2025
Stepwise neofunctionalization of the NF-kB family member c-Rel during vertebrate evolution.
Nature Immunology (accepted) (BioRxiv version here)
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.
2024
Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation
NAR PMID: 39166482
Inge MM*, Miller R*, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T
Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming
PLoS Biol. PMID: 39689157
Lawton ML, Inge MM, Blum BC, Smith-Mahoney EL, Bolzan D, Lin W, McConney C, Porter J, Moore J, Youssef A, Tharani Y, Varelas X, Denis GV, Wong WW, Padhorny D, Kozakov D, Siggers T, Wuchty S, Snyder-Cappione J, Emili A
2023
Starvation decreases immunity and immune regulatory factor NF-kB in the starlet sea anemone Nematostella vectensis
Commun. Biol 6:698 PMID:37420095
Carrion PJA, Desai N, Brennen JJ, Fifer JE, Siggers T, Davies SW, Gilmore TD.
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.
Nature Communications 14:688 PMID:36755019
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.
Widespread perturbation of ETS factor binding sites in cancer.
Nature Communications 14:913 PMID:36808133 (previous BioRxiv version here)
Carrasco Pro S*, Hook H*, Bray D, Berenzy D, Moyer D, Yin M, Labadorf AT, Tewhey R, Siggers T**, Fuxman Bass JI**.
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.
Gilmore TD, Siggers T
2022
CASCADE: High-throughput characterization of regulatory complex binding altered by non-coding variants.
Cell Genomics 2:100098 PMID:35252945 (previous BioRxiv version here)
Bray D*, Hook H*, Zhao R, Keenan JL, Penvose A, Osayame Y, Mohaghegh N, Chen X, Parameswaran S, Kottyan LC, Weirauch MT, Siggers T.
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
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.
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
Hook H*, Zhao RW*, Bray D, Keenan JL, Siggers T (2021)
2020
Transcription factor NF-kB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation.
Dev Comp Immunol PMID: 31751628
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
2019
Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.
Nature Immunology 20(10):1372 PMID:31451789
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
Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity
Nature Communications 10(1):2514 PMID:31175293
Penvose A*, Keenan J*, Bray D, Ramlall V, Siggers T, (
NextPBM: A platform to study cell-specific transcription factor binding and cooperativity
Nucleic Acids Research 47:e3 PMCID:PMC6451091
Mohaghegh N*, Bray D*, Keenan J, Penvose A, Andrilenas KK, Ramlall V, 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.
Andrilenas KK, Ramlall V, Kurland J, Leung G, Harbaugh AG, Siggers T,
2017
Transcription factor NF-kB is modulated by symbiotic status in a sea anemone of cnidarian bleaching
Sci Rep.7:16025 PMID:29167511.
Mansfield KM, Carter NM, Nguyen L, Cleves PA, Alshanbayeva A, William LM, Crowder C, Penvose AR, Finnerty JR, Weis VM, Siggers T, Gilmore TD
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.
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
Survey of variation in human transcription factors reveals prevalent DNA binding changes
Science 35:1450-1454.
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
Grhl2 is required in nonneural tissue for neural progenitor survival and forebrain development
Genesis 53(9):573-582.
Menke C, Cionni M, Siggers T, Bulyk ML, Beier DR, Stottmann RW
Characterizing the DNA binding site specificity of NF-kB with protein-binding microarrays (PBMs)
Methods Mol. Biol. 1280:609-630.
Siggers T**, Gilmore TD, Barron B, Penvose A
Using Protein-binding Microarrays to Study Transcription Factor Specificity: Homologs, Isoforms and Complexes
Briefings in Functional Genomics 14 :17-29.
Andrilenas K, Penvose A, Siggers T
2014
Diversification of transcription factor paralogs via noncanonical modularity in C2H2 Zinc finger DNA binding
Molecular Cell 55(4):640-648.
Siggers T**, Reddy J, Barron B, Bulyk ML**
Protein-DNA binding: complexities and multi-protein codes.
Nucleic Acids Res. 42(4):1551-1556.
Siggers T**, Gordan R**
2013
The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation
Genes Dev. 27(14):1551-1556.
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.
2012
Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding.
Nature Immunology 13(1):95-102
Siggers T*, Chang AB*, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML.
Faculty of 1000 Recommended
Click here to access the associated NF-kB PBM database and search tools.
Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.
Molecular Systems Biology 7:555
Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML.
Highlighted in Nature Review Genetics
2011
Extensive characterization of NF-KappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits.
Genome Biol. 12(7):R70
Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk ML, Angelov D, Dimitrov S, Udalova I, Ragoussis J.
2010
Precise temporal control of the eye regulatory gene Pax6 via enhancer binding site affinity.
Genes Dev. 24(10):980-985.
Rowan S*, Siggers T*, Lachke SA, Yue Y, Bulyk ML, Maas RL.
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.
Giorgetti L, Siggers T, Tiana G, Caprara G, Notarbartolo S, Corona T, Pasparakis M, Milani P, Bulyk ML, Natoli G.
Highlighted in Nature Review Genetics
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.
Viiri KM, Janis J, Siggers T, Heinonen TY, Valjakka J, Bulyk ML, Maki M, Lohi O.
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
Nucleic Acids Res. 35(5):1085-1097
Siggers T, Honig B.
2005
Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity.
JMB 345(5):1027-1045.
Siggers T, Silkov A, Honig B.
* Authors contributed equally
** Co-corresponding authors
