Computational Technique for Improvement of the Position-weight Matrices for the DNA/protein Binding Sites

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Apr 26

PMID 15849315

Citations 34

Authors

Naum I Gershenzon

Gary D Stormo

Ilya P Ioshikhes

Affiliations

Soon will be listed here.

Abstract

Position-weight matrices (PWMs) are broadly used to locate transcription factor binding sites in DNA sequences. The majority of existing PWMs provide a low level of both sensitivity and specificity. We present a new computational algorithm, a modification of the Staden-Bucher approach, that improves the PWM. We applied the proposed technique on the PWM of the GC-box, binding site for Sp1. The comparison of old and new PWMs shows that the latter increase both sensitivity and specificity. The statistical parameters of GC-box distribution in promoter regions and in the human genome, as well as in each chromosome, are presented. The majority of commonly used PWMs are the 4-row mononucleotide matrices, although 16-row dinucleotide matrices are known to be more informative. The algorithm efficiently determines the 16-row matrices and preliminary results show that such matrices provide better results than 4-row matrices.

Citing Articles

The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes.

Wanniarachchi D, Viswakula S, Wickramasuriya A BMC Bioinformatics. 2024; 25(1):371.

PMID: 39623329 PMC: 11613939. DOI: 10.1186/s12859-024-05995-0.

Investigating the sequence landscape in the initiator core promoter element using an enhanced MARZ algorithm.

Dresch J, Conrad R, Klonaros D, Drewell R PeerJ. 2023; 11:e15597.

PMID: 37366427 PMC: 10290830. DOI: 10.7717/peerj.15597.

Bayesian Markov models improve the prediction of binding motifs beyond first order.

Ge W, Meier M, Roth C, Soding J NAR Genom Bioinform. 2021; 3(2):lqab026.

PMID: 33928244 PMC: 8057495. DOI: 10.1093/nargab/lqab026.

Contribution of nonconsensus base pairs within ArsR binding sequences toward ArsR-DNA binding and arsenic-mediated transcriptional induction.

Chen X, Jiang X, Tie C, Yoo J, Wang Y, Xu M J Biol Eng. 2019; 13:53.

PMID: 31182975 PMC: 6555750. DOI: 10.1186/s13036-019-0181-4.

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

Andrabi M, Hutchins A, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K Sci Rep. 2017; 7(1):4071.

PMID: 28642456 PMC: 5481346. DOI: 10.1038/s41598-017-03199-6.

References

Stormo G . DNA binding sites: representation and discovery. Bioinformatics. 2000; 16(1):16-23. DOI: 10.1093/bioinformatics/16.1.16. View

Stormo G, Hartzell 3rd G . Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci U S A. 1989; 86(4):1183-7. PMC: 286650. DOI: 10.1073/pnas.86.4.1183. View

Man T, Stormo G . Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res. 2001; 29(12):2471-8. PMC: 55749. DOI: 10.1093/nar/29.12.2471. View

Praz V, Perier R, Bonnard C, Bucher P . The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res. 2001; 30(1):322-4. PMC: 99099. DOI: 10.1093/nar/30.1.322. View

Suzuki Y, Yamashita R, Nakai K, Sugano S . DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res. 2001; 30(1):328-31. PMC: 99097. DOI: 10.1093/nar/30.1.328. View

Bulyk M, Johnson P, Church G . Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 2002; 30(5):1255-61. PMC: 101241. DOI: 10.1093/nar/30.5.1255. View

Locker J, Ghosh D, Luc P, Zheng J . Definition and prediction of the full range of transcription factor binding sites--the hepatocyte nuclear factor 1 dimeric site. Nucleic Acids Res. 2002; 30(17):3809-17. PMC: 137408. DOI: 10.1093/nar/gkf484. View

Benos P, Bulyk M, Stormo G . Additivity in protein-DNA interactions: how good an approximation is it?. Nucleic Acids Res. 2002; 30(20):4442-51. PMC: 137142. DOI: 10.1093/nar/gkf578. View

Ponomarenko J, Bourne P, Shindyalov I . Building an automated classification of DNA-binding protein domains. Bioinformatics. 2002; 18 Suppl 2:S192-201. DOI: 10.1093/bioinformatics/18.suppl_2.s192. View

10.

King O, Roth F . A non-parametric model for transcription factor binding sites. Nucleic Acids Res. 2003; 31(19):e116. PMC: 206482. DOI: 10.1093/nar/gng117. View

11.

Djordjevic M, Sengupta A, Shraiman B . A biophysical approach to transcription factor binding site discovery. Genome Res. 2003; 13(11):2381-90. PMC: 403756. DOI: 10.1101/gr.1271603. View

12.

Cawley S, Bekiranov S, Ng H, Kapranov P, Sekinger E, Kampa D . Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004; 116(4):499-509. DOI: 10.1016/s0092-8674(04)00127-8. View

13.

Zhou Q, Liu J . Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics. 2004; 20(6):909-16. DOI: 10.1093/bioinformatics/bth006. View

14.

Stormo G, Schneider T, Gold L, Ehrenfeucht A . Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res. 1982; 10(9):2997-3011. PMC: 320670. DOI: 10.1093/nar/10.9.2997. View

15.

Harr R, Haggstrom M, Gustafsson P . Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res. 1983; 11(9):2943-57. PMC: 325935. DOI: 10.1093/nar/11.9.2943. View

16.

Staden R . Methods for calculating the probabilities of finding patterns in sequences. Comput Appl Biosci. 1989; 5(2):89-96. DOI: 10.1093/bioinformatics/5.2.89. View

17.

Stormo G . Consensus patterns in DNA. Methods Enzymol. 1990; 183:211-21. DOI: 10.1016/0076-6879(90)83015-2. View

18.

Bucher P . Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol. 1990; 212(4):563-78. DOI: 10.1016/0022-2836(90)90223-9. View

19.

Hertz G, Hartzell 3rd G, Stormo G . Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci. 1990; 6(2):81-92. DOI: 10.1093/bioinformatics/6.2.81. View

20.

Goodrich J, Schwartz M, McClure W . Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 1990; 18(17):4993-5000. PMC: 332103. DOI: 10.1093/nar/18.17.4993. View