Hi-C data sets can be binned at different resolutions. An important tradeoff between different formats is the size of the file sparse representations and especially the binary BUTLR and.hic formats require less disk space relative to uncompressed versions of other file formats. Most of the present file formats are very similar to one another, and conversion between most formats is straightforward using command line tools. The Epigenome Browser also supports the.hic format.Īs Hi-C datasets continue to accumulate, the scientific community will likely come to a consensus on standardized file formats to represent Hi-C datasets. These.hic files are built from sequenced read pair files from a Hi-C experiment. Juicebox uses a complementary software package, Juicer, to build.hic files that store binary contact matrices at different resolutions. The 3D Genome Browser uses its own sparse matrix representation in binary format, which can be created using the BUTLRTools software package. Hi-Browse and my5C also uses tab delimited text files, but unlike the Epigenome Browser format, the my5C and Hi-Browse formats require that every entry be explicitly represented in the input file, which includes pairs of loci with zero contacts. The Epigenome Browser represents Hi-C matrices using tab-delimited text files, similar to the browser extensible data (BED) files often used in Genomics. Most tools accept files that represent contact matrices however, the file format requirements differ by tool (Table (Table1). All five visualization tools can upload user data or data downloaded from repositories such as 3DGD or 4DGenome. Hi-C datasets are accumulating rapidly, and many users will need the capability to upload new datasets into these tools. The Hi-Browse, Juicebox, and my5C can be used with any genome. The Epigenome Browser supports a total of 19 genomes, and the 3D Genome browser supports human and mouse genomes. Most of these datasets are from Hi-C experiments performed on human cells, but each tool supports genomes of other organisms. Juicebox also offers datasets from 27 other studies, which includes data from a variety of organisms (Additional file 1). Datasets available for each tool are summarized in Table Table1. These three studies include nine human cell types from different lineages and tissues-IMR90, H1, GM06990, HMEC, NHEK, K562, HUVEC, HeLa, and KBM7-which makes them useful for many types of analyses. Available datasets include three influential studies that performed Hi-C experiments on several cell types, which we refer to using the last name of the first author on the respective publications: Lieberman-Aiden, Dixon, and Rao. This region contains the MNX1 gene, which is normally not expressed in human lymphocytes beyond embryonic development.įluorescence in situ hybridization (FISH) and Hi-C methods are largely used to investigate the three-dimensional organization of the genome in the cell nucleus and are applied here to study the organization of genes ( LMBR1, NOM1, MNX1, UBE3C, PTPRN2) localized in the human 7q36.3 band.Four of the five visualization software tools come with publicly available datasets, but my5C does not. However, this homeobox gene is frequently activated in leukemic cells and its expression is associated with an altered gene positioning in the leukemia cell nuclei. In this study, we used FISH on 3D-preserved nuclei to investigate the nuclear positioning of MNX1 in the leukemia-derived cell line K562. Of the five copies of the MNX1 gene present in K562, four alleles were positioned in the nuclear periphery and only one in the nuclear interior. Using the Juicebox’s Hi-C dataset, we identified five chromatin loops in the 7q36.3 band, with different extensions related to the size and orientation of the genes located here, and independent from their expression levels. We identified similar loops in 11 human and three mouse cell lines, showing that these loops are highly conserved in different human cell lines and during evolution. Moreover, the chromatin loop organization is well conserved also during neuronal cell differentiation, showing consistency in genomic organization of this region in development. In this report, we show that FISH and Hi-C are two different approaches that complement one another and together give complete information on the nuclear organization of specific chromosomal regions in different conditions, including cellular differentiation and genetic diseases.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |