{"id":73,"date":"2012-09-07T23:21:00","date_gmt":"2012-09-08T03:21:00","guid":{"rendered":"http:\/\/blogs.bu.edu\/tsiggers\/?page_id=73"},"modified":"2025-11-05T16:03:54","modified_gmt":"2025-11-05T21:03:54","slug":"73-2","status":"publish","type":"page","link":"https:\/\/blogs.bu.edu\/tsiggers\/73-2\/","title":{"rendered":"Publications"},"content":{"rendered":"

2025<\/span><\/p>\n

Targeting SUMOylation promotes cBAF complex stabiliziation and disruption of the SS18::SSX transcriptome in synovial sarcoma.<\/span>
\nNature communications<\/em> 16:9761 ( link<\/a>)
\nFloros KV, Fairchild Jr. CK, Li J, Zhang K, Roberts JL, Kurupi R, Paudel D, Xing Y, Hu B Kraskauskiene V, Hosseini N, Shen S, Inge MM<\/strong>, Smith-Fry K, Li L, Sotiriou A, Dalton KM, Jose A, Abdelfadiel EI, Hill RD, Slaughter JM, Shende M, Lorenz MR, Tanaka N, Kajino T, Nelson ML, Hinojosa MR, Kehinde VA, Belvin BR, Sugiokto FG, Lai Z, Dimopoulos AC, Boikos SA, Stamatouli AM, Lewis JP, Manjili MH, Edi H, Valerie K ,Li R, Poklepovic A, Koblinski JE, Siggers T, <\/strong>Banito A, Dozmorov MG, Jones KB, Radhakrishnan SK, Faber AC<\/p>\n

Stepwise neofunctionalization of the NF-kB family member c-Rel during vertebrate evolution.<\/span>
\nNature Immunology <\/em>26:760 ( PMID:40307452<\/a>)
\nDaly 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, <\/strong> Chen L, Smale ST.<\/span><\/strong><\/span><\/a><\/em><\/p>\n

 <\/p>\n

2024<\/span><\/p>\n

Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation<\/span>
\nNAR<\/em> PMID: <\/span><\/span><\/a>39166482<\/span><\/a>
\nInge MM*, Miller R*, Hook H, Bray D, Keenan JL, Zhao R,<\/strong> Gilmore TD, Siggers T\u00a0<\/strong><\/p>\n

Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming<\/span>
\nPLoS Biol. PMID: 39689157<\/span><\/span><\/a><\/em>
\nLawton ML, Inge MM<\/strong>, 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,\u00a0Siggers T<\/strong>, Wuchty S, Snyder-Cappione J, Emili A<\/p>\n

 <\/p>\n

2023<\/span><\/p>\n

Starvation decreases immunity and immune regulatory factor NF-kB in the starlet sea anemone Nematostella vectensis\u00a0<\/span>
\nCommun. Biol<\/em> 6:698 <\/span> PMID:37420095<\/a><\/span>
\nCarrion PJA, Desai N, Brennen JJ, Fifer JE, Siggers T,<\/strong> Davies SW, Gilmore TD.<\/p>\n

Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.<\/span>
\nNature Communications<\/em> 14:688 <\/span> PMID:36755019<\/a><\/span>
\nPaul I, Bolzan D, Youssef A, Gagnon K, Hook H<\/strong>, 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,<\/strong> Wuchty S, Muthuswamy S, Emili A.<\/p>\n

Widespread perturbation of ETS factor binding sites in cancer.<\/span>
\nNature Communications<\/em> 14:913 <\/span> PMID:36808133<\/a> (previous BioRxiv version here<\/a>)<\/span>
\nCarrasco Pro S*, Hook H*, Bray D, <\/strong>Berenzy D, Moyer D, Yin M, Labadorf AT, Tewhey R, Siggers T**, <\/strong>Fuxman Bass JI**.<\/p>\n

NF-kappaB and the Immune System<\/span>.
\nIn Encyclopedia of Cell Biology, Second Edition<\/em> (RA Bradshaw, GW Hart, PD Stahl eds) Elsevier. Volume 5:41-426. Oxford, Elsevier.
\nGilmore TD, Siggers T<\/strong><\/p>\n

 <\/p>\n

2022
\n<\/span><\/p>\n

CASCADE: High-throughput characterization of regulatory complex binding altered by non-coding variants.<\/span>
\nCell Genomics<\/em> 2:100098\u00a0 <\/span> PMID:35252945<\/a> (previous BioRxiv version here<\/a>)<\/span>
\nBray D*, Hook H*, Zhao R, Keenan JL, Penvose A, Osayame Y, Mohaghegh N<\/strong>, Chen X, Parameswaran S, Kottyan LC, Weirauch MT, Siggers T<\/strong>.<\/p>\n

 <\/p>\n

2021<\/span><\/p>\n

Comparison of NF-kB from the protists Capsaspora owczarzaki and Acanthoeca spectabilis reveals extensive evolutionary diversification of this transcription factor.<\/span>
\nCommun Biol. <\/em>4(1):1404
\nWilliam 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, <\/strong>Gilmore TD.<\/p>\n

High-Throughput Analysis of the Cell and DNA Site-Specific Binding of Native NF-kB Dimers using Nuclear Extract Protein-Binding Microarrays (NextPBMs).<\/span>
\nMethods Mol. Biol. 2366:43-66\u00a0<\/em> PMID:34236632<\/a>
\nHook H*, Zhao RW*, Bray D, Keenan JL,<\/strong> Siggers T<\/strong>\u00a0 <\/strong>(2021) <\/span><\/p>\n

2020<\/span><\/p>\n

Transcription factor NF-kB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation.<\/span>
\nDev Comp Immunol\u00a0<\/em> PMID: 31751628<\/a>
\nWilliams 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,\u00a0Siggers T<\/strong>, Gilmore T\u00a0 <\/strong> <\/span><\/p>\n

2019<\/span><\/p>\n

Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.<\/span>
\nNature Immunology <\/em>20(10):1372 PMID:31451789<\/a>
\nBruno L, Ramlall V,\u00a0<\/strong>Studer RA, Sauer S, Bradley D, Dharmalingam G, Carroll T, Ghoneim M, Chopin M, Nutt SL, Elderkin S, Rueda DS, Fisher AG,\u00a0Siggers T<\/strong>, Beltrao P, Merkenschlager M\u00a0\u00a0<\/strong><\/span><\/p>\n

Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity<\/span>
\nNature Communications <\/em>10(1):2514 PMID:31175293<\/a>
\nPenvose A*, Keenan J*, Bray D, Ramlall V, Siggers T, <\/strong>(<\/p>\n

NextPBM: A platform to study cell-specific transcription factor binding and cooperativity<\/span>
\nNucleic Acids Research <\/em> 47:e3 PMCID:PMC6451091 <\/a>
\nMohaghegh N*, Bray D*, Keenan J, Penvose A, Andrilenas KK, Ramlall V, Siggers T, <\/strong><\/span><\/p>\n

 <\/p>\n

2018<\/span><\/p>\n

DNA-binding landscape of IRF3, IRF5 and IRF7 dimers: implication for dimer-specific gene regulation<\/span>
\nNucleic Acids Research <\/em>46:2509-2520\u00a0PMID:29361124. <\/a>
\nAndrilenas KK, Ramlall V, Kurland J, Leung G,<\/strong> Harbaugh AG, Siggers T, <\/strong><\/span><\/p>\n

 <\/p>\n

2017<\/span><\/p>\n

Transcription factor NF-kB is modulated by symbiotic status in a sea anemone of cnidarian bleaching<\/span>
\nSci Rep.<\/em>7:16025\u00a0PMID:29167511. <\/a>
\nMansfield KM, Carter NM, Nguyen L, Cleves PA, Alshanbayeva A, William LM, Crowder C, Penvose AR<\/strong>, Finnerty JR, Weis VM, Siggers T, <\/strong> Gilmore TD <\/span><\/p>\n

 <\/p>\n

2016<\/span><\/p>\n

Expansion of GA Dinucleotdie Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation<\/span>
\nPLoS Genetics <\/em>12:e1006120:e1006120. <\/a>
\nKuzu G, Kaye EG, Chery J, Siggers T, <\/strong>Yang L, Dobson JR, Boor S, Bliss J, Liu W, Jogi, Rohs R, Singh ND, Bulyk ML, Tolstorukov MY, Larschan E <\/span><\/p>\n

Survey of variation in human transcription factors reveals prevalent DNA binding changes<\/span>
\nScience<\/em> 35:<\/span>1450-1454. <\/a>
\nBarrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, <\/strong>Shokri L, Gordan R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML<\/p>\n

Grhl2 is required in nonneural tissue for neural progenitor survival and forebrain development<\/span>
\nGenesis<\/em> 53(9):<\/span>573-582. <\/a>
\nMenke C, Cionni M, Siggers T<\/strong>, Bulyk ML, Beier DR, Stottmann RW<\/p>\n

Characterizing the DNA binding site specificity of NF-kB with protein-binding microarrays (PBMs)<\/span>
\nMethods Mol. Biol. 1280<\/em>:609-630.<\/a>
\nSiggers T**, <\/strong>Gilmore TD,\u00a0Barron B, Penvose A<\/strong><\/p>\n

Using Protein-binding Microarrays to Study Transcription Factor Specificity: Homologs, Isoforms and Complexes<\/span>
\nBriefings in Functional Genomics 14 <\/em>:17-29. <\/a>
\nAndrilenas K, Penvose A, Siggers T<\/strong> <\/span><\/p>\n

 <\/p>\n

2014<\/span><\/p>\n

Diversification of transcription factor paralogs via noncanonical modularity in C2H2 Zinc finger DNA binding<\/span>
\nMolecular Cell <\/em>55(4):640-648. <\/a>
\nSiggers T**, <\/strong>Reddy J, Barron B<\/strong>, Bulyk ML** <\/span><\/p>\n

Protein-DNA binding: complexities and multi-protein codes.<\/span>
\nNucleic Acids Res.\u00a0<\/em>42(4):1551-1556. <\/a>
\nSiggers T**,\u00a0<\/strong>Gordan R** <\/span><\/p>\n

 <\/p>\n

2013<\/span><\/p>\n

The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation<\/span>
\nGenes Dev<\/em>. 27(14):1551-1556. <\/a>
\nSoruco MM, Chery J, Bishop EP, Siggers T<\/strong>, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E. <\/span><\/span><\/p>\n

2012<\/span><\/p>\n

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-\u03baB family DNA binding.<\/span>
\nNature Immunology <\/em>13(1):95-102 <\/a>
\nSiggers T<\/strong>*, Chang AB*, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML.<\/p>\n

Faculty of 1000 Recommended\"\"
\nClick here<\/a> to access the associated NF-kB PBM database and search tools.
\n<\/span><\/p>\n

Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.<\/span>
\nMolecular Systems Biology <\/em>7:555 <\/a>
\nSiggers T<\/strong>, Duyzend MH, Reddy J, Khan S, Bulyk ML.
\n<\/span><\/span><\/span><\/p>\n

\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Highlighted in Nature Review Genetics<\/i><\/a><\/span><\/p>\n

 <\/p>\n

2011<\/span><\/p>\n

Extensive characterization of NF-KappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits.<\/span>
\nGenome Biol.<\/em> 12(7):R70<\/a>
\nWong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T,<\/strong> Bulyk ML, Angelov D, Dimitrov S, Udalova I, Ragoussis J.<\/p>\n

 <\/p>\n

2010<\/span><\/p>\n

Precise temporal control of the eye regulatory gene Pax6 via enhancer binding site affinity.<\/span>
\nGenes Dev<\/em>. 24(10):980-985. <\/a>
\nRowan S*, Siggers T*<\/strong>, Lachke SA, Yue Y, Bulyk ML, Maas RL.<\/span><\/p>\n

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses transcriptional responses to environmental inputs.<\/span>
\nMol. Cell.<\/em> 37(3):418-428.<\/a><\/span>
\nGiorgetti L, Siggers T<\/strong>, Tiana G, Caprara G, Notarbartolo S, Corona T, Pasparakis M, Milani P, Bulyk ML, Natoli G.<\/p>\n

Highlighted in Nature Review Genetics<\/i><\/a>
\n<\/span><\/p>\n

 <\/p>\n

2009<\/span><\/p>\n

DNA-binding and -bending activities of SAP30L and SAP30 are mediated by a zinc-dependent module and monophosphoinositides.<\/span> Mol. Cell Biol.<\/em> 29:342-356.<\/a>
\nViiri KM, Janis J, Siggers T<\/strong>, Heinonen TY, Valjakka J, Bulyk ML, Maki M, Lohi O.<\/p>\n

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.<\/span> <\/em><\/span><\/span>
\nNucleic Acids Res<\/em>. 35(5):1085-1097<\/a><\/span>
\nSiggers T<\/strong>, Honig B.<\/span><\/span><\/p>\n

 <\/p>\n

2005<\/span><\/p>\n

Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity.<\/span> <\/span><\/span><\/span>
\nJMB <\/em>345(5):1027-1045. <\/a><\/span>
\nSiggers T<\/strong>, Silkov A, Honig B.
\n<\/span><\/span><\/p>\n

* Authors contributed equally<\/p>\n

** Co-corresponding authors<\/p>\n","protected":false},"excerpt":{"rendered":"

2025 Targeting SUMOylation promotes cBAF complex stabiliziation and disruption of the SS18::SSX transcriptome in synovial sarcoma. Nature communications 16:9761 ( link) Floros KV, Fairchild Jr. CK, Li J, Zhang K, Roberts JL, Kurupi R, Paudel D, Xing Y, Hu B Kraskauskiene V, Hosseini N, Shen S, Inge MM, Smith-Fry K, Li L, Sotiriou A, Dalton […]<\/p>\n","protected":false},"author":3164,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"open","ping_status":"open","template":"links.php","meta":[],"_links":{"self":[{"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/pages\/73"}],"collection":[{"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/users\/3164"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/comments?post=73"}],"version-history":[{"count":50,"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/pages\/73\/revisions"}],"predecessor-version":[{"id":720,"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/pages\/73\/revisions\/720"}],"wp:attachment":[{"href":"https:\/\/blogs.bu.edu\/tsiggers\/wp-json\/wp\/v2\/media?parent=73"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}