Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy

Liu, Xuanyu; Ma, Yi; Yin, Kunlun; Li, Wenke; Chen, Wen; Zhang, Yujing; Zhu, Changsheng; Li, Tianjiao; Han, Bianmei; Li, Xuewen; Wang, Shuiyun; Zhou, Zhou

doi:10.1038/s41597-019-0094-6

Cited by 53 publications

(46 citation statements)

References 18 publications

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“…To that end, we analyzed RNA sequencing (RNA-seq) datasets generated from CMs isolated from adult mouse left ventricle ( Greco et al., 2016 ; Rosa-Garrido et al., 2017 ) ( Figure 1 A). We found 112,286 lncRNAs (FPKM >0.1) in mouse, 4,127 of which were expressed also in myocardial tissue from nine healthy human donors ( Liu et al., 2019 ) and in hiPSC-derived CMs at day 15 of differentiation. Selecting only those lncRNAs located in intergenic regions, we found 2,318 associated with a nearby protein-coding gene, 132 of which were enriched in heart.…”

Section: Resultsmentioning

confidence: 94%

Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions

et al. 2020

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Summary Enhancer RNAs (eRNAs) are a subset of long noncoding RNA generated from genomic enhancers: they are thought to act as potent promoters of the expression of nearby genes through interaction with the transcriptional and epigenomic machineries. In the present work, we describe two eRNAs transcribed from the enhancer of Nkx2-5— a gene specifying a master cardiomyogenic lineage transcription factor (TF)—which we call Intergenic Regulatory Element Nkx2-5 Enhancers ( IRENE s). The IRENE s are encoded, respectively, on the same strand (SS) and in the divergent direction (div) respect to the nearby gene. Of note, these two eRNAs have opposing roles in the regulation of Nkx2-5 : IRENE-SS acts as a canonical promoter of transcription, whereas IRENE-div represses the activity of the enhancer through recruitment of the histone deacetylase sirtuin 1. Thus, we have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription.

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Section: Resultsmentioning

confidence: 94%

Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions

et al. 2020

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“…LncRNAs belong to a large class of isoforms/transcripts with ≥200 nt in length which do not code for proteins [ 5 , 6 ], have been widely investigated in various physiological and pathological contexts using high-throughput RNA sequencing (RNA-seq) techniques and bioinformatic analyses. Some lncRNAs are expressed in a highly tissue-specific and cell-type manner, strongly suggesting that lncRNAs may play a cell-specific role [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Augustino

Liu

et al. 2020

BMC Genomics

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Background Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by high-throughput sequencing techniques and bioinformatics analysis. However, little is known about the regulatory mechanisms by which lncRNAs regulate genes that are associated with Enterotoxigenic Escherichia coli F4 fimbriae (ETEC-F4ac) adhesion phenotype in small intestine epithelial cells of Large White piglets. To address this, we used RNA sequencing to profile lncRNAs and mRNAs of small intestine epithelial cells in Large White piglets differing in their ETEC-F4 adhesion phenotypes and ITGB5 genotypes. Eight male piglets were used in this study and were divided into two groups on the basis of their adhesion phenotype and ITGB5 genotypes, a candidate gene for F4ac receptor. Non-adhesive group (n = 4) with CC genotype and adhesive group (n = 4) with TT genotype. Results In total, 78 differentially expressed lncRNAs (DE-lncRNA) and 223 differentially expressed mRNAs (log2 |FC| > 1, P < 0.05) were identified in the comparison of non-adhesive vs. adhesive small intestine epithelial cells. Furthermore, cis- and trans-regulatory target genes of DE-lncRNAs were identified, then interaction networks of lncRNAs and their cis- and trans-target differentially expressed genes (DEGs) were constructed separately. A total of 194 cis-targets were involved in the lncRNAs-cis genes interaction network and 61 trans-targets, were involved in lncRNA-trans gene interaction network that we constructed. We determined that cis-target genes were involved in alcoholism, systemic lupus erythematosus, viral carcinogenesis and malaria. Whereas trans-target DEGs were engaged in three important pathways related to the ETEC-F4 adhesion phenotype namely cGMP-PKG signaling pathway, focal adhesion, and adherens junction. The trans-target DEGs which directly involved in these pathways are KCNMB1 in cGMP-PKG signaling pathway, GRB2 in focal adhesion pathway and ACTN4 in focal adhesion and adherens junction pathways. Conclusion The findings of the current study provides an insight into biological functions and epigenetic regulatory mechanism of lncRNAs on porcine small intestine epithelial cells adhesion to ETEC-F4-ac and piglets’ diarrhea susceptibility/resistance.

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“…Because of unbiased analysis of the entire transcriptome, RNA sequencing enables us to identify previously undescribed transcripts, such as lncRNAs, gene isoforms, or pathways of gene expression regulated by enhancer RNAs. Another advantage of the RNA-seq method is the ability to identify non-human transcripts, for example, those of viral origin, that can confirm or exclude a potential infectious aetiology of human diseases [ 16 , 17 ].…”

Section: High-throughput Rna Sequencing Techniquesmentioning

confidence: 99%

Single-Cell Heterogeneity of Cutaneous T-Cell Lymphomas Revealed Using RNA-Seq Technologies

Rassek

Iżykowska

2020

Cancers

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Cutaneous T-cell lymphomas (CTCLs) represent a large, heterogeneous group of non-Hodgkin lymphomas that primarily affect the skin. Among multiple CTCL variants, the most prevalent types are mycosis fungoides (MF) and Sézary syndrome (SS). In the past decade, the molecular genetics of CTCL have been the target of intense study, increasing the knowledge of CTCL genomic alterations, discovering novel biomarkers, and potential targets for patient-specific therapy. However, the detailed pathogenesis of CTCL development still needs to be discovered. This review aims to summarize the novel insights into molecular heterogeneity of malignant cells using high-throughput technologies, such as RNA sequencing and single-cell RNA sequencing, which might be useful to identify tumour-specific molecular signatures and, therefore, offer guidance for therapy, diagnosis, and prognosis of CTCL.

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Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy

Cited by 53 publications

References 18 publications

Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions

Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Single-Cell Heterogeneity of Cutaneous T-Cell Lymphomas Revealed Using RNA-Seq Technologies

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