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YylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [human_2]

ABSTRACT: Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes. Methods: Paired end RNA-Seq was performed on key time-points of human ES cell differentiation to cardiomyocytes. The time-points include day2, day4, day6 and day8. Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the human genome (build hg38) and identified 781 novel yylncRNAs during ES cell differentiation to cardiomyocytes. Expression kinetics of a subset of yylncRNAs identified from RNA-Seq had a linear relationship with qRT–PCR . Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE115663 | GEO | 2019/01/29

REPOSITORIES: GEO

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yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [human_1]

Project description:Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes. Methods: Paired end RNA-Seq was performed on key time-points of human ES cell differentiation to cardiomyocytes. The time-points include day 0, day 1, day 2, day 4,day 6, day 8 and day 14. Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the human genome (build hg38) and identified 781 novel yylncRNAs during ES cell differentiation to cardiomyocytes. Expression kinetics of a subset of yylncRNAs identified from RNA-Seq had a linear relationship with qRT–PCR . Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content in the process of cardiac differentitation. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

2019-01-29 | GSE115575 | GEO

yylncT acts as a gatekeeper of the mesodermal transcriptional program by local modulation of DNMT3B [mouse]

Project description:Bidirectional transcription is a prevalent feature of eukaryotic promoters. The goal of this study is to identify novel divergent long-coding RNAs during differentiation of human ES to cardiomyocytes. Methods: Paired end RNA-Seq was performed on the tissue obtained from the cardiogenic region of the indicated embroynic stages of mice. Following stages of mouse development were used:- E8,E8.5,E9.5 and E14., Results: Using an optimized data analysis workflow, we mapped about ~70 million sequence reads per sample to the mouse genome (build mm10). Conclusions: Our study represents the detailed analysis of the genome wide identification of divergent long-coding RNA generated by paired end RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of long-non coding RNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

2019-01-29 | GSE115670 | GEO

RNA-seq analysis of global RNA levels at 4 stages of directed cardiac differentiation of mouse embryonic stem cells

Project description:We interrogated the transcriptome using RNA-seq at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of mRNAs and long non-coding RNAs (lncRNAs) and identified groups of genes with similar expression patterns during differentiation. RNA-seq analysis of global RNA levels at 4 stages of directed cardiac differentiation of mouse embryonic stem cells. Each stage in biological duplicates

2013-06-15 | E-GEOD-47948 | biostudies-arrayexpress

RNA-seq analysis of global RNA levels at 4 stages of directed cardiac differentiation of mouse embryonic stem cells

2013-06-15 | GSE47948 | GEO

usp11 overexpression in neuron derived from mESCs for proteome and ubiquitylome analyses

Project description:Using unbiased mass spectrometry-based screen to identify differences in ubiquitinated proteins in the overexpression of Usp11. To focus on potential substrates relevant for Usp11’s role in neurogenesis, we performed experiments with mouse embryonic stem (ES) cells, in which NPC and neurons are derived at Day8.

2021-01-29 | PXD021189 | Pride

Divergent transcription of lncRNA/mRNA gene pairs in embryonic stem cells

Project description:Many long non-coding RNA (lncRNA) species have been identified in mammalian cells, but the genomic origin, regulation and function of these molecules in individual cell types is poorly understood. We have generated comprehensive catalogs of lncRNA species expressed in human and murine embryonic stem cells (ESCs) and mapped their genomic origin. A surprisingly large fraction of these transcripts (>60%) originate from divergent transcription at promoters of active protein-coding genes. The divergently transcribed lncRNA/mRNA gene pairs exhibit coordinated changes in transcription when ESCs are differentiated into endoderm. A significant number of the divergently transcribed lncRNAs/mRNA pairs are conserved between human and mouse ESCs. Disruption of promoter-associated lncRNA orthologs in a zebrafish model of early development causes gross developmental defects. Our results reveal that transcription of most lncRNA genes is coordinated with transcription of protein-coding genes and that these lncRNAs have roles in early development. Analysis of genome-wide lncRNA transcription in human embryonic stem cells and early differentiation using RNA-seq, GRO-seq and ChIP-seq

2013-01-02 | E-GEOD-41009 | biostudies-arrayexpress

Identification of proteins that interact with the lncRNA Sarrah

Project description:Long non-coding RNAs (lncRNAs) contribute to (patho)physiological processes in the heart. Aging is the major risk factor for cardiovascular disease. Apoptosis of individual cardiomyocytes is one of the underlying causes for age-related cardiac dysfunction. Here, we identified the lncRNA Sarrah that is regulated during aging in cardiomyocytes and show that it has a protective effect on the myocardium. We used an RNA pulldown approach to identify proteins interacting with endogenous Sarrah to determine the mechanism by which Sarrah induces a cardioprotective gene expression pattern.

2020-04-01 | PXD018315 | Pride

Profiling of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer tissues and adjacent normal tissues

Project description:Purpose: To investigate the role and mechanism of mRNAs, long chain non-coding RNAs and circular RNAs in gastric cancer. Methods: RNA-seq of ribosomal RNA-depleted total RNA were performed to screen differential expressed mRNAs, long chain non-coding RNAs between paired gastric cancer tissues and adjacent normal tissues.For the linear RNA was digested with 3 U of RNase R per µg of RNA. Results: A total of 83672 mRNAs, 105998 long chain non-coding RNAs, 25441 distinct circRNAs were identified in these samples, and 13929 of these circRNAs were identified as novel circRNAs.

2022-03-15 | GSE193453 | GEO

Long Noncoding RNA Moderates microRNA Activity to Maintain Self-Renewal in Embryonic Stem Cells

Project description:Of the thousands of long non-coding RNAs expressed in embryonic stem (ES) cells, few have known roles and fewer have been functionally implicated in the regulation of self-renewal and pluripotency or reprogramming somatic cells to the pluripotent state. In ES cells, Cyrano is a stably expressed long intergenic non-coding RNA with no previously assigned role. We demonstrate that Cyrano contributes to ES cell maintenance, as its depletion results in loss of hallmarks of self-renewal. Delineation of Cyrano's network through transcriptomics revealed widespread effects on signaling pathways and gene expression networks that contribute to ES cell maintenance. Cyrano shares unique sequence complementarity with the differentiation-associated microRNA, mir-7, and mir-7 overexpression reduces expression of a key self-renewal factor to a similar extent as Cyrano knockdown. This suggests that Cyrano functions to restrain the action of mir-7. Altogether, we provide a view into the multifaceted function of Cyrano in ES cell maintenance.

2017-04-28 | GSE98297 | GEO

Genome-wide analysis of HoxBlinc lncRNA downstream targets in mouse ESC-derived embryonic bodies

Project description:We find a new non-coding transcript associated with active HoxB locus, which we named HoxBlinc lncRNA. We report that HoxBlinc RNA specifies Flk1+ mesoderm and then promotes the development of HS/PCs and cardiomyocytes. To understand the molecular pathways reguated by HoxBlinc, we generate two doxycycline inducible KD ES R1E cell lines, then differentiate these cell lines to day 6 via embryonic bodies stage. RNA-seq analysis were performed for day 6 EBs with or without doxycycline treatment starting at Flk1+ mesodermal stage. RNA from day 6 EBs targeting with 2 invidiual shRNAs with or without doxycycline treatment were combined together for RNA-seq analysis.

2015-11-11 | E-GEOD-74894 | biostudies-arrayexpress

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