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Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (CUT&Tag-seq)

ABSTRACT: Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (CUT&Tag-seq)

PROVIDER: PRJNA1101993 | ENA |

REPOSITORIES: ENA

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Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions

Project description:Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions

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Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (CUT&Tag-seq)

Project description:While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. We found extensive methylation differences, including CG methylation (mCG) and non-CG methylation (mCH; H represents A, C and T) between the rumen at fetal and adult stages and other tissues and PSCs. These differentially methylated regions (DMRs) are closely associated with other epigenetic regulatory components, such as transcription factors (TFs) and histone modifications. These DMRs can also combine to form large hypo CG-DMRs to regulate a cluster of functionally related genes. We elucidated the reasons for morphological and functional differences between fetal and adult rumen at the epigenetic level and the interactions between epigenetic modifications and gene expression. This study highlights the differences in methylation patterns between the rumen and other tissues during development and the role of DNA methylation in controlling gene expression and establishing tissue-specific functions.

2024-06-01 | GSE264339 | GEO

CUT&Tag and BioCUT&Tag enables investigation of the AT-rich and dynamic epigenome of Plasmodium falciparum from low input samples

Project description:This study aimed to adapt CUT&Tag to Plasmodium falciparum samples as an efficient and sensitive alternative to classical ChIP-sequencing. We compare H3K9me3 and HP1 CUT&Tag with ChIP-seq datasets, showing successful establishment of CUT&Tag in P. falciparum. Next we aimed to scale down required input material for our CUT&Tag reactions and generated high-quality HP1 tracks with as little as 10.000 nuclei. To minimise potential sample loss we tested feasibility of utilising (frozen) saponin parasite isolates as input material instead of nuclei, which proved to be viable. Lastly, we deployed our new technique Dimerisation-induced Biotinylation-CUT&Tag (DiBioCUT&Tag) to catch transient interactions by biotinylation of strongly associated proteins such as histones. We tested this technique on HP1 and compared standart CUT&Tag with DiBioCUT&Tag. Furthermore, we explored interactions of the transcription factor BDP5, which we were previously unable to succesfully ChIP.

2024-06-27 | GSE270104 | GEO

Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-06-01 | GSE264346 | GEO

Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (ATAC-seq)

2024-06-01 | GSE264333 | GEO

Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (ChIP-seq)

2024-06-01 | GSE264336 | GEO