The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors

Genes and Development

Volumn 27, Issue 6, 2013, Pages 602-614

  Dai, Qi ^a   Ren, Aiming ^b   Westholm, Jakub O ^a   Serganov, Artem A ^b   Patel, Dinshaw J ^b   Lai, Eric C ^a  

^a Department of Developmental Biology ^*  (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

BEN domain; Neurogenesis; Transcriptional repression

Indexed keywords

BEN PROTEIN; BEND5 PROTEIN; BINDING PROTEIN; DNA; DNA BINDING PROTEIN; DROSOPHILA PROTEIN; ENHANCER OF SPLIT PROTEIN COMPLEX; GENOMIC DNA; HOMODIMER; INSV PROTEIN; NUCLEOTIDE; REPRESSOR PROTEIN; SUH PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ALPHA HELIX; ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CHROMATIN IMMUNOPRECIPITATION; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; DROSOPHILA; GENE EXPRESSION; GENE REPRESSION; GENE TARGETING; IN VITRO STUDY; IN VIVO STUDY; NERVE CELL; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; REPRESSOR GENE; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CO-REPRESSOR PROTEINS; DNA-BINDING PROTEINS; DROSOPHILA; DROSOPHILA PROTEINS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MODELS, MOLECULAR; NERVOUS SYSTEM; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SEQUENCE ALIGNMENT;

EID: 84875328376     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.213314.113     Document Type: Article

References (35)

1. Abhiman S, Iyer LM, Aravind L. 2008. BEN: A novel domain in chromatin factors and DNA viral proteins. Bioinformatics 24: 458-461.
2. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. 2002. PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948-1954.
3. Aoki T, Sarkeshik A, Yates J, Schedl P. 2012. Elba, a novel developmentally regulated chromatin boundary factor is a hetero-tripartite DNA binding complex. eLife 1: e00171.
4. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
5. Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
6. Bang AG, Hartenstein V, Posakony JW. 1991. Hairless is required for the development of adult sensory organ precursor cells in Drosophila. Development 111: 89-104.
7. Barolo S, Stone T, Bang AG, Posakony JW. 2002. Default repression and Notch signaling: Hairless acts as an adaptor to recruit the corepressors Groucho and dCtBP to Suppressor of Hairless. Genes Dev 16: 1964-1976.
8. Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326: 1509-1512.
9. Chintapalli VR, Wang J, Dow JA. 2007. Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39: 715-720.
10. Dolfini D, Gatta R, Mantovani R. 2012. NF-Y and the transcriptional activation of CCAAT promoters. Crit Rev Biochem Mol Biol 47: 29-49.
11. Duan H, Dai Q, Kavaler J, Bejarano F, Medranda G, Nègre N, Lai EC. 2011. Insensitive is a novel corepressor of Suppressor of Hairless and regulates Notch-mediated cell fate decisions in the peripheral nervous system. EMBO J 30: 3120-3133.
12. Emsley P, Cowtan K. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
13. Heitzler P, Simpson P. 1991. The choice of cell fate in the epidermis of Drosophila. Cell 64: 1083-1092.
14. Korutla L, Wang P, Jackson TG, Mackler SA. 2009. NAC1, a POZ/BTB protein that functions as a corepressor. Neurochem Int 54: 245-252.
15. Lai EC. 2002. Keeping a good pathway down: Transcriptional repression of Notch pathway target genes by CSL proteins. EMBO Rep 3: 840-845.
16. Lai EC. 2004. Notch signaling: Control of cell communication and cell fate. Development 131: 965-973.
17. Lai EC, Orgogozo V. 2004. A hidden program in Drosophila peripheral neurogenesis revealed: Fundamental principles underlying sensory organ diversity. Dev Biol 269: 1-17.
18. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
19. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, et al. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476-482.
20. Lohse MB, Zordan RE, Cain CW, Johnson AD. 2010. Distinct class of DNA-binding domains is exemplified by a master regulator of phenotypic switching in Candida albicans. Proc Natl Acad Sci 107: 14105-14110.
21. Morel V, Lecourtois M, Massiani O, Maier D, Preiss A, Schweisguth F. 2001. Transcriptional repression by Suppressor of Hairless involves the binding of a Hairless-dCtBP complex in Drosophila. Curr Biol 11: 789-792.
22. Moscou MJ, Bogdanove AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326: 1501.
23. Nellesen DT, Lai EC, Posakony JW. 1999. Discrete enhancer elements mediate selective responsiveness of Enhancer of split complex genes to common transcriptional activators. Dev Biol 213: 33-53.
24. Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, et al. 2012. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489: 83-90.
25. Pape T, Schneider TR. 2004. HKL2MAP: A graphical user interface for phasing with SHELX programs. J Appl Crystallogr 37: 843-844.
26. Pavesi G, Mauri G, Pesole G. 2001. An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 17: S207-S214.
27. Reeves N, Posakony JW. 2005. Genetic programs activated by proneural proteins in the developing Drosophila PNS. Dev Cell 8: 413-425.
28. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, et al. 2010. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
29. Ryu JR, Arnosti DN. 2003. Functional similarity of Knirps CtBPdependent and CtBP-independent transcriptional repressor activities. Nucleic Acids Res 31: 4654-4662.
30. Saj A, Arziman Z, Stempfle D, van Belle W, Sauder U, Horn T, Durrenberger M, Paro R, Boutros M, Merdes G. 2010. A combined ex vivo and in vivo RNAi screen for notch regulators in Drosophila reveals an extensive notch interaction network. Dev Cell 18: 862-876.
31. Sathyan KM, Shen Z, Tripathi V, Prasanth KV, Prasanth SG. 2011. A BEN-domain-containing protein associates with heterochromatin and represses transcription. J Cell Sci 124: 3149-3163.
32. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, et al. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-232.
33. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. 2008. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5: 829-834.
34. Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA. 2009. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17: 904-912.
35. Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, et al. 2012. The transcription factor encyclopedia. Genome Biol 13: R24.