Affinity regression predicts the recognition code of nucleic acid-binding proteins

Nature Biotechnology

Volumn 33, Issue 12, 2015, Pages 1242-1249

  Pelossof, Raphael ^a   Singh, Irtisha ^a,b   Yang, Julie L ^a,b   Weirauch, Matthew T ^c,d   Hughes, Timothy R ^d   Leslie, Christina S ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b Weill Cornell Medical Center   (United States)

^c CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOCHEMISTRY; BIOMOLECULES; NUCLEIC ACIDS; RNA; THROUGHPUT;

ACID-BINDING PROTEINS; BINDING AFFINITIES; DNA-BINDING SPECIFICITY; INTERACTION MODEL; RNA-BINDING PROTEIN; RNA-BINDING RESIDUES; SEQUENCE DIVERGENCES; STATISTICAL APPROACH;

PROTEINS;

HOMEODOMAIN PROTEIN; NUCLEIC ACID BINDING PROTEIN; RNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

AFFINITY REGRESSION; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; DNA BINDING; DNA BINDING MOTIF; HIGH THROUGHPUT SCREENING; MICROARRAY ANALYSIS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN MICROARRAY; PROTEIN MOTIF; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN RNA BINDING; STATISTICAL ANALYSIS;

EID: 84949765648     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3343     Document Type: Article

References (36)

1. Berger, M.F. et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133, 1266-1276 (2008
2. Liu, J. & Stormo, G.D. Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. Bioinformatics 24, 1850-1857 (2008
3. Berger, M.F. et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol. 24, 1429-1435 (2006
4. Jolma, A. et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 20, 861-873 (2010
5. Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327-339 (2013
6. Noyes, M.B. et al. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133, 1277-1289 (2008
7. Ray, D. et al. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat. Biotechnol. 27, 667-670 (2009
8. Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172-177 (2013
9. Alleyne, T.M. et al. Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics 25, 1012-1018 (2009
10. Christensen, R.G. et al. Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics 28, i84-i89 (2012
11. Brunner, C., Fischer, A., Luig, K. & Thies, T. Pairwise support vector machines and their application to large scale problems. J. Mach. Learn. Res. 13, 2279-2292 (2012
12. Vert, J.P., Qiu, J. & Noble, W.S. A new pairwise kernel for biological network inference with support vector machines. BMC Bioinformatics 8 (suppl. 10), S8 (2007
13. Arvey, A., Agius, P., Noble, W.S. & Leslie, C. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res. 22, 1723-1734 (2012
14. Leslie, C., Eskin, E. & Noble, W.S. The spectrum kernel: a string kernel for SVM protein classification. Pac. Symp. Biocomputing 2012, 564-575 (2002
15. Tenenbaum, J.B. & Freeman, W.T. Separating style and content with bilinear models. Neural Comput. 12, 1247-1283 (2000
16. Hirsch, J.A. & Aggarwal, A.K. Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. EMBO J. 14, 6280-6291 (1995
17. Torrado, M. et al. Role of conserved salt bridges in homeodomain stability and DNA binding. J. Biol. Chem. 284, 23765-23779 (2009
18. Bürglin, T.R. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Nucleic Acids Res. 25, 4173-4180 (1997
19. Nagasaki, H., Sakamoto, T., Sato, Y. & Matsuoka, M. Functional analysis of the conserved domains of a rice KNOX homeodomain protein, OSH15. Plant Cell 13, 2085-2098 (2001
20. Weirauch, M.T. et al. Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol. 31, 126-134 (2013
21. Weirauch, M.T. et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158, 1431-1443 (2014
22. Zhao, Y., Granas, D. & Stormo, G.D. Inferring binding energies from selected binding sites. PLOS Comput. Biol. 5, e1000590 (2009
23. Auweter, S.D. et al. Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO J. 25, 163-173 (2006
24. Chen, X., Hughes, T.R. & Morris, Q. RankMotif.: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics 23, i72-i79 (2007
25. Agius, P., Arvey, A., Chang, W., Noble, W.S. & Leslie, C. High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput. Biol. 6, e1000916 (2010
26. Kazan, H., Ray, D., Chan, E.T., Hughes, T.R. & Morris, Q. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput. Biol. 6, e1000832 (2010
27. Zhao, Y. & Stormo, G.D. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat. Biotechnol. 29, 480-483 (2011
28. Gordân, R. et al. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Reports 3, 1093-1104 (2013
29. Bellucci, M., Agostini, F., Masin, M. & Tartaglia, G.G. Predicting protein associations with long noncoding RNAs. Nat. Methods 8, 444-445 (2011
30. Foat, B.C. & Stormo, G.D. Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol. Syst. Biol. 5, 268 (2009
31. Maticzka, D., Lange, S.J., Costa, F. & Backofen, R. GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol. 15, R17 (2014
32. Lambert, N. et al. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol. Cell 54, 887-900 (2014
33. Buenrostro, J.D. et al. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nat. Biotechnol. 32, 562-568 (2014
34. Osmanbeyoglu, H.U., Pelossof, R., Bromberg, J.F. & Leslie, C.S. Linking signaling pathways to transcriptional programs in breast cancer. Genome Res. 24, 1869-1880 (2014
35. Golub, G.H. & Van Loan, C.F. Matrix Computations 4th edn. (The Johns Hopkins University Press, Baltimore, 2013
36. Penrose, R. A generalized inverse for matrices. Math. Proc. Camb. Philos. Soc. 51, 406-413 (1955