SC-EpiTranscriptome · Investigating differentiation using parallel single cell transcriptomic and epigenomic analysis

Investigating differentiation using parallel single cell transcriptomic and epigenomic analysis

Nearly every cell in our body contains the same genetic information in the form of DNA. Yet, to fulfil its tissue specific roles and to adapt to changing environments, each cell needs a specific protein composition. A crucial step therein is the selective transcription of coding and non-coding regions of the genome. Transcription is induced by the binding of transcription factors to specific gene cis-regulatory sequences, which stabilizes in turn the binding and processivity of the core transcriptional machinery. Interestingly, the same transcription factors were shown to bind to and activate different target genes in different cell types (Arvey et al. 2012), and the presence of transcription factor binding sites at cis-regulatory sequences, have been insufficient to predict the actual presence of the transcription factor. Epigenetic mechanisms including histone modifications are suggested to explain this discrepancy. Different chromatin states are defined by the combination of these histone modifications that are thought to contain instructive information like a “histone code”. Recent studies compared the genome wide histone code between undifferentiated and a variety of differentiated cell types, generating a very detailed picture of their distribution in different cell types (Zhu et al. 2013). They observe clear cell-type specific patterns that allow them to distinguish different cell types. With both the transcriptional activity as well as the distribution of histone modifications changing in the process of differentiation the question stays which changes first and potentially regulates the other. Understanding the instructive potential of epigenetic pathways was shown to be important for two medical fields. In the field of cancer, a whole genome sequencing studies of human cancer samples revealed mutations in epigenetic pathways in half of the patients, opening up the possibility for reversible tumor supporting cell states (Flavahan et al. 2017). Additional in regenerative medicine researchers identified that removal of de-differentiation inhibiting Chromatin marks can increase the otherwise low efficiency induced pluripotent stem cell generation (Watanbe et al. 2013). Therefore, the main objective of this work was to use genome wide co-acquisition of transcriptional and epigenetic changes in single cells, to provide the first systematic description of the coordinated changes in transcription and epigenetic landscape during differentiation. Based on these experiments, we aimed to identify changes with a potentially instructive role of histone modifications and to proof this instructive nature through knockout experiments.

Текст от CORDIS, на английски · Данни: CORDIS, © Европейски съюз