Dataset Information

Kinetics of transcriptome during hepatic conversion [RNA-seq]

ABSTRACT: Cell plasticity endows differentiated cells with competence to be reprogrammed to other identities. While reprogramming factors-induced epigenetic changes have been characterized, intrinsic chromatin features underlying cell plasticity remain elusive. By characterizing kinetics of high-order chromatin structures during transdifferentiation from fibroblasts to hepatocytes, we identified contiguous compartment switchable regions (CSRs). Compartment B to A CSRs (B-to-A CSRs), enriched with hepatocyte genes and demarcated by loop anchors, displayed a chimeric status of pre-existing chromatin accessibility in repressive compartment in fibroblasts. Pre-existing accessibility allowed the occupancy of pioneer factor Foxa3 to B-to-A CSRs, triggering compartment switch, H3K27ac gain and H3K27me3 reduction, and hepatocyte gene activation. Moreover, chimeric chromatin status appeared to be related with fibroblasts reprogramming to neurons, cardiomyocytes and pluripotent stem cells. Together, pre-existing accessibility in compartment B defines a chimeric chromatin status that may constitute intrinsic attribute for cell plasticity.

ORGANISM(S): Mus musculus

PROVIDER: GSE148833 | GEO | 2023/04/17

REPOSITORIES: GEO

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Project description:Hematopoiesis consists of step-wise commitment of multiple distinct intermediate differentiation stages before mature blood cells are generated1,2. Early progenitor cells have multiple cell fate potentials and retain plasticity to differentiate to alternative lineages, while later stages are fully committed to certain cell lineages and rarely alter their fates3,4. Although extensive studies have been performed on regulatory pathways in mature blood cells5-8, few have examined chromatin re-organization underlying the transcription programs in early progenitors of hematopoiesis. In particular, what roles chromatin organization plays in the cell fate commitment during the differentiation of early hematopoietic progenitor cells remains unclear. Here, we carried out an integrative analysis of 3D nucleome, chromatin accessibility and gene expression during early T cell development from hematopoietic stem cells (HSC) to CD4/CD8 double positive (DP) T cells. Analysis of these data sets revealed extensive A/B compartment flips and dynamic changes of chromatin accessibility at regulatory regions including promoters and enhancers during the development process. Remarkably, both the compartment flip and changes in chromatin accessibility display a monotonic pattern. While gradual and progressive changes in chromatin re-organization was observed at most development stages, an abrupt and striking genome-wide change in A/B compartment structure and chromatin accessibility occurred during the transition from double negative stage 2 (DN2) to DN3, which was accompanied with the loss of cell fate plasticity of DN3 to differentiate to alternative lineages, suggesting that a chromatin barrier is established at the DN3 stage to lock the cells in the T cell fate. The binding of PU.1, a key factor for the fate choice of early progenitor cells, and BCL11B, critically required for T cell commitment at late stages, was associated with increased long-distance interaction and chromatin accessibility and may coordinately contribute to the establishment of the 3D nucleome structure required for the lineage differentiation and commitment.