Matthew Slattery, PhD

Associate Professor, Medical School, Duluth Campus

Matthew Slattery

Contact Info

Office Phone 218-726-7223

Fax 218-726-8014

Office Address:
Department of Biomedical Sciences
255 SMed
1035 University Drive
Duluth, MN 55812

Associate Professor, Medical School, Duluth Campus

Department of Biomedical Sciences

Postdoc, Columbia University and University of Chicago

PhD, Pharmaceutical Sciences, University of Wisconsin

BS, Pharmacology/Toxicology, University of Wisconsin


Professional Associations


Research Summary/Interests

Whole genome sequencing has become increasingly straightforward in recent years, though our understanding of the regulatory genome – the noncoding portion of the genome dictating where, when, and to what level genes are expressed – remains incomplete. Research in the Slattery lab explores the mechanisms by which transcription factors interact with noncoding regulatory DNA elements, also known as enhancers, to influence cell fate decisions. We use an integrative approach centered on three major themes – DNA binding specificity, context-specific genomics, and cis-regulatory element dissection – to characterize gene regulatory networks controlling the response to environmental stress. Importantly, this approach also allows us to identify and test noncoding DNA variants linking the response to cell stress with various disease states.



1. Lacher SE, Slattery M*. Gene regulatory effects of disease-associated variation in the NRF2 network. Current Opinion in Toxicology. 1:71-79, 2016. [Review] *Corresponding author

2. Wang X, Campbell MR, Lacher SE, Cho HY, Wan M, Crowl CL, Chorley BN, Bond GL, Kleeberger SR, Slattery M, Bell DA. A polymorphic antioxidant response element links NRF2/sMAF binding to enhanced MAPT expression and reduced risk of parkinsonian disorders. Cell Reports. 15(4):830-42, 2016.

3. Zhang Y, Lee JK, Toso EA, Lee JS, Choi SH, Slattery M, Aihara H, Kyba M. DNA-binding sequence specificity of DUX4. Skeletal Muscle. 6:8, 2016.

4. Loganathan R, Lee JS, Wells MB, Grevengoed E, Slattery M, Andrew DJ. Ribbon regulates morphogenesis of the Drosophila embryonic salivary gland through transcriptional activation and repression. Developmental Biology. 409(1):234-50, 2016.

5. Lacher SE, Lee JS, Wang X, Campbell MR, Bell DA, Slattery M*. Beyond antioxidant genes in the ancient NRF2 regulatory network. Free Radical Biology & Medicine. 88(Pt B):452-65, 2015. *Corresponding author

6. Bieli D, Kanca O, Córdoba S, Hamaratoglu F, Gohl D, Schedl P, Affolter M, Slattery M, Müller M, Estella C. Establishment of a developmental compartment requires interactions between three synergistic cis-regulatory modules. PLoS Genetics. 11(10):e1005376, 2015.

7. Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS. Deconvolving the recognition of DNA shape from sequence. Cell. 161(2):307-18, 2015.

8. Slattery M*, Zhou T, Yang L, Dantas Machado AC, Gordan R*, Rohs R*. Absence of a simple code: How transcription factors read the genome. Trends in Biochemical Sciences. 39(9):381-99, 2014. [Review] *Corresponding authors

9. Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, Obar RA, White KP, Celniker SE, Przytycka T, Gygi SP, Artavanis-Tsakonas S. Transcription Factor Networks in Drosophila melanogaster. Cell Reports. 8(6):2031-43, 2014.

10. Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng, Y, Gardner K, Hillier L, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Comparative analysis of regulatory information and circuits across distant species. Nature. 512(7515):453-6, 2014.

11. Oh H, Slattery M, Ma L, White KP, Mann RS, Irvine KD. Yorkie Promotes Transcription by Recruiting a Histone Methyltransferase Complex. Cell Reports. 8(2):449-59, 2014.

12. Riley T*, Slattery M*, Mann RS, Bussemaker HJ. SELEX-seq, a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. Methods in Molecular Biology. 1196:255-78, 2014. *Equal contribution

13. Slattery M*, Ma L*, Spokony RF*, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel B,Grundstad AJ, Gao W, Moran JR, EJ, Grossman RL, Kellis M, White KP. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Research24(7):1224-35, 2014. *Equal contribution

14. Arthur R, Ma L, Slattery M, Spokony R, Ostapenko A, Négre N, White KP. Evolution of histone H3 lysine 27 trimethylation in Drosophila is linked to gene expression evolution and to patterns of gene duplication and diversification. Genome Research. 24(7):1115-24, 2014.

