Abstract
BackgroundFragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. Based on the frequency of fragile site induction, they are categorized as common and rare fragile sites. Common fragile sites are sensitive to replication stress and often rearranged in cancer. Rare fragile sites are the archetypal trinucleotide repeats. Fragile sites are known to be involved in chromosomal rearrangements in tumors. Human miRNA genes are also present at fragile sites. A better understanding of genes and miRNAs lying in the fragile site regions and their association with disease progression is required.ResultHumCFS is a manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites. Protein coding genes in the fragile sites were identified by mapping the coordinates of fragile sites with human genome Ensembl (GRCh38/hg38). Genes present in fragile sites were further mapped to DisGenNET database, to understand their possible link with human diseases. Human miRNAs from miRBase was also mapped on fragile site coordinates. In brief, HumCFS provides useful information about 125 human chromosomal fragile sites and their association with 4921 human protein-coding genes and 917 human miRNA’s.ConclusionUser-friendly web-interface of HumCFS and hyper-linking with other resources will help researchers to search for genes, miRNAs efficiently and to intersect the relationship among them. For easy data retrieval and analysis, we have integrated standard web-based tools, such as JBrowse, BLAST etc. Also, the user can download the data in various file formats such as text files, gff3 files and Bed-format files which can be used on UCSC browser.Database URL:http://webs.iiitd.edu.in/raghava/humcfs/
Highlights
Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population
User-friendly web-interface of Human chromosomal fragile site (HumCFS) and hyper-linking with other resources will help researchers to search for genes, miRNAs efficiently and to intersect the relationship among them
HumCFS: database statistics, significant findings and analysis HumCFS is a unique repository of human Chromosomal Fragile Sites (CFS) and their genes associated with diseases and human miRNAs
Summary
Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. The genetic instability at fragile sites often results in aberrant expression of oncogenes and tumor-suppressing genes, a step towards initiation of cancer progression [8]. It has been shown by in vitro studies that translocation, deletion, intra-chromosomal gene arrangement and sister chromatid exchange of cancer-specific genomic regions occur as a consequence of cell treatment with fragile site inducers [9, 10]. Common fragile sites even co-localize with breakpoints and deletions specific to various tumors [11, 12] Epigenetic alterations such as histone hypo-acetylation and methylation contribute towards genomic instability at CFS [13]. The differential expression of miR218 due to chromosomal rearrangement is allied with bladder cancer development [18, 19]
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