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Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

ABSTRACT: We performed in situ Hi-C experiments to determine the 3D chromatin organization in pig spleen

ORGANISM(S): Sus scrofa

PROVIDER: GSE237035 | GEO | 2023/12/31

REPOSITORIES: GEO

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Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

Project description:Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

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Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.

Project description:This study explores the relationship between three-dimensional genome organization and ultraconserved elements (UCEs), an enigmatic set of DNA elements that are perfectly conserved between the reference genomes of distantly related species. Examining both human and mouse genomes, we interrogate the relationship of UCEs to three features of chromosome organization derived from Hi-C studies. We find that UCEs are enriched within contact domains and, further, that the subset of UCEs within domains shared across diverse cell types are linked to kidney-related and neuronal processes. In boundaries, UCEs are generally depleted, with those that do overlap boundaries being overrepresented in exonic UCEs. Regarding loop anchors, UCEs are neither overrepresented nor underrepresented, but those present in loop anchors are enriched for splice sites. Finally, as the relationships between UCEs and human Hi-C features are conserved in mouse, our findings suggest that UCEs contribute to interspecies conservation of genome organization and, thus, genome stability.

| S-EPMC6363003 | biostudies-literature

Reprogramming the spleen into a functioning “liver” in vivo III

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Organization and evolution of transposable elements along the bread wheat chromosome 3B.

Project description:BACKGROUND: The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far. RESULTS: We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation. CONCLUSION: Accurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.

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Chromosomal organization and evolutionary history of Mariner transposable elements in Scarabaeinae coleopterans.

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Project description:Long non-coding RNAs and mRNAs profiling during spleen development in pig

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Project description:We describe a total 222.19 Gb of pig RNA-seq sequences generated from the 18 libraries

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