Figuring out how genes coordinate the complex phenomena of life involves more than deciphering a DNA sequence. Proteins called transcription factors control genes by attaching to DNA; discovering where each of these proteins binds is critical to understanding how genes regulate working cells.

Research Overview 

The ability of a cell to respond to environmental stresses, differentiate properly, and progress normally through the cell cycle requires a specific and coordinated gene expression program involving regulated transcription of thousands of genes. The initiation of transcription is in large part controlled by the sequence-specific DNA binding of transcriptional activators and repressors. Despite their importance, the sequence specificities of most transcription factors (TFs) remain unknown, underscoring the need for a rapid and universal method to discover TF binding sites.


Previously we developed a novel DNA microarray-based in vitro technology, termed protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the DNA binding site sequence specificities of TFs in a single day (Mukherjee et al., Nature Genetics (2004) 36(12):1331-9; Berger et al., Nature Biotechnology (2006) 24(11):1429-1435). Using PBMs, we have identified the DNA binding site sequence specificities of a large number of TFs from a wide range of organisms, including Vibrio harveyi, Plasmodium falciparum, yeast, worm, fly, mouse, and human. In addition to identifying novel sequence-specific putative regulatory proteins, PBM data aid in the identification of cis regulatory elements and gene regulatory networks, as the resulting binding specificity data allow for improved prediction of genomic TF binding sites and TFs' combinatorial co-regulation of target genes.


To this effect, we have developed computational approaches for analyzing cis regulatory modules (including transcriptional enhancers). We have developed algorithms that include a rigorous statistical consideration of TF binding site clustering, their combinatorial co-occurrences, and cross-species conservation in order to identify candidate cis regulatory modules (CRMs). We have seen that our predicted CRMs are bound by the corresponding TFs in mammalian cells, and that predicted transcriptional enhancers drive temporal- and cell-specific gene expression in the developing Drosophila embryo. A newer algorithm of ours can refine a prior hypothesis of TFs' combinatorial co-regulation of the expression of their target genes. These and newer strategies under development in our lab can be applied widely for analyzing metazoan transcriptional regulatory networks.

Publications 

Original Research

*Grove CA, *de Masi F, Barrasa MI, Newburger DE, Alkema MJ, †Bulyk ML, †Walhout AJM. A multi-parameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (accepted) (*co-1st authors; †co-corresponding authors).
*Badis G, *Berger MF, *Philippakis AA, *Talukder S, *Gehrke AR, *Jaeger SA, *Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang C-F, Coburn D, Newburger D, Morris QD, †Hughes TR, †Bulyk ML. Diversity and complexity in DNA recognition by transcription factors. Science. (accepted) (*co-1st authors; †co-corresponding authors).
†Estep PW III, Warner JB, Bulyk ML. Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways. PLoS ONE (2009) 4(4):e5242- (†corresponding author: This e-mail address is being protected from spambots. You need JavaScript enabled to view it )
Lesch BJ, Gehrke AR, Bulyk ML, Bargmann CI. Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans. Genes and Development (2009) 23(3):345-58.
*Zhu C, *Byers K, *McCord RP, Shi Z, Berger MF, Newburger D, Saulrieta K, Smith Z, Shah M, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A , Murthy TVS, LaBaer J, Bulyk ML. High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors. Genome Research. 2009 Apr;19(4):556-66. Epub 2009 Jan 21. doi:10.1101/gr.090233.108 (*co-1st authors). Supplemental Information
Berger MF and Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature Protocols. (2009) 4(3):393-411
Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR. Predicting the Binding Preference of Transcription Factors to Individual DNA k-mers. Bioinformatics. 2009 Apr 15;25(8):1012-8. Epub 2008 Dec 16.
Scharer CD, McCabe CD, Ali-Seyed M, Berger MF, Bulyk ML, Moreno CS. Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer. Cancer Research. January 15, 2009. 69(2). Supplemental Information
Viiri KM, Janis J, Siggers T, Heinonen TY, Valjakka J, Bulyk ML, Maki M, Lohi O. DNA-binding and -bending activities of SAP30L and SAP30 are mediated by a zinc-dependent module and monophosphoinositides. Mol Cell Biol. 2009 Jan;29(2):342-56. Epub 2008 Nov 17.
Newburger DE and Bulyk ML. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucl. Acids Res. 2009 37: D77-D82; doi:10.1093/nar/gkn660. Epub October 8, 2008. Click here to access the UniPROBE database.
Pompeani AJ, Irgon JJ, Berger MF, Bulyk ML, Wingreen NS, and Bassler BL. The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Molecular Microbiology. (2008) 70(1):76-88.
 A Faculty of 1000 Recommended. Supplemental Information
*Berger MF, *Badis G, *Gehrke AR, *Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, †Bulyk ML, †Hughes TR. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell June 27, 2008; 133:1266-1276 (doi:10.1016/j.cell.2008.05.024) (*co-1st authors; †co-corresponding authors). Supplemental Data. Additional Supplementary Information. Click here to access the mouse homeodomains PBM database.
De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398 (10.1073/pnas.0801993105).
 A Faculty of 1000 Must Read.Supplemental Information
*Warner JB, *Philippakis AA, *Jaeger SA, He FS, Lin J, Bulyk ML. Systematic identification of mammalian regulatory motifs' target genes and functions. Nature Methods. 2008 Apr; 5(4):347-53. Epub 2008 Mar 2 (10.1038/nmeth.1188) (* co-1st authors) Supplementary Information. Read the News and Views highlight of this paper in Nature Methods.
McCord RP and Bulyk ML. Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Pacific Symposium on Biocomputing 13:441-452 (2008). Supplementary Information.
Choi Y, Qin Y, Berger MF, Ballow DJ, Bulyk ML, Rajkovic A. Microarray Analyses of Newborn Mouse Ovaries Lacking Nobox. Biology of Reproduction 2007 Jul;77(2):312-9. Epub 2007 May 9.
McCord RP, Berger MF, Philippakis AA, Bulyk ML. Inferring condition-specific transcription factor function from DNA binding and gene expression. Molecular Systems Biology, 2007; 3:100. Supplemental Information.
Yanhui Hu, Andreas Rolfs, Bhupinder Bhullar, Tellamraju V. S. Murthy, Cong Zhu, Michael F. Berger, Anamaria A. Camargo, Fontina Kelley, Seamus McCarron, Daniel Jepson, Aaron Richardson, Jacob Raphael, Donna Moreira, Elena Taycher, Dongmei Zuo, Stephanie Mohr, Michael F. Kane, Janice Williamson, Andrew Simpson, Martha L. Bulyk, Edward Harlow, Gerald Marsischky, Richard D. Kolodner and Joshua LaBaer. Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae. Genome Research 2007 Apr;17(4):536-43.Epub 2007 Feb 23.
*Philippakis AA, *Qureshi A, Berger MF, Bulyk ML. Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. RECOMB 2007, published in Journal of Computational Biology (2008) 15(7):655-665, doi: 10.1089/cmb.2007.0114 (* co-1st authors)
*Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors) Supplemental Information.
*Philippakis AA, *Busser B, Gisselbrecht SS, He FS, Estrada B, Michelson AM, Bulyk ML. Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells. PLoS Computational Biology, (2006) 2(5):e53. (* co-1st authors)
Huber BR and Bulyk ML. Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. BMC Bioinformatics. 2006; 7:229.
*Philippakis AA, *He FS, Bulyk ML. ModuleFinder: a tool for computational discovery of cis regulatory modules. Pacific Symposium on Biocomputing. 2005; p. 519-530. (* co-1st authors)
Click here to get ModuleFinder software.
*Mukherjee S, *Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML. Rapid analysis of the DNA binding specificities of transcription factors with DNA microarrays. Nature Genetics. 2004 Dec; 36(12):1331-1339. Epub 2004 Nov 14. (* co-1st authors) Supplemental Information. Read the highlight of this paper in Nature Methods.
 Faculty of 1000 Recommended.
*Bulyk ML, *McGuire AM, Masuda N, Church GM. A motif co-occurrence approach for genome-wide prediction of transcription factor binding sites in E. coli. Genome Research. 2004; 14(2):201-208. (* co-1st authors)
Lee M-LT, Bulyk ML, Whitmore GA, Church GM. A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics. 2002 Dec; 58(4):981-988.
Benos P, Bulyk ML, Stormo GD. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Research. 2002; 30(20):4442-4451.
Bulyk ML, Johnson PLF, Church GM. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Research 2002 Mar 1; 30(5):1255-1261. Supplemental data.
Bulyk ML, Huang XH, Choo Y, Church GM. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. U.S.A. 2001 Jun 12; 98(13):7158-7163. Supplemental data. (News & Comment in Trends in Genetics)
Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J. Comparison of systematic computations on the human genome. Nature 2001 Feb 15; 409:856-9.
Bulyk ML, Gentalen E, Lockhart DJ, Church GM. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nature Biotechnology 1999 Jun; 17(6):573-7.
Flores JF, Walker GJ, Glendening JM, Haluska FG, Castresana JS, Rubio MP, Pastorfide GC, Boyer LA, Kao WH, Bulyk ML, Barnhill RL, Hayward NK, Housman DE, Fountain JW. Loss of the p16INK4a and p15INK4b genes, as well as neighboring 9p21 markers, in sporadic melanoma. Cancer Research 1996 Nov 1; 56(21):5023-32.

Review articles, commentaries, book chapters, etc.

Busser BW, †Bulyk ML, †Michelson AM. Toward a systems-level understanding of developmental regulatory networks. Current Opinion in Genetics & Development. (2008) 18:521-529. Epub 2008 Oct 9 (†co-corresponding authors)
Bulyk ML. DNA microarray technologies for measuring protein-DNA interactions. Current Opinion in Biotechnology. 2006 July 11; 17(4)
Bulyk ML. Protein binding microarrays for the characterization of protein-DNA interactions. Chapter in "Analytics of protein-DNA interactions", 2007, volume 104, pages 65-85, Advances in Biochemical Engineering / Biotechnology.Springer-Verlag, Inc. Edited by Harald Steitz.
Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenetic and Genome Research 114:1-15 (2006)
Michelson AM and Bulyk ML. Biological code breaking in the 21st century. Molecular Systems Biology. 2006; 2:2006.0018. Epub 2006 May 2 (News & Views).
Berger MF and Bulyk ML. Protein binding microarrays (PBMs) for the rapid, high-throughout characterization of the sequence specificities of DNA binding proteins. Chapter 13 in "Gene mapping, discovery, and expression", 2006; Volume 338, pages 245-260, Methods in Molecular Biology. The Humana Press, Inc. Edited by Minou Bina.
Bulyk ML. Determining DNA binding specificity using microarrays. Chapter 15 in DNA "Microarrays Part A: Array Platforms and Wet-Bench Protocols" 2006, volume 411, pages 276-296, Methods in Enzymology. Elsevier Life Sciences. Edited by Brian Oliver and Alan Kimmel.
Bulyk ML. Discovering DNA regulatory elements with bacteria. Nature Biotechnology. 2005 Aug; 23(8):942-4. (News & Views)
Bulyk ML. Integrative functional genomics. Genome Biology. 2004; 5:331. (Meeting Report)
Bulyk ML. Computational prediction of transcription-factor binding site locations. Genome Biology. 2003; 5(1):201. (Click here for the abridged version.)

Patents

United States Patent 6,548,021. Church GM and Bulyk ML. "Surface-bound, double-stranded DNA protein arrays". April 15, 2003.
International Patent Application No. WO 02/18648 A2. Church GM, Bulyk ML, and Choo Y. "Analysis of Binding Interactions". March 7, 2002.
United States Patent 6,326,489. Church GM and Bulyk ML. "Surface-bound, bimolecular, double-stranded DNA arrays". December 4, 2001.