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Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins.

Treiber N, Treiber T, Zocher G, Grosschedl R
Genes Dev 24 2270-5 (2010)
Related entries: 3mlo, 3mlp

Cited: 34 times
EuropePMC logo PMID: 20876732

Abstract

Early B-cell factor 1 (Ebf1) is a key transcriptional determinant of B-lymphocyte differentiation whose DNA-binding domain has no sequence similarity to other transcription factor families. Here we report the crystal structure of an Ebf1 dimer bound to its palindromic recognition site. The DNA-binding domain adopts a pseudoimmunoglobulin-like fold with novel topology, but is structurally similar to the Rel homology domains of NFAT and NF-κB. Ebf1 contacts the DNA with two loop-based modules and a unique Zn coordination motif whereby each Ebf1 monomer interacts with both palindromic half-sites. This unusual mode of DNA recognition generates an extended contact area that may be crucial for the function of Ebf1 in chromatin.

Articles - 3mln mentioned but not cited (2)

  1. Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins. Treiber N, Treiber T, Zocher G, Grosschedl R. Genes Dev 24 2270-2275 (2010)
  2. PiDNA: Predicting protein-DNA interactions with structural models. Lin CK, Chen CY. Nucleic Acids Res 41 W523-30 (2013)


Reviews citing this publication (3)

  1. The regulatory network of B-cell differentiation: a focused view of early B-cell factor 1 function. Boller S, Grosschedl R. Immunol Rev 261 102-115 (2014)
  2. B-lineage transcription factors and cooperating gene lesions required for leukemia development. Tijchon E, Havinga J, van Leeuwen FN, Scheijen B. Leukemia 27 541-552 (2013)
  3. B lymphocyte lineage specification, commitment and epigenetic control of transcription by early B cell factor 1. Hagman J, Ramírez J, Lukin K. Curr Top Microbiol Immunol 356 17-38 (2012)

Articles citing this publication (29)

  1. Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Okosun J, Bödör C, Wang J, Araf S, Yang CY, Pan C, Boller S, Cittaro D, Bozek M, Iqbal S, Matthews J, Wrench D, Marzec J, Tawana K, Popov N, O'Riain C, O'Shea D, Carlotti E, Davies A, Lawrie CH, Matolcsy A, Calaminici M, Norton A, Byers RJ, Mein C, Stupka E, Lister TA, Lenz G, Montoto S, Gribben JG, Fan Y, Grosschedl R, Chelala C, Fitzgibbon J. Nat Genet 46 176-181 (2014)
  2. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R. Cell 155 1507-1520 (2013)
  3. Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Zhao B, Zou J, Wang H, Johannsen E, Peng CW, Quackenbush J, Mar JC, Morton CC, Freedman ML, Blacklow SC, Aster JC, Bernstein BE, Kieff E. Proc Natl Acad Sci U S A 108 14902-14907 (2011)
  4. Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition. Lopez-Atalaya JP, Ito S, Valor LM, Benito E, Barco A. Nucleic Acids Res 41 8072-8084 (2013)
  5. Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming. Boller S, Ramamoorthy S, Akbas D, Nechanitzky R, Burger L, Murr R, Schübeler D, Grosschedl R. Immunity 44 527-541 (2016)
  6. Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. Monahan K, Schieren I, Cheung J, Mumbey-Wafula A, Monuki ES, Lomvardas S. Elife 6 e28620 (2017)
  7. EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex. Shapira SN, Lim HW, Rajakumari S, Sakers AP, Ishibashi J, Harms MJ, Won KJ, Seale P. Genes Dev 31 660-673 (2017)
  8. Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism. Harms FL, Girisha KM, Hardigan AA, Kortüm F, Shukla A, Alawi M, Dalal A, Brady L, Tarnopolsky M, Bird LM, Ceulemans S, Bebin M, Bowling KM, Hiatt SM, Lose EJ, Primiano M, Chung WK, Juusola J, Akdemir ZC, Bainbridge M, Charng WL, Drummond-Borg M, Eldomery MK, El-Hattab AW, Saleh MAM, Bézieau S, Cogné B, Isidor B, Küry S, Lupski JR, Myers RM, Cooper GM, Kutsche K. Am J Hum Genet 100 117-127 (2017)
  9. De Novo Mutations in EBF3 Cause a Neurodevelopmental Syndrome. Sleven H, Welsh SJ, Yu J, Churchill MEA, Wright CF, Henderson A, Horvath R, Rankin J, Vogt J, Magee A, McConnell V, Green A, King MD, Cox H, Armstrong L, Lehman A, Nelson TN, Deciphering Developmental Disorders study, CAUSES study, Williams J, Clouston P, Hagman J, Németh AH. Am J Hum Genet 100 138-150 (2017)
  10. Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Jankowski A, Szczurek E, Jauch R, Tiuryn J, Prabhakar S. Genome Res 23 1307-1318 (2013)
  11. Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. Lindqvist CM, Lundmark A, Nordlund J, Freyhult E, Ekman D, Carlsson Almlöf J, Raine A, Övernäs E, Abrahamsson J, Frost BM, Grandér D, Heyman M, Palle J, Forestier E, Lönnerholm G, Berglund EC, Syvänen AC. Oncotarget 7 64071-64088 (2016)
  12. EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. Glaser LV, Rieger S, Thumann S, Beer S, Kuklik-Roos C, Martin DE, Maier KC, Harth-Hertle ML, Grüning B, Backofen R, Krebs S, Blum H, Zimmer R, Erhard F, Kempkes B. PLoS Pathog 13 e1006664 (2017)
  13. Interaction of CCR4-NOT with EBF1 regulates gene-specific transcription and mRNA stability in B lymphopoiesis. Yang CY, Ramamoorthy S, Boller S, Rosenbaum M, Rodriguez Gil A, Mittler G, Imai Y, Kuba K, Grosschedl R. Genes Dev 30 2310-2324 (2016)
  14. TgrC1 mediates cell-cell adhesion by interacting with TgrB1 via mutual IPT/TIG domains during development of Dictyostelium discoideum. Chen G, Wang J, Xu X, Wu X, Piao R, Siu CH. Biochem J 452 259-269 (2013)
  15. Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function. Li Y, Osuma A, Correa E, Okebalama MA, Dao P, Gaylord O, Aburas J, Islam P, Brown AE, Kratsios P. Elife 9 e59464 (2020)
  16. Novel de novo variant in EBF3 is likely to impact DNA binding in a patient with a neurodevelopmental disorder and expanded phenotypes: patient report, in silico functional assessment, and review of published cases. Blackburn PR, Barnett SS, Zimmermann MT, Cousin MA, Kaiwar C, Pinto E Vairo F, Niu Z, Ferber MJ, Urrutia RA, Selcen D, Klee EW, Pichurin PN. Cold Spring Harb Mol Case Stud 3 a001743 (2017)
  17. Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer. Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Poon PSY, Lam YN, Lin JS, Tay ST, Lee MH, Tan ALK, Ong X, White K, Rozen SG, Beer M, Foo RSY, Grabsch HI, Skanderup AJ, Li S, Teh BT, Tan P. J Clin Invest 130 3005-3020 (2020)
  18. Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis. Heydarian M, Luperchio TR, Cutler J, Mitchell CJ, Kim MS, Pandey A, Sollner-Webb B, Reddy K. J Proteomics Bioinform 7 1000302 (2014)
  19. The structure, splicing, synteny and expression of lamprey COE genes and the evolution of the COE gene family in chordates. Lara-Ramírez R, Poncelet G, Patthey C, Shimeld SM. Dev Genes Evol 227 319-338 (2017)
  20. EBF2 Links KMT2D-Mediated H3K4me1 to Suppress Pancreatic Cancer Progression via Upregulating KLLN. Yao B, Xing M, Meng S, Li S, Zhou J, Zhang M, Yang C, Qu S, Jin Y, Yuan H, Zen K, Ma C. Adv Sci (Weinh) 11 e2302037 (2024)
  21. Negative Regulation of TLR Signaling by BCAP Requires Dimerization of Its DBB Domain. Lauenstein JU, Scherm MJ, Udgata A, Moncrieffe MC, Fisher DI, Gay NJ. J Immunol 204 2269-2276 (2020)
  22. Case Reports Neuroimaging Findings in Patients with EBF3 Mutations: Report of Two Cases. Jiménez de la Peña M, Jiménez de Domingo A, Tirado P, Calleja-Pérez B, Alcaraz LA, Álvarez S, Williams J, Hagman JR, Németh AH, Fernández-Jaén A. Mol Syndromol 12 186-193 (2021)
  23. Retraction of Publication Retracted: EBF1 gene promotes the proliferation and inhibits the apoptosis of bone marrow CD34+ cells in patients with myelodysplastic syndrome through negative regulation of mitogen-activated protein kinase axis. Hou S, Hao J, Wang YY, Zhao BB, Xiao GW, Li YQ, Liu X, Zou ZL, Yao Y, Xiong H. J Cell Biochem 120 1407-1419 (2019)
  24. Age-Progressive and Gender-Dependent Bone Phenotype in Mice Lacking Both Ebf1 and Ebf2 in Prrx1-Expressing Mesenchymal Cells. Nieminen-Pihala V, Rummukainen P, Wang F, Tarkkonen K, Ivaska KK, Kiviranta R. Calcif Tissue Int 110 746-758 (2022)
  25. EBF1 promotes triple-negative breast cancer progression by surveillance of the HIF1α pathway. Qiu Z, Guo W, Dong B, Wang Y, Deng P, Wang C, Liu J, Zhang Q, Grosschedl R, Yu Z, Deng J, Wu Y. Proc Natl Acad Sci U S A 119 e2119518119 (2022)
  26. EBF1-JAK2 inhibits the PAX5 function through physical interaction with PAX5 and kinase activity. Kojima Y, Kawashima F, Yasuda T, Odaira K, Inagaki Y, Yamada C, Muraki A, Noura M, Okamoto S, Tamura S, Iwamoto E, Sanada M, Matsumura I, Miyazaki Y, Kojima T, Kiyoi H, Tsuzuki S, Hayakawa F. Int J Hematol 118 65-74 (2023)
  27. Further delineation of EBF3-related syndromic neurodevelopmental disorder in twelve Chinese patients. Zhu J, Li W, Yu S, Lu W, Xu Q, Wang S, Qian Y, Guo Q, Xu S, Wang Y, Zhang P, Zhao X, Ni Q, Liu R, Li X, Wu B, Zhou S, Wang H. Front Pediatr 11 1091532 (2023)
  28. Terri Grodzicker: 35 years of shaping scientific publishing and communication. Grosschedl R. Genes Dev 37 2-3 (2023)
  29. Tnpo3 enables EBF1 function in conditions of antagonistic Notch signaling. Bayer M, Boller S, Ramamoothy S, Zolotarev N, Cauchy P, Iwanami N, Mittler G, Boehm T, Grosschedl R. Genes Dev 36 901-915 (2022)


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