Actual ligation frequencies in the chromosome conformation capture procedure. [PDF]
PLoS ONE, 2013 Chromosome conformation capture (3C) and derivative experimental procedures are used to estimate the spatial proximity between different genomic elements, thus providing information about the 3D organization of genomic domains and whole genomes within ...
Alexey A Gavrilov +2 more
doaj +2 more sources
A cautionary note on the use of chromosome conformation capture in plants [PDF]
Plant Methods, 2017 Background The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin ...
Suraj Jamge +3 more
doaj +2 more sources
STRIDE: A Sequencing Depth Robust Metric for Sparse Chromosome Conformation Capture Data Comparison. [PDF]
Adv Sci (Weinh)A mean first passage time (MFPT)‐based representation transforms sparse Hi‐C contact maps into robust topological representations, preserving biologically meaningful chromatin features and facilitating robust analysis of TADs, chromatin loops, differential chromatin contacts, and sparse single‐cell Hi‐C data.
Xu B, Gao X, Tao W, Zhang Z, Li F.
europepmc +2 more sources
ELF5-Mediated Enhancer-Promoter Interaction Regulates LALBA Expression in Ovine Mammary Gland. [PDF]
Adv Sci (Weinh)In the study, we systematically investigate the epigenetic mechanisms underlying lactation traits in sheep by integrating transcriptomic, chromatin accessibility, histone modification, and functional analyses. We identify a super‐enhancer at the LALBA locus and demonstrate that enhancer E4 functions as its core regulatory element.
Wu X +11 more
europepmc +2 more sources
Capture-C: a modular and flexible method for high-resolution chromosome conformation capture [PDF]
, 2021 Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample 3C material, including the Capture-C family of protocols.
Rue-Albrecht, K. +30 more
core +2 more sources
3C-seq-captured chromosome conformation of the hyperthermophilic archaeon Thermofilum adornatum [PDF]
, 2021 Abstract Three-dimensional structure of chromosomes displays diverse patterns across the tree of life, with compartments, interaction domains and loops being quite universally observed. The archaeal kingdom remains understudied to this extent so far, despite representing an interesting area from evolutionary and other perspectives.
Andrey Sobolev +7 more
openaire +1 more source
Application of Hi-C and other omics data analysis in human cancer and cell differentiation research
Computational and Structural Biotechnology Journal, 2021 With the development of 3C (chromosome conformation capture) and its derivative technology Hi-C (High-throughput chromosome conformation capture) research, the study of the spatial structure of the genomic sequence in the nucleus helps researchers ...
Haiyan Gong +4 more
doaj +1 more source
CTCF mediates the cell-type specific spatial organization of the Kcnq5 locus and the local gene regulation. [PDF]
PLoS ONE, 2012 Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial ...
Licheng Ren +5 more
doaj +1 more source
Simultaneous Profiling of Chromosome Conformation and Gene Expression in Single Cells
Bio-Protocol, 2023 Rapid development in single-cell chromosome conformation capture technologies has provided valuable insights into the importance of spatial genome architecture for gene regulation.
Yujie Chen +3 more
doaj +1 more source
3D genomics and its applications in precision medicine
Cellular & Molecular Biology Letters, 2023 Three-dimensional (3D) genomics is an emerging discipline that studies the three-dimensional structure of chromatin and the three-dimensional and functions of genomes.
Mengjie Chen +4 more
doaj +1 more source