15. Slattery M*, White KP*. Enhanced dissection of the regulatory genome. Nature Methods. 10(8):710-2, 2013 [Commentary/News & Views] *Corresponding authors

16. Slattery M, Voutev R, Ma L, Négre N, White KP, Mann RS. Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. PLoS Genetics. 9(9):e1003753, 2013.

17. Hattori T, Taft J, Swist K, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Strahl BD, White KP,Farnham PJ, Zhao Y, Koide S. Renewable, recombinant antibodies to histone posttranslational modifications. Nature Methods. 10(10):992-5, 2013.

18. Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD. Association of Yorkie with chromatin and chromatin remodeling complexes. Cell Reports. 3(2):309-18, 2013.

19. Jory A, Estella C, Giorgianni MW, Slattery M, Laverty TR, Rubin GM, and Mann RS. A survey of 6300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Reports. 2(4):1014-24, 2012.

20. Nagaraj R, Rao S, Jones K, Slattery M, Négre N, Christofk H, White KP, Mann RS, Banerjee U. Control of mitochondrial structure and function by the Yorkie/YAP oncogenic pathway. Genes & Development. 26(18):2027-37, 2012.

21. Slattery M, Négre N, White KP. Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster. Briefings in Functional Genomics. 11(5):336-46, 2012. [Review]

22. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein B, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Katherine Fisher-Aylor K, Euskirchen G, Gerstein M, Gertz J, Guigo R?, Hartemink AJ, Hoffman MM, Iyer V, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White K, Xi S, Farnham P, Lieb J, Wold B, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE Consortia. Genome Research. 22(9): 1813-31, 2012.

23. Chen Y, Négre N, Li Q, Mieczkowska JO, Slattery M, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS. Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods. 9(6):609-14, 2012.

24. Lelli K, Slattery M, Mann RS. Disentangling the many layers of eukaryotic transcriptional regulation. Annual Reviews of Genetics. 46:43-68, 2012. [Review]

25. Slattery M*, Riley T*, Liu P*, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. 147(6): 1270-82, 2011. *Equal contribution

26. Slattery M, Ma L, Négre N, White KP, Mann RS. Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. PLoS One. 6(4):e14686, 2011.

27. Peng W, Slattery M, Mann RS. Transcription factor choice in the Hippo signaling pathway: homothorax and yorkie regulation of the microRNA bantam in the progenitor domain of the Drosophila eye imaginal disc. Genes & Development. 23(19):2307-19, 2009.

28. Affolter M, Slattery M, Mann RS. A lexicon for homeodomain-DNA recognition. Cell. 133(7):1133-5, 2008 [Commentary/Preview]

29. Slattery MG, Liko D, Heideman W. PKA, TOR and glucose transport control the response to nutrient repletion in Saccharomyces cerevisiae. Eukaryotic Cell. 7(2):358-67, 2008.

30. Liko D, Slattery MG, Heideman W. Stb3 binds to RRPE motifs that control transcriptional responses to growth in Saccharomyces cerevisiae. Journal of Biological Chemistry. 282(36):26623-8, 2007.

31. Slattery MG, Heideman W. Coordinated regulation of growth genes in Saccharomyces cerevisiae. Cell Cycle. 6(10):1210-9, 2007.

32. Kanin EI, Kipp RT, Kung C, Slattery M, Viale A, Hahn S, Shokat KM, Ansari AZ. Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis. Proceedings of the National Academy of Sciences. 104(14):5812-7, 2007.

33. Liko D, Slattery MG, Phillips CL, Heideman W. Using the yeast gene deletion collection to customize gene expression. Biotechniques. 40(6):728-32, 2006.

34. Slattery MG, Liko D, Heideman W. The function and properties of the Azf1 transcriptional regulator change with growth conditions in Saccharomyces cerevisiae. Eukaryotic Cell. 5(2):313-20, 2006.

35. Laabs TL, Markwardt DD, Slattery MG, Newcomb LL, Stillman DJ, Heideman W. ACE2 is required for daughter cell-specific G1 delay in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences. 100(18):10275-80, 2003.

36. Newcomb LL, Diderich JA, Slattery MG, Heideman W. Glucose regulation of Saccharomyces cerevisiae cell cycle genes. Eukaryotic Cell. 2(1):143-9, 2003


Teaching Areas

Pharmacology (Neuropharmacology)

Mentoring/Advising: undergraduate students, graduate students, and post doctoral researchers.