In an effort to identify a chromatin-associated pluripotent network, Rafiee et al., (2016) developed a powerful ChIP-MS technique and discovered a novel protein, TRIM24, enriched on OCT4-, SOX2-, and NANOG-associated chromatin, paving the way for future proteomic studies on chromatin.
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Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.
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Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step, allowing genome-wide identification of chromatin contacts mediated by a protein of interest. In mammalian cells, cohesin protein complex is one of the major players in the establishment of chromatin loops.
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Background: The regulation of chromatin accessibility is essential in eukaryotic cells as one of several mechanisms that ensure gene activation occurs at appropriate times and in appropriate cell types. Accordingly, mutations in chromatin remodeling proteins are linked to many different developmental disorders and cancers. One example of a chromatin protein that has been linked to both developmental abnormalities and cancer is BPTF/NURF301, the largest subunit of the Nucleosome Remodeling Factor (NuRF) complex.
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Biallelic loss of expression/function variants in cause the inherited peripheral neuropathy Charcot-Marie-Tooth type 4B3. There is an incomplete understanding of the disease pathomechanism(s) underlying Charcot-Marie-Tooth type 4B3, and despite its severe clinical presentation, currently no disease-modifying therapies. A key barrier to the study of Charcot-Marie-Tooth type 4B3 is the lack of pre-clinical models that recapitulate the clinical and pathologic features of the disease.
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School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea; Department of Bioinformatics & Life Science, Soongsil University, Seoul, Republic of Korea.
The study of chromatin interactions has advanced considerably with technologies such as high-throughput chromosome conformation capture (Hi-C) sequencing, providing a genome-wide view of physical interactions within the nucleus. These techniques have revealed the existence of hierarchical chromatin structures such as compartments, topologically associating domains (TADs), and chromatin loops, which are crucial in genome organization and regulation. However, identifying and analyzing these structural features require advanced computational methods.
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Mammalian behaviour and physiology undergo major changes in early life. Young animals rely on conspecifics to meet their needs and start showing nutritional independence and sex-specific social interactions at weaning and puberty, respectively. How neuronal populations regulating homeostatic functions and social behaviours develop during these transitions remains unclear.
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