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Hi-C data reveals interactions within and among chromosomes.
, 2018 A. Each element of the matrix reflects the frequency of contacts between two genomic windows in an exemplar region of chromosome 3. Repeat density and the locations of AT-rich regions (blue) are plotted below the matrix, as in Fig 2.
Daniel Berry (3482828) +9 more
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Rich chromatin structure prediction from Hi-C data [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015 ABSTRACT Recent studies involving the 3-dimensional conformation of chromatin have revealed the important role it has to play in different processes within the cell. These studies have also led to the discovery of densely interacting segments of the chromosome, called topologically associating domains.
Laraib Malik, Rob Patro
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Methods for the Analysis of Topologically Associating Domains (TADs)
, 2021 Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus ...
Giovanni Ciriello +5 more
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BEKVAEM: INTEGRATIVE DATA EXPLORER FOR HI-C DATA
Journal of Bioinformatics and Genomics, 2019 Motivation: The browser-based visualization of Hi-C contact maps alongside complementary data tracks is a computationally challenging task and requires an efficient software implementation to run on small clients. Few software packages have yet been shared with the community to address this problem and modification of these is cumbersome.
Hofmann, Andreas +3 more
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Inferring chromosome radial organization from Hi-C data [PDF]
BMC Bioinformatics, 2019 Abstract Background The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome
Priyojit Das +2 more
openaire +3 more sources
FEBS Letters, EarlyView.Biomolecular condensates formed by fused in sarcoma (FUS) are dissolved by high ATP concentrations yet persist in cells. Using a reconstituted system, we demonstrate that valosin‐containing protein (VCP), an AAA+ ATPase, counteracts ATP‐driven dissolution of FUS condensates through its D2 ATPase activity.
Hitomi Kimura +2 more
wiley +1 more source
Molecular Oncology, EarlyView.CIN85 is highly expressed in osteosarcoma, particularly in metastatic lesions. Its overexpression increases cell migration and Matrigel invasion, while silencing CIN85 suppresses these behaviors. Transcriptome analysis shows that CIN85 regulates MMP2, COL3A1, and Akt/mTOR signaling. Targeting these pathways reverses CIN85‐induced motility, highlighting
Iryna Horak +10 more
wiley +1 more source
Analyses of significant chromatin interactions identified by Fit-Hi-C software.
, 2020 (a) Three representative sub-regions (1 Mb × 1 Mb) from chromosomes 17 and 22 (GM12878 cell line), with significant loci-pairs (cut-off is the 0.5 percentile of q-values) being marked with yellow points in the upper triangle of the heatmaps.
Guifang Du (8479452) +14 more
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A Deep Learning Method For Comparing Hi-C Data
, 2021 The rapidly increasing three-dimensional genome-wide data produced by chromosome conformation capture presents many challenges in computational biology to understand the genome.
Krishnamurthy, Sughosh
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Evolutionarily divergent DUF4465 domains have a common vitamin B12‐binding function
FEBS Open Bio, EarlyView.We show that DUF4465 family proteins, widespread across bacteria from gut microbiomes, hydrothermal vents, and soil, share a common vitamin B12‐binding function. These augmented β‐jellyroll proteins bind vitamin B12 via extended loops. Our findings establish sequence‐diverse DUF4465 proteins as a widespread class of B12‐binding proteins, highlighting ...
Charlea Clarke +4 more
wiley +1 more source