PUBLICATION
Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation
- Authors
- Wragg, J.W., Roos, L., Vucenovic, D., Cvetesic, N., Lenhard, B., Müller, F.
- ID
- ZDB-PUB-200704-17
- Date
- 2020
- Source
- Nucleic acids research 48(15): 8374-8392 (Journal)
- Registered Authors
- Müller, Ferenc
- Keywords
- none
- MeSH Terms
-
- Transcription Initiation Site*
- Animals
- Morphogenesis/genetics
- TATA Box/genetics
- Promoter Regions, Genetic/genetics*
- Sp1 Transcription Factor/genetics
- Cell Differentiation/genetics
- Embryonic Development/genetics
- Humans
- Transcription, Genetic*
- Zebrafish/genetics
- Gene Regulatory Networks/genetics*
- Binding Sites/genetics
- Cell Cycle/genetics
- Cell Proliferation/genetics
- PubMed
- 32619237 Full text @ Nucleic Acids Res.
Citation
Wragg, J.W., Roos, L., Vucenovic, D., Cvetesic, N., Lenhard, B., Müller, F. (2020) Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation. Nucleic acids research. 48(15):8374-8392.
Abstract
The core-promoter, a stretch of DNA surrounding the transcription start site (TSS), is a major integration-point for regulatory-signals controlling gene-transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell-cycling behaviour between cells of different fates. The role promoter-associated gene-regulatory-networks play in development-associated transitions in cell-cycle-dynamics is poorly understood. This study demonstrates in a vertebrate embryo, how core-promoter variations define transcriptional output in cells transitioning from a proliferative to cell-lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo segmentation, using the FUCCI transgenic cell-cycle-phase marker, revealed a spatial and lineage-specific separation in cell-cycling behaviour. To investigate the role differential promoter usage plays in this process, cap-analysis-of-gene-expression (CAGE) was performed on cells segregated by cycling dynamics. This analysis revealed a dramatic increase in tissue-specific gene expression, concurrent with slowed cycling behaviour. We revealed a distinct sharpening in TSS utilization in genes upregulated in slowly cycling, differentiating tissues, associated with enhanced utilization of the TATA-box, in addition to Sp1 binding-sites. In contrast, genes upregulated in rapidly cycling cells carry broad distribution of TSS utilization, coupled with enrichment for the CCAAT-box. These promoter features appear to correspond to cell-cycle-dynamic rather than tissue/cell-lineage origin. Moreover, we observed genes with cell-cycle-dynamic-associated transitioning in TSS distribution and differential utilization of alternative promoters. These results demonstrate the regulatory role of core-promoters in cell-cycle-dependent transcription regulation, during embryo-development.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping