Gregory E. Crawford

Professor in Pediatrics

My primary research interest is understanding how the genome is regulated.  The human genome contains approximately 25,000 genes, which are encoded in ~2% of the genome. The overarching goal of my research program is to identify and characterize how these genes are turned on and off in different cell types, tissues, development states, environmental responses, diseases, and individuals. By understanding where all gene regulatory elements are located, how they work to regulate gene expression, and how non-coding variants within these regions affect function, my research program can address a number of important basic and clinical questions.

Appointments and Affiliations

  • Professor in Pediatrics
  • Associate Professor in Molecular Genetics and Microbiology
  • Affiliate of the Duke Regeneration Center

Contact Information

  • Office Location: Room 2111 Ciemas, Durham, NC 27708
  • Office Phone: +1 919 684 8196
  • Email Address: greg.crawford@duke.edu
  • Websites:

Education

  • Ph.D. University of Michigan, Ann Arbor, 2001
  • National Institutes of Health, 2006

Courses Taught

  • UPGEN 778B: University Program in Genetics and Genomics Biological Solutions Module Il
  • UPGEN 778A: University Program in Genetics and Genomics Biological Solutions Module I

In the News

Representative Publications

  • Shibata, Yoichiro, Nathan C. Sheffield, Olivier Fedrigo, Courtney C. Babbitt, Matthew Wortham, Alok K. Tewari, Darin London, et al. “Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.” PLoS Genet 8, no. 6 (June 2012): e1002789. https://doi.org/10.1371/journal.pgen.1002789.
  • Balasubramanian, Dheepa, Batool Akhtar-Zaidi, Lingyun Song, Cynthia F. Bartels, Martina Veigl, Lydia Beard, Lois Myeroff, et al. “H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites.” Genome Medicine 4, no. 5 (May 2012): 47. https://doi.org/10.1186/gm346.
  • Reddy, Timothy E., Jason Gertz, Florencia Pauli, Katerina S. Kucera, Katherine E. Varley, Kimberly M. Newberry, Georgi K. Marinov, et al. “Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.” Genome Research 22, no. 5 (May 2012): 860–69. https://doi.org/10.1101/gr.131201.111.
  • Bischof, Jared M., Christopher J. Ott, Shih-Hsing Leir, Nehal Gosalia, Lingyun Song, Darin London, Terrence S. Furey, Calvin U. Cotton, Gregory E. Crawford, and Ann Harris. “A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function.” Thorax 67, no. 5 (May 2012): 385–91. https://doi.org/10.1136/thoraxjnl-2011-200880.
  • Degner, Jacob F., Athma A. Pai, Roger Pique-Regi, Jean-Baptiste Veyrieras, Daniel J. Gaffney, Joseph K. Pickrell, Sherryl De Leon, et al. “DNase I sensitivity QTLs are a major determinant of human expression variation.” Nature 482, no. 7385 (February 5, 2012): 390–94. https://doi.org/10.1038/nature10808.
  • Gaffney, Daniel J., Jean-Baptiste Veyrieras, Jacob F. Degner, Roger Pique-Regi, Athma A. Pai, Gregory E. Crawford, Matthew Stephens, Yoav Gilad, and Jonathan K. Pritchard. “Dissecting the regulatory architecture of gene expression QTLs.” Genome Biol 13, no. 1 (January 31, 2012): R7. https://doi.org/10.1186/gb-2012-13-1-r7.
  • Zhang, W., Y. Wu, J. C. Schnable, Z. Zeng, M. Freeling, G. E. Crawford, and J. Jiang. “High-resolution mapping of open chromatin in the rice genome.” Genome Research 22, no. 1 (January 2012): 151–62. https://doi.org/10.1101/gr.131342.111.
  • Lee, B. K., A. A. Bhinge, A. Battenhouse, R. M. McDaniell, Z. Liu, L. Song, Y. Ni, et al. “Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.” Genome Research 22, no. 1 (January 2012): 9–24. https://doi.org/10.1101/gr.127597.111.
  • Song, Lingyun, Zhancheng Zhang, Linda L. Grasfeder, Alan P. Boyle, Paul G. Giresi, Bum-Kyu Lee, Nathan C. Sheffield, et al. “Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.” Genome Res 21, no. 10 (October 2011): 1757–67. https://doi.org/10.1101/gr.121541.111.
  • Wu, Weisheng, Yong Cheng, Cheryl A. Keller, Jason Ernst, Swathi Ashok Kumar, Tejaswini Mishra, Christapher Morrissey, et al. “Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.” Genome Res 21, no. 10 (October 2011): 1659–71. https://doi.org/10.1101/gr.125088.111.
  • Tsumagari, Koji, Shao-Chi Chang, Michelle Lacey, Carl Baribault, Sridar V. Chittur, Janet Sowden, Rabi Tawil, Gregory E. Crawford, and Melanie Ehrlich. “Gene expression during normal and FSHD myogenesis.” BMC Med Genomics 4 (September 27, 2011): 67. https://doi.org/10.1186/1755-8794-4-67.
  • Boyle, Alan P., Lingyun Song, Bum-Kyu Lee, Darin London, Damian Keefe, Ewan Birney, Vishwanath R. Iyer, Gregory E. Crawford, and Terrence S. Furey. “High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.” Genome Res 21, no. 3 (March 2011): 456–64. https://doi.org/10.1101/gr.112656.110.
  • Stitzel, Michael L., Praveen Sethupathy, Daniel S. Pearson, Peter S. Chines, Lingyun Song, Michael R. Erdos, Ryan Welch, et al. “Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.” Cell Metab 12, no. 5 (November 3, 2010): 443–55. https://doi.org/10.1016/j.cmet.2010.09.012.
  • Birney, Ewan, Jason D. Lieb, Terrence S. Furey, Gregory E. Crawford, and Vishwanath R. Iyer. “Allele-specific and heritable chromatin signatures in humans.” Hum Mol Genet 19, no. R2 (October 15, 2010): R204–9. https://doi.org/10.1093/hmg/ddq404.
  • Balasubramani, Anand, Yoichiro Shibata, Gregory E. Crawford, Albert S. Baldwin, Robin D. Hatton, and Casey T. Weaver. “Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli.” Immunity 33, no. 1 (July 23, 2010): 35–47. https://doi.org/10.1016/j.immuni.2010.07.004.
  • Schnetz, Michael P., Lusy Handoko, Batool Akhtar-Zaidi, Cynthia F. Bartels, C Filipe Pereira, Amanda G. Fisher, David J. Adams, et al. “CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.” PLoS Genet 6, no. 7 (July 15, 2010): e1001023. https://doi.org/10.1371/journal.pgen.1001023.
  • Mukasa, Ryuta, Anand Balasubramani, Yun Kyung Lee, Sarah K. Whitley, Benjamin T. Weaver, Yoichiro Shibata, Gregory E. Crawford, Robin D. Hatton, and Casey T. Weaver. “Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage.” Immunity 32, no. 5 (May 28, 2010): 616–27. https://doi.org/10.1016/j.immuni.2010.04.016.
  • McDaniell, Ryan, Bum-Kyu Lee, Lingyun Song, Zheng Liu, Alan P. Boyle, Michael R. Erdos, Laura J. Scott, et al. “Heritable individual-specific and allele-specific chromatin signatures in humans.” Science 328, no. 5975 (April 9, 2010): 235–39. https://doi.org/10.1126/science.1184655.
  • Song, Lingyun, and Gregory E. Crawford. “DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.” Cold Spring Harb Protoc 2010, no. 2 (February 2010): pdb.prot5384. https://doi.org/10.1101/pdb.prot5384.
  • Xu, Xueqing, Koji Tsumagari, Janet Sowden, Rabi Tawil, Alan P. Boyle, Lingyun Song, Terrence S. Furey, Gregory E. Crawford, and Melanie Ehrlich. “DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.” Nucleic Acids Research 37, no. 22 (December 2009): 7381–93. https://doi.org/10.1093/nar/gkp833.
  • Ott, Christopher J., Neil P. Blackledge, Jenny L. Kerschner, Shih-Hsing Leir, Gregory E. Crawford, Calvin U. Cotton, and Ann Harris. “Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus.” Proc Natl Acad Sci U S A 106, no. 47 (November 24, 2009): 19934–39. https://doi.org/10.1073/pnas.0900946106.
  • Heintzman, Nathaniel D., Gary C. Hon, R David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, et al. “Histone modifications at human enhancers reflect global cell-type-specific gene expression.” Nature 459, no. 7243 (May 7, 2009): 108–12. https://doi.org/10.1038/nature07829.
  • Ott, Christopher J., Magdalena Suszko, Neil P. Blackledge, Jane E. Wright, Gregory E. Crawford, and Ann Harris. “A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter.” J Cell Mol Med 13, no. 4 (April 2009): 680–92. https://doi.org/10.1111/j.1582-4934.2008.00621.x.
  • Bina, Minou, Phillip Wyss, Sheryl A. Lazarus, Syed R. Shah, Wenhui Ren, Wojciech Szpankowski, Gregory E. Crawford, Sang P. Park, and Xiaohui C. Song. “Discovering sequences with potential regulatory characteristics.” Genomics 93, no. 4 (April 2009): 314–22. https://doi.org/10.1016/j.ygeno.2008.11.008.
  • Schnetz, M. P., C. F. Bartels, K. Shastri, D. Balasubramanian, G. E. Zentner, R. Balaji, X. Zhang, et al. “Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns.” Genome Research 19, no. 4 (April 2009): 590–601. https://doi.org/10.1101/gr.086983.108.
  • Shibata, Yoichiro, and Gregory E. Crawford. “Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).” Methods Mol Biol 556 (2009): 177–90. https://doi.org/10.1007/978-1-60327-192-9_13.
  • Boyle, Alan P., Justin Guinney, Gregory E. Crawford, and Terrence S. Furey. “F-Seq: a feature density estimator for high-throughput sequence tags.” Bioinformatics 24, no. 21 (November 1, 2008): 2537–38. https://doi.org/10.1093/bioinformatics/btn480.
  • Boyle, Alan P., Sean Davis, Hennady P. Shulha, Paul Meltzer, Elliott H. Margulies, Zhiping Weng, Terrence S. Furey, and Gregory E. Crawford. “High-resolution mapping and characterization of open chromatin across the genome.” Cell 132, no. 2 (January 25, 2008): 311–22. https://doi.org/10.1016/j.cell.2007.12.014.
  • Eguchi, Jun, Qing-Wu Yan, Dustin E. Schones, Michael Kamal, Chung-Hsin Hsu, Michael Q. Zhang, Gregory E. Crawford, and Evan D. Rosen. “Interferon regulatory factors are transcriptional regulators of adipogenesis.” Cell Metab 7, no. 1 (January 2008): 86–94. https://doi.org/10.1016/j.cmet.2007.11.002.
  • Xi, Hualin, Hennady P. Shulha, Jane M. Lin, Teresa R. Vales, Yutao Fu, David M. Bodine, Ronald D. G. McKay, et al. “Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.” PLoS Genet 3, no. 8 (August 2007): e136. https://doi.org/10.1371/journal.pgen.0030136.
  • ENCODE Project Consortium, Pieter J., Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R. Gingeras, Elliott H. Margulies, et al. “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.” Nature 447, no. 7146 (June 14, 2007): 799–816. https://doi.org/10.1038/nature05874.
  • Heintzman, Nathaniel D., Rhona K. Stuart, Gary Hon, Yutao Fu, Christina W. Ching, R David Hawkins, Leah O. Barrera, et al. “Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.” Nat Genet 39, no. 3 (March 2007): 311–18. https://doi.org/10.1038/ng1966.
  • Nagel, Stefan, Michaela Scherr, Alexander Kel, Klaus Hornischer, Gregory E. Crawford, Maren Kaufmann, Corinna Meyer, Hans G. Drexler, and Roderick A. F. MacLeod. “Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1.” Cancer Res 67, no. 4 (February 15, 2007): 1461–71. https://doi.org/10.1158/0008-5472.CAN-06-2615.
  • Crawford, Gregory E., Sean Davis, Peter C. Scacheri, Gabriel Renaud, Mohamad J. Halawi, Michael R. Erdos, Roland Green, Paul S. Meltzer, Tyra G. Wolfsberg, and Francis S. Collins. “DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.” Nat Methods 3, no. 7 (July 2006): 503–9. https://doi.org/10.1038/nmeth888.
  • Bernat, John A., Gregory E. Crawford, Aleksey Y. Ogurtsov, Francis S. Collins, David Ginsburg, and Alexey S. Kondrashov. “Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs.” Hum Mol Genet 15, no. 13 (July 1, 2006): 2098–2105. https://doi.org/10.1093/hmg/ddl133.
  • Lewinski, Mary K., Masahiro Yamashita, Michael Emerman, Angela Ciuffi, Heather Marshall, Gregory Crawford, Francis Collins, et al. “Retroviral DNA integration: viral and cellular determinants of target-site selection.” PLoS Pathog 2, no. 6 (June 2006): e60. https://doi.org/10.1371/journal.ppat.0020060.
  • Scacheri, Peter C., Sean Davis, Duncan T. Odom, Gregory E. Crawford, Stacie Perkins, Mohamad J. Halawi, Sunita K. Agarwal, et al. “Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis.” PLoS Genet 2, no. 4 (April 2006): e51. https://doi.org/10.1371/journal.pgen.0020051.
  • Yan, Jizhou, Lisha Xu, Gregory Crawford, Zenfeng Wang, and Shawn M. Burgess. “The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure.” Mol Cell Biol 26, no. 1 (January 2006): 155–68. https://doi.org/10.1128/MCB.26.1.155-168.2006.
  • Scacheri, Peter C., Gregory E. Crawford, and Sean Davis. “Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays.” Methods Enzymol 411 (2006): 270–82. https://doi.org/10.1016/S0076-6879(06)11014-9.
  • Crawford, Gregory E., Ingeborg E. Holt, James Whittle, Bryn D. Webb, Denise Tai, Sean Davis, Elliott H. Margulies, et al. “Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).” Genome Res 16, no. 1 (January 2006): 123–31. https://doi.org/10.1101/gr.4074106.
  • Crawford, Gregory E., Ingeborg E. Holt, James C. Mullikin, Denise Tai, Robert Blakesley, Gerard Bouffard, Alice Young, et al. “Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites.” Proc Natl Acad Sci U S A 101, no. 4 (January 27, 2004): 992–97. https://doi.org/10.1073/pnas.0307540100.
  • Crawford, G. E., Q. L. Lu, T. A. Partridge, and J. S. Chamberlain. “Suppression of revertant fibers in mdx mice by expression of a functional dystrophin.” Hum Mol Genet 10, no. 24 (November 15, 2001): 2745–50. https://doi.org/10.1093/hmg/10.24.2745.
  • Crawford, G. E., J. A. Faulkner, R. H. Crosbie, K. P. Campbell, S. C. Froehner, and J. S. Chamberlain. “Assembly of the dystrophin-associated protein complex does not require the dystrophin COOH-terminal domain.” J Cell Biol 150, no. 6 (September 18, 2000): 1399–1410. https://doi.org/10.1083/jcb.150.6.1399.
  • Lumeng, C., S. Phelps, G. E. Crawford, P. D. Walden, K. Barald, and J. S. Chamberlain. “Interactions between beta 2-syntrophin and a family of microtubule-associated serine/threonine kinases.” Nat Neurosci 2, no. 7 (July 1999): 611–17. https://doi.org/10.1038/10165.