Of these techniques, circular chromosome conformation capture sequencing (4C-seq) is used to identify all chromatin interactions occurring with a single chromosomal location (one versus all). Here we describe a 4C-seq protocol that has been optimized for primary adherent cells, for which the first...
Sonication-based Circular Chromosome Conformation Capture with next-generation sequencing analysis for the detection of chromatin interactions. Protocol Exchange: Protocol. 2010.Huang P. Y. et al. Protocol: Sonication-based Circular Chromosome Conformation Capture with next-generation sequencing analysis for ...
To test this hypothesis, we profiled the accessible chromatin of 25 medulloblastoma tumors (11 ecDNA+, 14 ecDNA−) using ATAC-seq44, as well as chromatin interactions of 17 medulloblastoma tumors (eight ecDNA+, nine ecDNA−) using chromatin conformation capture (Hi-C)45. Consistent with ...
Advanced eccDNA structure research methods. Five research methods can be used to study the advanced structure of eccDNA.ACircle-Sequencing (Circle-Seq).BChromatin Immunoprecipitation Sequencing (ChIP-seq).CCircular chromosome conformation capture combined with high-throughput sequencing (4C-seq).DProximity...
More recently, higher resolution assays such as Chromatin Conformation Capture have provided more evidence that genome organization is linked to the regulation of replication initiation. Notably, large topologically associating domains (TADs) of chromosomes, which consist of long-range interactions have...
mapped the nucleosome position on ecDNA and found the high accessibility of chromatin residing on ecDNA [50]. They also illustrated the ultra-long-range chromatin contacts in ecDNA with the help of proximity ligation-assisted CHIP-seq (PLAC-seq) and circular chromosome conformation capture combined ...
we briefly summarize recent progress in the metabolism and functions of circRNAs and elaborately discuss the patterns of circRNA-protein interactions, including altering interactions between proteins, tethering or sequestering proteins, recruiting proteins to chromatin, forming circRNA-protein-mRNA ternary compl...
doi:10.1002/9783527678679.dg01701This article has no abstract.Wiley‐VCH Verlag GmbH & Co. KGaAThe Dictionary of Genomics, Transcriptomics and Proteomics
T. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J. Struct. Biol. 156, 262–272 (2006). Article CAS PubMed Google Scholar Japaridze, A. et al. Hyperplectonemes: a higher order compact and dynamic DNA self-...
(Supplementary Figs.5and6). Enhancer e4 was characterized by increased chromatin accessibility and active enhancer histone marks as determined by ATAC-seq, H3K4me1, and H3K27ac ChIP-seq (Fig.3c). Importantly, 4C chromatin conformation capture analysis showed that e4 spatially interacted with the...