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Maintenance of the ES Cell State

Maintenance of the ES Cell State

The cells of the blastocyst inner cell mass only remain pluripotent for a short time. This state of pluripotency and self-renewal can be maintained in embryonic stem (ES) cell culture by adding specific chemicals or growth factors to ensure the cells can continue dividing and later differentiate into different cell types. In some cases, the cells are grown on a feeder layer of differentiated cells, which provides the growth factors and extracellular matrix components necessary for stem cell...

Somatic to iPS Cell Reprogramming

Somatic to iPS Cell Reprogramming

Reprogramming alters the gene expression in somatic cells, transforming them into induced pluripotent stem (iPS) cells over several generations. Scientists can reprogram cells by introducing genes for four transcription factors—Oct4, Sox2, Klf4, and c-Myc (OSKM) by viral or non-viral methods. These factors are also known as Yamanaka factors after Shinya Yamanaka, who first generated iPS cells using mouse skin cells. Yamanaka was awarded the Nobel Prize in Physiology or Medicine in 2012 for this...

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...

Embryonic Stem Cells

Embryonic Stem Cells

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.
ES cells are grown in a culture medium where they can divide indefinitely, creating ES cell lines. Under certain conditions, ES cells can differentiate, either spontaneously into a variety of...

Embryonic Stem Cells

Embryonic Stem Cells

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.

Chromatin Modification in iPS Cells

Chromatin Modification in iPS Cells

Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...

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Related Experiment Video

Updated: Jul 4, 2026

Oct4GiP Reporter Assay to Study Genes that Regulate Mouse Embryonic Stem Cell Maintenance and Self-renewal

Oct4GiP Reporter Assay to Study Genes that Regulate Mouse Embryonic Stem Cell Maintenance and Self-renewal

Published on: May 30, 2012

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation.

Marcel E Dinger¹, Paulo P Amaral, Tim R Mercer

¹ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia.

Genome Research

|June 20, 2008

Summary

Long noncoding RNAs (ncRNAs) are newly found to be critical regulators in embryonic stem cell (ES cell) differentiation. These ncRNAs are involved in pluripotency and lineage specification, potentially through epigenetic mechanisms.

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Neural Differentiation of Mouse Embryonic Stem Cells in Serum-free Monolayer Culture

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Published on: May 14, 2015

Area of Science:

Developmental Biology
Epigenetics
Transcriptomics

Background:

Studies on embryonic stem cell (ES cell) pluripotency and lineage specification have primarily focused on protein-coding transcripts.
Recent analyses reveal thousands of long noncoding RNAs (ncRNAs) in mammals, many developmentally regulated, but their functions are largely unknown.

Purpose of the Study:

To identify novel ncRNAs involved in mouse ES cell differentiation.
To investigate the role of ncRNAs in regulating pluripotency and lineage specification during development.

Main Methods:

Custom-designed microarray analysis of mouse ES cells differentiating into embryoid bodies (EBs) over 16 days.
Integrated analysis of expression profiles, genomic context, chromatin state, and promoter regions for candidate ncRNAs.
Chromatin immunoprecipitation (ChIP) to assess histone modifications and associated proteins.

Main Results:

Identified 945 ncRNAs during EB differentiation, with 174 differentially expressed, correlating with pluripotency or differentiation.
Found coordinated expression between many ncRNAs and associated developmental genes (e.g., Dlx1, Gata6).
Characterized two novel ncRNAs (Evx1as, Hoxb5/6as) linked to homeotic loci and epigenetic regulation via H3K4 trimethylation and MLL1.

Conclusions:

Long ncRNAs play significant roles in directing ES cell pluripotency and differentiation pathways.
Some ncRNAs may exert their functions by interacting with the epigenetic machinery, influencing gene expression during development.