Abstract
In this work, we performed a systematic study of perfect and nonspacer palindromes present in human genomic DNA, and we investigated palindrome distribution over the entire human genome and over the functional regions such as the exon, intron, intergenic, and upstream regions (2,000 bp upstream from translational start site). We found that 24 palindrome-abundant intervals are mostly located on G-bands, which condense early, replicate late, and are relatively A+T rich. In general, palindromes are overrepresented in introns but underrepresented in exons. Upstream region has enriched palindrome distribution, where palindromes can serve as transcription factor binding sites. We created a Human DNA Palindrome Database (HPALDB) which is accessible at http://vhp.ntu.edu.sg/hpaldb. It contains 12,556,994 entries covering all palindromes in the human genome longer than 6 bp. Queries can be performed in different ways. Each entry in the database is linked to its location on NCBI’s human chromosome Map Viewer.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bendall AJ, Molloy PL (1994) Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgCl2 on specificity and comparison with binding of Myc family members. Nucleic Acids Res 22:2801–2810
Boyd KE, Farnham PJ (1999) Coexamination of site-specific transcription factor binding and promoter activity in living cells. Mol Cell Biol 19:8393–8399
Bzymek M, Lovett ST (2001) Evidence for two mechanisms of palindrome-stimulated deletion in Escherichia coli: single-strand annealing and replication slipped mispairing. Genetics 158:527–540
Chew DSH, Choi KP, Leung M-Y (2005) Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses. Nucleic Acids Res 33:e134
Coffin JM, Hughes SH, Varmus HE (1997) Retroviral sequences. Cold Spring Harbor Laboratory Press, New York
Cunningham LA, Cote AG, Cam-Ozdemir C, Lewis SM (2003) Rapid, stabilizing palindrome rearrangements in somatic cells by the center-break mechanism. Mol Cell Biol 23:8740–8750
Dröge P (1994) Protein tracking-induced supercoiling of DNA: a tool to regulate DNA transactions in vivo? Bioessays 16:91–99
Dröge P, Müller-Hill B (2001) High local protein concentrations at promoters: strategies in prokaryotic and eukaryotic cells. Bioessays 23:179–183
Durbin R, Eddy S, Krogh A (1998) Biological sequences analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, UK
FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C (2004) Clustering of DNA sequences in human promoters. Genome Res 14:1562–1574
Gotter AL, Shaikh TH, Budarf ML, Rhodes CH, Emanuel BS (2004) A palindrome-mediated mechanism distinguishes translocations involving LCR-B of chromosome 22q11.2. Hum Mol Genet 13:103–115
Henthorn PS, Mager DL, Huisman THJ, Smithies O (1986) A gene deletion ending within a complex array of repeated sequences 3′ to the human {beta}-globin gene cluster. Proc Natl Acad Sci USA 83:5194–5198
Kornberg A, Baker TA (1992) DNA replication. Freeman, New York
Leach DRF (1996) Cloning and characterization of DNAs with palindromic sequences. Genet Eng (N Y) 18:1–11
LeBlanc MD, Aspeslagh G, Buggia NP, Dyer BD (2000) An annotated catalog of inverted repeats of Caenorhabditis elegans chromosomes III and X, with observations concerning odd/even biases and conserved motifs. Genome Res 10:1381–1392
Lewis SM, Cote AG (2006) Palindromes and genomic stress fractures: bracing and repairing the damage. DNA Repair 5:1146–1160
Lewis SM, Chen S, Strathern JN, Rattray AJ (2005) New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus. Nucleic Acids Res 33:e186
Lisnic B, Svetec I-K, Saric H, Nikolic I, Zgaga Z (2005) Palindrome content of the yeast Saccharomyces cerevisiae genome. Curr Genet 47(5):289–297
Mattick JS (2004) RNA regulation: a new genetics? Nat Rev Genet 5:316–323
Mayr B, Montminy M (2001) Transcriptional regulation by the phosphorylation-dependent factor CREB. Nat Rev Mol Cell Biol 2:599–609
Scarpulla RC (2002) Transcriptional activators and coactivators in the nuclear control of mitochondrial function in mammalian cells. Gene 286:81–89
Shaywitz AJ, Greenberg ME (1999) CREB: a stimulus-induced transcription factor activated by a diverse array of extracellular signals. Annu Rev Biochem 68:821–861
Shen WH, Wang J, Wu J, Zhurkin VB, Yin Y (2006) Mitogen-activated protein kinase phosphatase 2: a novel transcription target of p53 in apoptosis. Cancer Res 66:6033–6039
Silver LM (1995) Mouse genetics. Oxford University Press, London, UK
Tokuhisa JG, Singh K, Dennis ES, Peacock WJ (1990) A DNA-binding protein factor recognizes two binding domains within the octopine synthase enhancer element. Plant Cell 2:215–224
Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981
Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G (2004) Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res 14:1861–1869
Acknowledgments
We acknowledge the financial support of Nanyang Technological University, Singapore. We are particularly grateful to the two anonymous reviewers for their constructive comments and suggestions that significantly improved the presentation of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Lu, L., Jia, H., Dröge, P. et al. The human genome-wide distribution of DNA palindromes. Funct Integr Genomics 7, 221–227 (2007). https://doi.org/10.1007/s10142-007-0047-6
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10142-007-0047-6