Dataset Information

Next Generation Sequencing Facilitates Quantitative Analysis of transcriptome and epigenome in skeletal stem cell sorted from Ptipfl/fl and Ptipf/f;Col2-Cre mice

ABSTRACT: Purpose: the goals of this study are to map epigenetic alterations drive the trajectory of skeletal stem and progenitor cells by integrating their cis-regulatory landscape(ChIP-seq) with the transcriptomic profiling(RNA-seq) Methods: freshly sorted SSCs, pBCSPs, and BCSPs by FACS (Fluorescence activated Cell Sorting) from 3-day-old Ptipf/f mice and conditional knockout Ptip by crossing col2a1-cre mice and Ptipfl/fl mice (Ptipf/f;Col2-Cre mice) were performed RNA-seq and ChIP-seq (H3K4me1/H3K4me3/H3K27ac-ChIPseq). Results: using an optimized data analysis workflow, we integrated their cis-regulatory landscape with the transcriptomic profiling. As expected, expression levels of genes were associated with the activity of their related cis-regulatory elements in SSCs, pBCSPs and BCSPs. Conclusions: Ptip play a crucial role in epigenetic alterations governing the developmental trajectory of skeletal stem and progenitor cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE183543 | GEO | 2024/09/06

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Methylation of histone H3 lysine 4 (H3K4me) at actively expressed, cell type-specific genes is established during development by the Trithorax group of epigenetic regulators. In mammals, the Trithorax family includes KMT2A-D (MLL1-4), a family of SET domain proteins that function in large complexes to impart mono-, di-, and trimethylation at H3K4. Individual KMT2s and their co-factors are essential for embryonic development and the establishment of correct gene expression patterns, presumably by demarcating the active and accessible regions of the genome in a cell specific and heritable manner. Despite the importance of H3K4me marks in development, little is known about the importance of histone methylation in maintaining gene expression patterns in fully differentiated and non-dividing cell types. In this report, we utilized an inducible cardiac-specific Cre driver to delete the PTIP protein, a key component of a H3K4me complex, and ask whether this activity is still required to maintain the phenotype of terminally differentiated cardiomyocytes. Our results demonstrate that reducing the H3K4me3 marks is sufficient to alter gene expression patterns and significantly augment systolic heart function. These results clearly show that maintenance of H3K4me3 marks is necessary for the stability of the transcriptional program in differentiated cells. The array we performed allowed us to identify genes that are regulated by PTIP and histone methylation. 8-week-old littermate mice on a mixed C57B6 and B6129 background were utilized. Three mice were on a background with a PTIP floxed allele and a wild type PTIP allele (PTIP+1, PTIP+2, PTIP+3). Three mice had a transgene that expresses a modified estrogen receptor -Cre recombinase fusion protein under the control of a cardiac-specific driver (alpha myosin heavy chain, Jackson Lab stock #005650) and a floxed PTIP allele and a null PTIP (PTIPKO1, PTIPKO2, PTIPKO3). Both groups of mice were injected with tamoxifen at 8 weeks of age. Tamoxifen deletes the floxed PTIP allele in the PTIPKO mice. 5 days after tamoxifen injection, RNA was harvested from left ventricle (LV) apices in both groups. RNA was then sent to the University of Michigan microarray facility core for analysis.

Dataset Information

Next Generation Sequencing Facilitates Quantitative Analysis of transcriptome and epigenome in skeletal stem cell sorted from Ptipfl/fl and Ptipf/f;Col2-Cre mice

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets