2024
Inge MM*, Miller R*, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (2024) NAR PMID: 39166482
Daly AE, Chang AB, Purbey P, Williams KJ, Yeh G, Li S, Pope SD, Venkatesh B, Redelings BD, Li S, Nguyen K, Rodrigues J, Jorgensen K, Siggers T, Chen L, Smale ST. Stepwise neofunctionalization of the NF-kB family member c-Rel during vertebrate evolution. (BioRxiv version here)
2023
Carrion PJA, Desai N, Brennen JJ, Fifer JE, Siggers T, Davies SW, Gilmore TD. Starvation decreases immunity and immune regulatory factor NF-kB in the starlet sea anemone Nematostella vectensis (2023) Commun. Biol 6:698 PMID:37420095
Paul I, Bolzan D, Youssef A, Gagnon K, Hook H, Karemore G, Oliphant M, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen C, Hu P, Denis G, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy S, Emili A. Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT. (2023) Nature Communications 14:688 PMID:36755019
Carrasco Pro S*, Hook H*, Bray D, Berenzy D, Moyer D, Yin M, Labadorf AT, Tewhey R, Siggers T**, Fuxman Bass JI**. Widespread perturbation of ETS factor binding sites in cancer. (2023) Nature Communications 14:913 PMID:36808133 (previous BioRxiv version here)
Gilmore TD, Siggers T (2023) NF-kappaB and the Immune System. In Encyclopedia of Cell Biology, Second Edition (RA Bradshaw, GW Hart, PD Stahl eds) Elsevier. Volume 5:41-426. Oxford, Elsevier.
2022
Bray D*, Hook H*, Zhao R, Keenan JL, Penvose A, Osayame Y, Mohaghegh N, Chen X, Parameswaran S, Kottyan LC, Weirauch MT, Siggers T. (2022) CASCADE: Hight-throughput characterization of regulatory complex binding altered by non-coding variants. Cell Genomics 2:100098 PMID:35252945 (previous BioRxiv version here)
2021
William LM, Sridhar S, Samaroo J, Peart J, Adindu EK, Addanki A, DiRusso CJ, BB522 Molecular Biology Laboratory, Aguirre Carrion PJ, Rodriguez-Sastre N, Siggers T, Gilmore TD. (2021) Comparison of NF-kB from the protists Capsaspora owczarzaki and Acanthoeca spectabilis reveals extensive evolutionary diversification of this transcription factor. Commun Biol. 4(1):1404
Hook H*, Zhao RW*, Bray D, Keenan JL, Siggers T (2021) High-Throughput Analysis of the Cell and DNA Site-Specific Binding of Native NF-kB Dimers using Nuclear Extract Protein-Binding Microarrays (NextPBMs). Methods Mol. Biol. 2366:43-66 PMID:34236632
2020
Williams LM, Inge MM, Mansfield KM, Rasmussen A, Afghani J, Agrba M, Albert C, Andersson C, Babaei M, Babaei M, Badsasaryants A, Bonilla A, Browne A, Carpenter S, Chen T, Christie B, Cyr A, Dam K, Dulock N, Erdene G, Esau L, Esonwune S, Hanchate A, Huang X, Jennings T, Kasabwala A, Kehoe L, Kobayashi R, Lee M, LeVan A, Liu Y, Murphy E, Nambiar A, Olive M, Patel D, Pavesi F, Petty CA, Samofalova Y, Sanchez S, Stejskal C, Tang Y, Yapo A, Cleary JP Jr, Yunes CA, Siggers T, Gilmore T (2020) Transcription factor NF-kB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation. Dev Comp Immunol PMID: 31751628
2019
Bruno L, Ramlall V, Studer RA, Sauer S, Bradley D, Dharmalingam G, Carroll T, Ghoneim M, Chopin M, Nutt SL, Elderkin S, Rueda DS, Fisher AG, Siggers T, Beltrao P, Merkenschlager M (2019) Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system. Nature Immunology 20(10):1372 PMID:31451789
Penvose A*, Keenan J*, Bray D, Ramlall V, Siggers T, (2019) Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding recpetor specificity Nature Communications 10(1):2514 PMID:31175293
Mohaghegh N*, Bray D*, Keenan J, Penvose A, Andrilenas KK, Ramlall V, Siggers T, (2019) NextPBM: A platform to study cell-specific transcription factor binding and cooperativity Nucleic Acids Research 47:e3 PMCID:PMC6451091
2018
Andrilenas KK, Ramlall V, Kurland J, Leung G, Harbaugh AG, Siggers T, (2018) DNA-binding landscape of IRF3, IRF5 and IRF7 dimers: implication for dimer-specific gene regulation Nucleic Acids Research 46:2509-2520 PMID:29361124.
2017
Mansfield KM, Carter NM, Nguyen L, Cleves PA, Alshanbayeva A, William LM, Crowder C, Penvose AR, Finnerty JR, Weis VM, Siggers T, Gilmore TD (2017) Transcription factor NF-kB is modulated by symbiotic status in a sea anemone of cnidarian bleachin Sci Rep.7:16025 PMID:29167511.
2016
Kuzu G, Kaye EG, Chery J, Siggers T, Yang L, Dobson JR, Boor S, Bliss J, Liu W, Jogi, Rohs R, Singh ND, Bulyk ML, Tolstorukov MY, Larschan E (2016) Expansion of GA Dinucleotdie Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation PLoS Genetics 12:e1006120:e1006120.
Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordan R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML (2016) Survey of variation in human transcription factors reveals prevalent DNA binding changes Science 35:1450-1454.
2015
Menke C, Cionni M, Siggers T, Bulyk ML, Beier DR, Stottmann RW (2015) Grhl2 is required in nonneural tissue for neural progenitor survival and forebrain development Genesis 53(9):573-582.
Siggers T**, Gilmore TD, Barron B, Penvose A (2015) Characterizing the DNA binding site specificity of NF-kB with protein-binding microarrays (PBMs) Methods Mol. Biol. 1280:609-630.
Andrilenas K, Penvose A, Siggers T (2015) Using Protein-binding Microarrays to Study Transcription Factor Specificity: Homologs, Isoforms and Complexes Briefings in Functional Genomics 14:17-29.
2014
Siggers T**, Reddy J, Barron B, Bulyk ML** (2014) Diversification of transcription factor paralogs via noncanonical modularity in C2H2 Zinc finger DNA binding Molecular Cell55(4):640-648.
Siggers T**, Gordan R** (2014) Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res. 42(4):1551-1556.
2013
Soruco MM, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E. (2013) The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation Genes Dev. 27(14):1551-1556.
2012
Siggers T*, Chang AB*, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML. (2012). Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding. Nature Immunology 13(1):95-102
Faculty of 1000 Recommended
Click here to access the associated NF-kB PBM database and search tools.
Pre-2012
Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML. (2011). Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Molecular Systems Biology 7:555
Highlighted in Nature Review Genetics
Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk ML, Angelov D, Dimitrov S, Udalova I, Ragoussis J. (2011). Extensive characterization of NF-KappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol. 12(7):R70
Rowan S*, Siggers T*, Lachke SA, Yue Y, Bulyk ML, Maas RL. (2010). Precise temporal control of the eye regulatory gene Pax6 via enhancer binding site affinity. Genes Dev. 24(10):980-985.
Giorgetti L, Siggers T, Tiana G, Caprara G, Notarbartolo S, Corona T, Pasparakis M, Milani P, Bulyk ML, Natoli G. (2010). Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses transcriptional responses to environmental inputs. Mol. Cell. 37(3):418-428.
Highlighted in Nature Review Genetics
Viiri KM, Janis J, Siggers T, Heinonen TY, Valjakka J, Bulyk ML, Maki M, Lohi O. (2009). DNA-binding and -bending activities of SAP30L and SAP30 are mediated by a zinc-dependent module and monophosphoinositides. Mol. Cell Biol. 29:342-356.
Siggers T, Honig B. (2007). Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res. 35(5):1085-1097
Siggers T, Silkov A, Honig B. (2005). Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity. JMB 345(5):1027-1045.
* Authors contributed equally
** Co-corresponding authors
