Dynamics of Chromatin Opening across Larval Development in the Urochordate Ascidian Ciona savignyi .
Muchun HeYuting LiYajuan LiBo DongHaiyan YuPublished in: International journal of molecular sciences (2024)
Ascidian larvae undergo tail elongation and notochord lumenogenesis, making them an ideal model for investigating tissue morphogenesis in embryogenesis. The cellular and mechanical mechanisms of these processes have been studied; however, the underlying molecular regulatory mechanism remains to be elucidated. In this study, assays for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) were applied to investigate potential regulators of the development of ascidian Ciona savignyi larvae. Our results revealed 351 and 138 differentially accessible region genes through comparisons of ATAC-seq data between stages 21 and 24 and between stages 24 and 25, respectively. A joint analysis of RNA-seq and ATAC-seq data revealed a correlation between chromatin accessibility and gene transcription. We further verified the tissue expression patterns of 12 different genes. Among them, Cs -matrix metalloproteinase 24 ( MMP24 ) and Cs -krüppel-like factor 5 ( KLF5 ) were highly expressed in notochord cells. Functional assay results demonstrated that both genes are necessary for notochord lumen formation and expansion. Finally, we performed motif enrichment analysis of the differentially accessible regions in different tailbud stages and summarized the potential roles of these motif-bearing transcription factors in larval development. Overall, our study found a correlation between gene expression and chromatin accessibility and provided a vital resource for understanding the mechanisms of the development of ascidian embryos.
Keyphrases
- single cell
- rna seq
- transcription factor
- genome wide
- gene expression
- genome wide identification
- high throughput
- dna methylation
- dna damage
- copy number
- drosophila melanogaster
- aedes aegypti
- electronic health record
- poor prognosis
- induced apoptosis
- machine learning
- big data
- climate change
- oxidative stress
- data analysis
- single molecule
- cell proliferation
- ultrasound guided
- bioinformatics analysis
- zika virus