Dumbović, Gabrijela Sanjuan, Xavier Perucho, Manuel Forcales, Sonia-V
Published in
Methods (San Diego, Calif.)
Super resolution microscopy has changed our capability to visualize and understand spatial arrangements of RNA- and protein-containing domains in individual cells. In a previous study, we described a novel lncRNA, Tumor-associated NBL2 transcript (TNBL), which originates from a primate specific macrosatellite repeat. We aimed to describe several as...
Liang, Zhen Lou, Jieqiong Scipioni, Lorenzo Gratton, Enrico Hinde, Elizabeth
Published in
Data in brief
The nanometer spacing between nucleosomes throughout global chromatin organisation modulates local DNA template access, and through continuous dynamic rearrangements, regulates genome function [1]. However, given that nucleosome packaging occurs on a spatial scale well below the diffraction limit, real time observation of chromatin structure in liv...
Liang, Zhen Lou, Jieqiong Scipioni, Lorenzo Gratton, Enrico Hinde, Elizabeth
The nanometer spacing between nucleosomes throughout global chromatin organisation modulates local DNA template access, and through continuous dynamic rearrangements, regulates genome function [1]. However, given that nucleosome packaging occurs on a spatial scale well below the diffraction limit, real time observation of chromatin structure in liv...
Mebrek, Majda Lyna Clède, Sylvain de Chalus, Aliénor Heide, Solveig Ruoso, Léa Rogers, Eli Lédée, Nathalie Prat-Ellenberg, Laura Cassuto, Nino Guy Siffroi, Jean-Pierre
...
Published in
Journal of assisted reproduction and genetics
Interphasic DNA has a constant three-dimensional conformation, which is particularly striking for spermatic DNA, with distinct chromosomal territories and a constant chromosomal conformation. We hypothesized that this organization is fragile, and that an excess or a lack of chromosomal segments could hinder the genomic structure as a whole. Five hu...
Guh, Chia-Yu Hsieh, Yu-Hung Chu, Hsueh-Ping
Published in
Journal of Biomedical Science
Protein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes t...
Mizi, Athanasia Gade Gusmao, Eduardo Papantonis, Argyris
Published in
Methods (San Diego, Calif.)
Genome organization is now understood to be tightly linked to all genomic functions. Thus, the high-resolution mapping of higher-order chromosomal structures via 3C-based approaches has become an integral tool for studying transcriptional and cell cycle regulation, signaling effects or disease onset. Nonetheless, 3C-based protocols are not without ...
Stachecka, Joanna Nowacka-Woszuk, Joanna Kolodziejski, Pawel A Szczerbal, Izabela
Published in
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Proper expression of the PPARG gene, which encodes a key transcription factor of adipogenesis, is indispensable in the formation of mature adipocytes. The positioning of a gene within the nuclear space has been implicated in gene regulation. We here report on the significance of the PPARG gene's nuclear positioning for its activity during in vitro ...
Hu, Shibin Lv, Pin Yan, Zixiang Wen, Bo
Published in
Epigenetics & Chromatin
BackgroundNuclei of eukaryotes contain various higher-order chromatin architectures and nuclear bodies (NBs), which are critical for proper nuclear functions. Recent studies showed that active chromatin regions are associated with nuclear speckles (NSs), a type of NBs involved in RNA processing. However, the functional roles of NSs in 3D genome org...
Knoch, Tobias A
Published in
Seminars in cell & developmental biology
Despite all the efforts the three-dimensional higher-order architecture and dynamics in the cell nucleus are still debated. The regulation of genes, their transcription, replication, as well as differentiation in Eukarya is, however, closely connected to this architecture and dynamics. Here, an evaluation and review framework is setup to investigat...
See, Kelvin Lan, Yemin Rhoades, Joshua Jain, Rajan Smith, Cheryl L Epstein, Jonathan A
Published in
Development (Cambridge, England)
Dynamic organization of chromatin within the three-dimensional nuclear space has been postulated to regulate gene expression and cell fate. Here, we define the genome-wide distribution of nuclear peripheral heterochromatin as a multipotent P19 cell adopts either a neural or a cardiac fate. We demonstrate that H3K9me2-marked nuclear peripheral heter...
