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Related Concept Videos

Embryonic Stem Cells00:58

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Embryonic stem (ES) cells are undifferentiated pluripotent cells, meaning they can produce any cell type in the body. This gives them tremendous potential in science and medicine since they can generate specific cell types for use in research or to replace body cells lost due to damage or disease.
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Embryonic Stem Cells00:57

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Embryonic stem (ES) cells were first discovered in mice in 1981 by Martin Evans. In 1998, James Thomson identified a method to isolate embryonic stem cells from humans. Human embryonic stem cells (hESCs) are obtained from 3-5 day old embryos that remain unused after an in vitro fertilization procedure.
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Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells
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Integrative Analysis Reveals Conserved R-Loop Features in Mouse Embryonic Stem Cells.

Ohbeom Kwon1, Hyeonwoo La1, Seonho Yoo1

  • 1Department of Stem Cell and Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea.

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Summary
This summary is machine-generated.

Conserved RNA-DNA hybrid structures, or R-loops, are key to genome stability and RNA biology in mouse stem cells. Integrating multiple datasets revealed common R-loop regions linked to active gene expression and RNA processing.

Keywords:
G-quadruplexGC skewR-loopRNA metabolismchromatin statesmouse embryonic stem cellpost-transcriptional regulationtranscription regulation

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Area of Science:

  • Molecular Biology
  • Genomics
  • RNA Biology

Background:

  • R-loops (RNA-DNA hybrids) are crucial for transcription and genome stability.
  • Platform-specific biases complicate the identification of conserved R-loops.
  • Mouse embryonic stem cells offer a model for studying stable R-loops due to high transcriptional activity.

Purpose of the Study:

  • To identify and characterize conserved R-loop regions in mouse embryonic stem cells.
  • To investigate the genomic and functional context of these conserved R-loops.
  • To understand the role of R-loops in RNA biology and gene regulation.

Main Methods:

  • Integrated analysis of 13 R-loop profiling datasets from four experimental platforms.
  • Characterization of chromatin environment and associated biological functions of common R-loop regions.
  • Sequence feature analysis and transcription factor motif analysis.

Main Results:

  • Defined 27,950 Common R-loop regions reproducibly detected across platforms.
  • Common R-loops are located in promoter-proximal and genic regions, enriched in CpG islands.
  • Associated genes show high, stable expression and enrichment in RNA metabolic processes.
  • R-loops are enriched in transcriptionally active contexts with GC skew and specific transcription factor motifs (OCT4-SOX2-TCF-NANOG, CTCF, YY1).

Conclusions:

  • This study provides the first integrated analysis of conserved R-loops in mouse embryonic stem cells.
  • Conserved R-loops are preferentially located at regulatory loci involved in RNA metabolism.
  • R-loops function as critical structural and functional nodes in RNA biology.