Results 51 to 60 of about 388,478 (262)

Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO

Nature Communications, 2022
High-resolution reconstruction of spatial chromosome organisation is in demand. Here the authors report FLAMINGO, for reconstructing high-resolution 3D Genome Organisation from HiC data which they use to generate both 5 kb and 1 kb-resolution 3D ...
Hao Wang, Jiaxin Yang, Yu Zhang, Jianliang Qian, Jianrong Wang   +4 more
doaj   +1 more source

Investigating transcription factor dynamics in health and disease using FRAP

FEBS Letters, EarlyView.
FRAP analysis of GFP‐tagged transcription factors reveals how molecular mobility and target engagement change in response to drug treatment. By combining live‐cell imaging, quantitative model fitting, and statistical analysis, this approach uncovers transcription factor dynamics linked to disease mechanisms, providing a powerful framework for ...
Kannan Govindaraj, Carolina Vazquez Garzon, Jose Joaquin Velasco, Janine N. Post   +3 more
wiley   +1 more source

The 3D Genome in Transcriptional Regulation and Pluripotency [PDF]

Cell Stem Cell, 2014
It can be convenient to think of the genome as simply a string of nucleotides, the linear order of which encodes an organism's genetic blueprint. However, the genome does not exist as a linear entity within cells where this blueprint is actually utilized.
Gorkin, David U., Leung, Danny, Ren, Bing   +2 more
openaire   +4 more sources

Identification of the plant mitochondrial OrfX protein: A mass spectrometry approach

FEBS Letters, EarlyView.
The mitochondrial genome of plants contains an open reading frame, orfx, which encodes a rare protein that has so far escaped mass spectrometric detection. The protein resembles the c‐subunit of bacterial twin‐arginine‐motif‐dependent protein translocases (TatC).
Matthias Döring, Jan de Jonge, Hans‐Peter Braun, Nils Rugen   +3 more
wiley   +1 more source

3D genome organization and its study in livestock breeding

Journal of Integrative Agriculture
Eukaryotic genomes are hierarchically packaged into cell nucleus, affecting gene regulation. The genome is organized into multiscale structural units, including chromosome territories, compartments, topologically associating domains (TADs), and DNA loops.
Jie Cheng, Xiukai Cao, Shengxuan Wang, Jiaqiang Zhang, Binglin Yue, Xiaoyan Zhang, Yongzhen Huang, Xianyong Lan, Gang Ren, Hong Chen   +9 more
doaj   +1 more source

Three-Dimensional Genome Map of the Filamentous Fungus Penicillium oxalicum

Microbiology Spectrum, 2022
Higher-order spatial organization of the chromatin in the nucleus plays crucial roles in the maintenance of cell functions and the regulation of gene expression. Three-dimensional (3D) genome sequencing has been used to great effect in mammal and plants,
Cheng-Xi Li, Lin Liu, Ting Zhang, Xue-Mei Luo, Jia-Xun Feng, Shuai Zhao   +5 more
doaj   +1 more source

The 3DGD: a database of genome 3D structure [PDF]

Bioinformatics, 2014
Abstract Summary: The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines.
Chao Li, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding 0001, Yixue Li   +5 more
openaire   +2 more sources

An epithelial GPR35 isoform supports tumor‐associated transcriptional and metabolic phenotypes

FEBS Letters, EarlyView.
GPR35 generates two functionally distinct isoforms with previously unresolved roles. GPR35‐short mediates immune‐cell chemotaxis, while GPR35‐long is enriched in colorectal cancer epithelium, where it supports increased metabolism, proliferation, and tumor‐associated transcriptional programs.
Jørgen D. Rønneberg, Martine Hjeltnes, Josephine Krieger, Joshua E. Elias, Maria Stensland, Kristian Holm, Xiaojun Jiang, Chuki Khangsar, Tuula A. Nyman, Arthur Kaser, Johannes R. Hov, Tom H. Karlsen, Nicole C. Kaneider, Frode L. Jahnsen, Georg Schneditz   +14 more
wiley   +1 more source

Open for connections: HiCAR reveals the interactions of accessible DNA

Cell Genomics, 2022
Hi-C is a powerful technology for exploring 3D genome organization on a genome-wide scale, yet it can be financially and computationally challenging. In a recent issue of Molecular Cell, Wei et al.1 introduce HiCAR, which simplifies Hi-C by targeting the
Benoit Moindrot, Daan Noordermeer
doaj   +1 more source

Structure‐forward targeting of claudins with synthetic binders

FEBS Letters, EarlyView.
Claudins form the paracellular barriers between epithelial and endothelial tissues at tight junctions and are targets for molecular binders with the goal of modulating barrier permeability. Claudin‐binding molecules are relevant in drug delivery or in altering claudin interactions with disease‐causing proteins.
Alex J. Vecchio
wiley   +1 more source