Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

| PRJNA993593 | ENA

DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.

Project description:IntroductionPolyploidy is a major force in plant evolution and the domestication of cultivated crops.ObjectivesThe study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication.MethodsThe 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication.ResultsWe found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes.ConclusionThe study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.

| S-EPMC9788948 | biostudies-literature

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

Project description:We restored liver function in the spleen by direct reprogramming splenic fibroblasts in situ and thereby transformed the spleen into a “liver” with sufficient physiological functions within a living animal.

2021-04-17 | GSE172244 | GEO

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

2021-04-17 | GSE172243 | GEO

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

2021-04-17 | GSE172242 | GEO

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.

| S-EPMC4290129 | biostudies-literature

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

Project description:BackgroundWith the aim to increase the knowledge on the evolution of coleopteran genomes, we investigated through cytogenetics and nucleotide sequence analysis Mariner transposons in three Scarabaeinae species (Coprophanaeus cyanescens, C. ensifer and Diabroctis mimas).ResultsThe cytogenetic mapping revealed an accumulation of Mariner transposon in the pericentromeric repetitive regions characterized as rich in heterochromatin and C0t-1 DNA fraction (DNA enriched with high and moderately repeated sequences). Nucleotide sequence analysis of Mariner revealed the presence of two major groups of Mariner copies in the three investigated coleoptera species.ConclusionsThe Mariner is accumulated in the centromeric area of the coleopteran chromosomes probably as a consequence of the absence of recombination in the heterochromatic regions. Our analysis detected high diversification of Mariner sequences during the evolutionary history of the group. Furthermore, comparisons between the coleopterans sequences with other insects and mammals, suggest that the horizontal transfer (HT) could have acted in the spreading of the Mariner in diverse non-related animal groups.

| S-EPMC3906913 | biostudies-literature

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

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

| PRJNA416652 | ENA

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

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

2018-02-16 | GSE106381 | GEO