SELEX-seq: A method for characterizing the complete repertoire of binding site preferences for transcription factor complexes

Methods in Molecular Biology

Volumn 1196, Issue , 2014, Pages 255-278

  Riley, Todd R ^a   Slattery, Matthew ^a   Abe, Namiko ^a   Rastogi, Chaitanya ^a   Liu, Dahong ^a   Mann, Richard S ^a   Bussemaker, Harmen J ^a  

^a NONE

Author keywords

Computational analysis; Extradenticle; Hox proteins; Next generation sequencing; Pbx; SELEX; Transcription factor specificity

Indexed keywords

DNA BINDING PROTEIN; DNA DIRECTED DNA POLYMERASE BETA; DOUBLE STRANDED DNA; HOX PROTEIN; MULTIPROTEIN COMPLEX; OLIGONUCLEOTIDE; TAQ POLYMERASE; TRANSCRIPTION FACTOR; DNA;

ARTICLE; BINDING AFFINITY; BINDING SITE; COMBINATORIAL CHEMISTRY; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DISSOCIATION CONSTANT; DNA BINDING; DNA BINDING MOTIF; DNA FLANKING REGION; DNA LIBRARY; DNA PROBE; DNA PROTEIN COMPLEX; DNA SEQUENCE; GEL MOBILITY SHIFT ASSAY; GENE AMPLIFICATION; IN VITRO STUDY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN EXPRESSION; RNA SEQUENCE; SELEX SEQ; THERMODYNAMICS; BIOLOGY; CHEMISTRY; HIGH THROUGHPUT SEQUENCING; METABOLISM; PROCEDURES; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT APTAMER TECHNIQUE;

BINDING SITES; COMPUTATIONAL BIOLOGY; DNA; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SELEX APTAMER TECHNIQUE; TRANSCRIPTION FACTORS;

EID: 84927137392     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1242-1_16     Document Type: Article

References (18)

1. Hueber SD, Lohmann I (2008) Shaping segments: Hox gene function in the genomic age. Bioessays 30(10):965-979. doi:10.1002?bies.20823
2. Young T, Deschamps J (2009) Hox, Cdx, and anteroposterior patterning in the mouse embryo. Curr Top Dev Biol 88:235-255. doi:10.1016/S0070-2153(09)88008-3
3. Abramovich C, Humphries RK (2005) Hox regulation of normal and leukemic hematopoietic stem cells. Curr Opin Hematol 12(3):210-216
4. Mann RS, Lelli KM, Joshi R (2009) Hox specificity unique roles for cofactors and collaborators. Curr Top Dev Biol 88:63-101. doi:10.1016/S0070-2153(09)88003-4
5. Conlon FL, Fairclough L, Price BM, Casey ES, Smith JC (2001) Determinants of T box protein specificity. Development 128(19): 3749-3758
6. Jones S (2004) An overview of the basic helixloop-helix proteins. Genome Biol 5(6):226. doi:10.1186/gb-2004-5-6-226
7. Hollenhorst PC, McIntosh LP, Graves BJ (2011) Genomic and biochemical insights into the specificity of ETS transcription factors. Annu Rev Biochem 80:437-471. doi:10.1146?annurev.biochem.79.081507.103945
8. Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131(3):530-543. doi:10.1016/j.cell.2007.09.024
9. Abu-Shaar M, Ryoo HD, Mann RS (1999) Control of the nuclear localization of Extradenticle by competing nuclear import and export signals. Genes Dev 13(8):935-945
10. Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147(6):1270-1282. doi:10.1016/j.cell.2011.10.053
11. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249(4968):505-510
12. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287):818-822. doi:10.1038/346818a0
13. Slattery M, Ma L, Negre N, White KP, Mann RS (2011) Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. PLoS One 6(4):e14686. doi:10.1371/journal.pone.0014686
14. Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J (2013) DNA-binding specificities of human transcription factors. Cell 152(1-2):327-339. doi:10.1016/j.cell.2012.12.009
15. Levine HA, Nilsen-Hamilton M (2007) A mathematical analysis of SELEX. Comput Biol Chem 31(1):11-35. doi:10.1016/j.compbiolchem.2006.10.002
16. Gebelein B, Culi J, Ryoo HD, Zhang W, Mann RS (2002) Specificity of Distalless repression and limb primordia development by abdominal Hox proteins. Dev Cell 3(4):487-498
17. Noro B, Lelli K, Sun L, Mann RS (2011) Competition for cofactor-dependent DNA binding underlies Hox phenotypic suppression. Genes Dev 25(22):2327-2332. doi:10.1101/gad.175539.111
18. Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpaa MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 20(6):861-873. doi:10.1101/gr.100552.109