Open chromatin interactions

Author: aipv

August undefined, 2024

Web25 de jan. de 2024 · Open chromatin regions (OCRs) allow direct interaction between cis-regulatory elements and trans-acting factors. Therefore, predicting all potential OCR-mediated loops is essential for deciphering the regulation mechanism of gene expression. However, existing loop prediction tools are restricted to specific anchor types. Web24 de jan. de 2024 · Genome-wide open chromatin interactions in hexaploid wheat. To investigate global open chromatin interactions in wheat, we performed OCEAN-C …

In the loop: promoter–enhancer interactions and bioinformatics

Web17 de mar. de 2024 · Here, we report a new method HiCAR (Hi-C on accessible regulatory DNA), which utilizes Tn5 transposase and chromatin proximity ligation, for the analysis of open-chromatin-anchored interactions with low-input cells. By applying HiCAR in … Web31 de jul. de 2024 · Here we developed a computational method, Chromatin Interaction Neural Network (CHINN), to predict chromatin interactions between open chromatin … cynthia bingham obituary

The 3D Genome Browser: a web-based browser for visualizing 3D …

Web1 de fev. de 2002 · How the transcriptional apparatus gains access to and subsequently opens compacted chromatin has remained a mystery. Now in this issue of Molecular … Web24 de abr. de 2024 · OCEAN-C can detect HOCI-mediated chromatin interactions that are strongly associated with gene expression, super-enhancers, and broad H3K4me3 domains and can detect large-scale topological structures, including topologically associated domains and A/B compartments. We develop a method called open chromatin enrichment and … WebHá 2 dias · reported the results of a complex comparative analysis of gene transcription, chromatin accessibility, and its active/repressive states, as well as spatial chromatin … cynthia binns

Remembering through the genome: the role of chromatin states …

Chromatin interaction maps reveal genetic regulation for …

WebNuclear chromatin is organized into nucleosomes, with each unit consisting of 146 base pairs of DNA wrapped twice around eight core histone proteins (i.e., two copies each of … WebChINN is able to predict CTCF-, RNA polymerase II- and HiC- associated chromatin interactions between open chromatin regions. ChINN was able to identify convergent CTCF motifs, AP-1 transcription family member motifs such as FOS, and other transcription factors such as MYC as being important in predicting chromatin interactions. cynthia bingerWeb24 de jan. de 2024 · The open chromatin enrichment and network Hi-C (OCEAN-C) is a powerful antibody-independent method to detect chromatin interactions between open … cynthia bilodeau thèse

"WebHoje · Comprehensive maps of chromatin contacts in fetal and adult cattle muscle. To construct and compare chromatin structures between fetal and adult stages, we determined genome-wide chromatin interaction frequency by carrying out the Hi-C experiments in Longissimus dorsi muscle. Four individuals with two biological replicates of each stage … " - Open chromatin interactions

Open chromatin interactions

Dissecting the plant chromatin interactome using mass …

Web24 de abr. de 2024 · Genome-wide open chromatin interaction assay using OCEAN-C. We first performed in situ Hi-C and FAIRE-seq experiments using U266 multiple … Web14 de jun. de 2024 · Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in …

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Web24 de abr. de 2024 · We develop a method called open chromatin enrichment and network Hi-C (OCEAN-C) for antibody-independent mapping of global open chromatin … Web1 de jul. de 2024 · Background Chromatin physical interactions provide essential information for understanding the regulation of cis-elements like enhancers, promoters, …

Web28 de set. de 2024 · Topologically associated domains (TADs) are spatial and functional units of metazoan chromatin structure. Interpretation of the interplay between regulatory factors and chromatin structure... Web13 de abr. de 2024 · In recent years, four other Hi-C derivatives have been developed to target 3D interactions of accessible regions in the genome ( Figure 1 B). These assays …

WebThe open chromatin enrichment and network Hi-C (OCEAN-C) was developed not only for identifying large-scale chromatin structures, including topologically associated domains … Web9 de out. de 2009 · Hi-C allows unbiased identification of chromatin interactions across an entire genome.We briefly summarize the process: cells are crosslinked with formaldehyde; DNA is digested with a restriction enzyme that leaves a 5′ overhang; the 5′ overhang is filled, including a biotinylated residue; and the resulting blunt-end fragments are ligated under …

Web1 de fev. de 2024 · Here, we present nicking enzyme-assisted open chromatin interaction capture (NicE-C), a method that leverages nicking enzyme mediated open chromatin …

WebHá 1 dia · One of the most attractive and well-described mechanisms that has been proposed to facilitate E-P communication is through extrusion of DNA loops by the Cohesin complex 12, 13 (Figure 1 A). Cohesin is a ring-shaped protein complex critical for the cohesion of sister chromatids during mitosis, as well as 3D chromatin folding, especially … billy ray cyrus homeWeb1 de fev. de 2024 · To enrich enhancer–promoter interactions in a probe-free way, we attempt to select open chromatin–associated chromatin interactions via combining in … cynthia binger boyntonWebThe open chromatin enrichment and network Hi-C (OCEAN-C) was developed not only for identifying large-scale chromatin structures, including topologically associated domains (TADs) and A/B compartments, but also for globally mapping hubs of open chromatin interactions (HOCIs) and their interaction ne … cynthia bioteauWebHere, we present nicking enzyme-assisted open chromatin interaction capture (NicE-C), a method that leverages nicking enzyme-mediated open chromatin profiling and … billy ray cyrus lil nas lyricsWeb11 de abr. de 2024 · Regions of open chromatin can more favorably bind proteins, such as ... Barrera A, Hong LK, Leichter SM, Bartelt LC, et al. Pre-established chromatin … cynthia binnyWeb20 de nov. de 2014 · The procedure involves the initial crosslinking of chromatin with formaldehyde to capture in vivo protein-DNA interactions, and subsequent shearing of chromatin with sonication. Following phenol-chloroform extraction, nucleosome-depleted areas of the genome are released to the aqueous phase of the solution due to much … cynthia binder mdWeb9 de fev. de 2024 · The concept of 3D genomics encompasses chromatin interactions and 3D spatial structures of the genome in the nucleus and its effects on gene transcription, DNA replication and repair, and other biological functions in combination with linear genome sequence information (Dekker et al ., 2013 ). cynthia bird facebook