3d genome organization

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3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes

Studying the dynamics of three-dimensional (3D) chromatin structure is essential to the understanding of biological processes in the nucleus. Integrative analysis of multi-omics data in recent publications have provided comprehensive and multilevel insight into 3D genome organization emphasizing its...

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

2024-07-30 | MSV000095480 | MassIVE

Loss of neuronal 3D chromatin organization causes transcriptional and behavioral deficits related to serotonergic dysfunction [ChIP-seq]

The interior of the neuronal cell nucleus is a highly organized 3-dimensional (3D) structure in which regions of the genome that are millions of bases apart participate in specialized sub-structures with dedicated functions. To investigate neuronal chromatin organization and dynamics in vivo, we gen...

ORGANISM(S): Mus musculus

2014-07-18 | E-GEOD-56809 | biostudies-arrayexpress

Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases

Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D)...

ORGANISM(S): Mus musculus (Mouse)

2021-08-05 | PXD024756 | Pride

Histone h3 methylation

Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

Understanding the topological configurations of chromatin can reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor...

ORGANISM(S): Mus musculus

2013-05-24 | E-GEOD-36203 | biostudies-arrayexpress

Differential protein and glycan packaging into extracellular vesicles in response to 3D gastric cancer cellular organization

Alterations of the glycosylation machinery are a common event in cancer that leads to the synthesis of aberrant glycan structures by tumor cells. Extracellular vesicles (EVs) play a modulator role in cancer communication and progression, and interestingly, several tumor-associated glycans have alrea...

ORGANISM(S): Homo sapiens (Human)

2023-10-24 | PXD035650 | Pride

Glycosylation 3d Evs Gastric cancer

Clustering of CpG islands constitutes an important determinant of the interphase chromosome 3D organization [4C-Seq]

Using 4C-Seq experimental procedure we have characterized, in cultured chicken lymphoid and erythroid cells, genome-wide patterns of spatial contacts of several CpG islands scattered along the chromosome 14. A clear tendency for interaction of CpG islands present within the same and different chromo...

ORGANISM(S): Gallus gallus

2014-03-01 | E-GEOD-51937 | biostudies-arrayexpress

Cohesin Regulates 3D Accessible Genome Organization and Function

PRJNA603822 | ENA

Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation [RNA-seq]

In mouse embryonic stem cells (mES cells), ubiquitylation of histone H2A lysine 119 represses a large number of developmental genes and maintains mES cell pluripotency. It has been suggested that a number of H2A ubiquitin ligases as well as deubiquitylases and related peptide fragments contribute to...

ORGANISM(S): Mus musculus

2015-12-08 | E-GEOD-71882 | biostudies-arrayexpress

Deterioration of multi-level 3D genome organization during breast cancer progression

PRJNA1035141 | ENA

Deterioration of multi-level 3D genome organization during breast cancer progression

PRJNA1033691 | ENA

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