AuthorsKamanu, Frederick Kinyua
Medvedeva, Yulia A.
Jankovic, Boris R.
Archer, John A.C.
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
MetadataShow full item record
AbstractMutations in any genome may lead to phenotype characteristics that determine ability of an individual to cope with adaptation to environmental challenges. In studies of human biology, among the most interesting ones are phenotype characteristics that determine responses to drug treatments, response to infections, or predisposition to specific inherited diseases. Most of the research in this field has been focused on the studies of mutation effects on the final gene products, peptides, and their alterations. Considerably less attention was given to the mutations that may affect regulatory mechanism(s) of gene expression, although these may also affect the phenotype characteristics. In this study we make a pilot analysis of mutations observed in the regulatory regions of 24,667 human RefSeq genes. Our study reveals that out of eight studied mutation types, insertions are the only one that in a statistically significant manner alters predicted transcription factor binding sites (TFBSs). We also find that 25 families of TFBSs have been altered by mutations in a statistically significant manner in the promoter regions we considered. Moreover, we find that the related transcription factors are, for example, prominent in processes related to intracellular signaling; cell fate; morphogenesis of organs and epithelium; development of urogenital system, epithelium, and tube; neuron fate commitment. Our study highlights the significance of studying mutations within the genes regulatory regions and opens way for further detailed investigations on this topic, particularly on the downstream affected pathways. 2012 Kamanu, Medvedeva, Schaefer, Jankovic, Archer and Bajic.
CitationKamanu FK, Medvedeva YA, Schaefer U, Jankovic BR, Archer JAC, et al. (2012) Mutations and Binding Sites of Human Transcription Factors. Front Gene 3. doi:10.3389/fgene.2012.00100.
PublisherFrontiers Media SA
JournalFrontiers in Genetics
PubMed Central IDPMC3365286
The following license files are associated with this item:
- Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.
- Authors: Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E
- Issue date: 2013 Dec 1
- Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.
- Authors: Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP
- Issue date: 2015 Apr 23
- Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.
- Authors: Kim SY, Kim Y
- Issue date: 2006 Jul 4
- Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding.
- Authors: Laurila K, Lähdesmäki H
- Issue date: 2009
- CpG deamination creates transcription factor-binding sites with high efficiency.
- Authors: Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M
- Issue date: 2011