Results 21 to 30 of about 4,889,916 (279)

Advancements in mapping 3D genome architecture. [PDF]

Methods, 2020
McKay DJ, Stutzman AV, Dowen JM.
europepmc   +4 more sources

Single-cell DNA methylation and 3D genome architecture in the human brain. [PDF]

Science, 2023
Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non ...
Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li YE, Siletti K, Liem M, Claffey N, O'Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR.   +38 more
europepmc   +5 more sources

Organizational principles of 3D genome architecture. [PDF]

Nat Rev Genet, 2018
Studies of 3D chromatin organization have suggested that chromosomes are hierarchically organized into large compartments composed of smaller domains called topologically associating domains (TADs). Recent evidence suggests that compartments are smaller than previously thought and that the transcriptional or chromatin state is responsible for ...
Rowley MJ, Corces VG.
europepmc   +4 more sources

Three-dimensional chromatin architecture in plants – General features and novelties

European Journal of Cell Biology, 2023
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades.
Edouard Tourdot, Stefan Grob
doaj   +1 more source

The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome architecture. [PDF]

Nucleic Acids Res
Abstract The 3D Genome Browser 2.0 (https://3dgenome.fsm.northwestern.edu) is a significantly enhanced online platform designed for the exploration and analysis of 3D genome architecture data, with easy integration with other omics data such as ChIP-seq and ATAC-seq. This major update introduces a completely redesigned user interface (
Yu S, Fu Y, Wong JH, Wang J, Zhao H, Zhao J, Yue F.   +6 more
europepmc   +3 more sources

A CTCF Code for 3D Genome Architecture. [PDF]

Cell, 2015
The architectural protein CTCF plays a complex role in decoding the functional output of the genome. Guo et al. now show that the orientation of a CTCF site restricts its choice of interacting partner, thus creating a code that predicts the three-dimensional organization of the genome.
Nichols MH, Corces VG.
europepmc   +4 more sources

RNA gradients: Shapers of 3D genome architecture

Current Opinion in Cell Biology, 2022
A growing body of evidence points to a role of nuclear RNAs (nucRNAs) in shaping the three-dimensional (3D) architecture of the genome within the nucleus of a eukaryotic cell. nucRNAs are non-homogeneously distributed within the nucleus where they can form global and local gradients that might contribute to instructing the formation and coordinating ...
Bouwman, Britta A.M., Crosetto, Nicola, Bienko, Magda   +2 more
openaire   +3 more sources

Unraveling the 3D Genome Architecture in Plants: Present and Future [PDF]

Molecular Plant, 2020
The eukaryotic genome has a hierarchical three-dimensional (3D) organization with functional implications for DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation ...
Weizhi Ouyang, Dan Xiong, Guoliang Li, Xingwang Li   +3 more
openaire   +2 more sources

Analysis methods for studying the 3D architecture of the genome [PDF]

Genome Biology, 2015
The rapidly increasing quantity of genome-wide chromosome conformation capture data presents great opportunities and challenges in the computational modeling and interpretation of the three-dimensional genome. In particular, with recent trends towards higher-resolution high-throughput chromosome conformation capture (Hi-C) data, the diversity and ...
Ay, Ferhat, Noble, William S.
openaire   +2 more sources

Demystifying cancer etiology via 3D genome mapping [PDF]

, 2020
Ramanand et al. perform the first high-resolution 3D genome mapping via ChIA-PET to capture RNAPII-associated chromatin interactions in normal prostate epithelial and prostate cancer cells.
Yuliang Feng, Siim Pauklin
core   +1 more source