Transcriptome during cell differentiation

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Development in animal involves cell proliferation, growth and differentiation that are regulated by genes in our genome. During the process, cells that are previously have potentials to become every cell in the body change to a certain type of cell with a specific function. Since every cell in the multicellular organism have the same genome there must be differential regulation of gene expression during differentiation. The most important regulators are genes encode for transmembrane proteins, transcription factors, epigenetic and also signal molecules present in the environment that affect transcription factor binding towards gene promoters. During differentiation specific transcription factors are activated to allow gene expression for certain cell lineage and suppress on the other lineage. Some signal molecules known to affect transcription factors include proteins belong to the TGFß superfamily, Wnt, Hedgehog and Notch. From the epigenetic aspect, the chromatin structure in the undifferentiated cells is distinct from that of differentiated cells. Chromatin in the undifferentiated indicates transcriptionally active state enable more gene expressed probably not in specific manner at low levels. Whereas in the differentiated cells less genes are expressed but more specific to certain lineage. One of the example of this differential gene expression is in the differentiation of neuroectoderm during human embryogenesis. In the differentiation of human neuroectoderm there is decrease expression in the pluripotent genes such as POU5F1, SOX2 and NANOG and increase expression of neuroectoderm genes such as POU3F1, ZNF521 and neuroepithelial markers such as PAX6 and SOX1 that reach the highest expression at day 12 post fertilization. Based on the gene expression profiling, there is a critical transition period in which undifferentiated (stem cell) transform to differentiated cells. In the human embryonic stem invitro differentiation, it occurs at day 8[HYPHEN]10. Several transcription factors identified during this stage include PAX6, SIX3, HESX1 and ID3. As a conclusion, cell differentiation involves differential gene transcription regulated by signaling molecules, transcription factors and epigenetic mechanisms. During cell differentiation transcription of pluripotent genes reduced, while transcription of cell-type specific gene increased.

Original languageEnglish
Title of host publicationEncyclopedia of Bioinformatics and Computational Biology
Subtitle of host publicationABC of Bioinformatics
Number of pages5
ISBN (Electronic)9780128114322
ISBN (Print)9780128114148
Publication statusPublished - 1 Jan 2018


  • Cell differentiation
  • Epigenetic
  • Gene transcription
  • Signaling molecules
  • Transcription factors


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