erefinder: Genome-wide detection of oestrogen response elements.
gene regulation
genome
oestrogen
transcription factor
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Sep 2019
Sep 2019
Historique:
received:
25
10
2018
revised:
31
05
2019
accepted:
31
05
2019
pubmed:
10
6
2019
medline:
18
1
2020
entrez:
10
6
2019
Statut:
ppublish
Résumé
Oestrogen response elements (EREs) are specific DNA sequences to which ligand-bound oestrogen receptors (ERs) physically bind, allowing them to act as transcription factors for target genes. Locating EREs and ER responsive regions is therefore a potentially important component of the study of oestrogen-regulated pathways. Here, we report the development of a novel software tool, erefinder, which conducts a genome-wide, sliding-window analysis of oestrogen receptor binding affinity. We demonstrate the effects of adjusting window size and highlight the program's general agreement with ChIP studies. We further provide two examples of how erefinder can be used for comparative approaches. erefinder can handle large input files, has settings to allow for broad and narrow searches, and provides the full output to allow for greater data manipulation. These features facilitate a wide range of hypothesis testing for researchers and make erefinder an excellent tool to aid in oestrogen-related research.
Identifiants
pubmed: 31177626
doi: 10.1111/1755-0998.13046
doi:
Substances chimiques
Estrogens
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1366-1373Informations de copyright
© 2019 John Wiley & Sons Ltd.
Références
Anstead, G. M., Carlson, K. E., & Katzenellenbogen, J. A. (1997). The estradiol pharmacophore: Ligand structure-estrogen receptor bining affinity relationships and a model for the receptor binding site. Steroids, 62, 268-303.
Arnal, J.-F., Lenfant, F., Metivier, R., Flouriot, G., Henrion, D., Adlanmerini, M., … Katzenellenbogen, J. (2017). Membrane and nuclear estrogen receptor alpha actions: From tissue specificity to medical implications. Physiology Review, 97, 1045-1087. https://doi.org/10.1152/physrev.00024.2016
Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006). MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34, W369-W373. https://doi.org/10.1093/nar/gkl198
Bajic, V. B., Tan, S. L., Chong, A., Tang, S., Strom, A., Gustafsson, J. A., … Liu, E. T. (2003). Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes. Nucleic Acids Research, 31(13), 3605-3607.
Bourdeau, V., Deschênes, J., Métivier, R., Nagai, Y., Nguyen, D., Bretschneider, N., … Mader, S. (2004). Genome-wide identification of high-affinity estrogen response elements in human and mouse. Molecular Endocrinology, 18(6), 1411-1427. https://doi.org/10.1210/me.2003-0441
Boyer, M., Poujol, N., Margeat, E., & Royer, C. A. (2000). Quantitative characterization of the interaction between purified human estrogen receptor alpha and DNA using fluorescence anisotropy. Nucleic Acids Research, 28(13), 2494-2502.
Bulyk, M. L., Johnson, P. L. F., & Church, G. M. (2002). Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Research, 30(5), 1255-1261. https://doi.org/10.1093/nar/30.5.1255
Callard, G. V., Tchoudakova, A. V., Kishida, M., & Wood, E. (2001). Differential tissue distribution, developmental programming, estrogen regulationand promoter characteristics of cyp19 genes in teleost fish. The Journal of Steroid Biochemistry and Molecular Biology, 79, 305-314. https://doi.org/10.1016/S0960-0760(01)00147-9
Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., … Brown, M. (2005). Chromosome-wise mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell, 122, 33-43.
Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., … Brown, M. (2006). Genome-wide analysis of estrogen receptor binding sites. Nature Genetics, 38(11), 1289-1297. https://doi.org/10.1038/ng1901
Charif, D., & Lobry, J. R. (2007). Seqin{R} 1.0-2: A contributed package to the {R} project for statistical computing devoted to biological sequences retrieval and analysis. In U. Bastolla, M. Porto, E. Roman, & M. Vendruscolo (Eds.), Structural approaches to sequence evolution: molecules, networks, populations (pp. 207-232). New York, NY: Springer Verlag.
Cuellar-Partida, G., Buske, F. A., McLeay, R. C., Whitington, T., Nobel, W. S., & Bailey, T. L. (2012). Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics, 28(1), 56-62. https://doi.org/10.1093/bioinformatics/btr614
Deegan, B. J., Bhat, V., Seldeen, K. L., McDonald, C. B., & Farooq, A. (2011). Genetic variation within the ERE motif modulate plasticity and energetics of binding of DNA to the ERalpha receptor. Archives of Biochemistry and Biophysics, 507, 262-270.
Frankl-Vilches, C., Kuhl, H., Werber, M., Klages, S., Kerick, M., Bakker, A., … Leitner, S. (2015). Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. Genome Biology, 16(1), 19.
Frith, M. C., Li, M. C., & Weng, Z. (2003). Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Research, 31(13), 3666-3668. https://doi.org/10.1093/nar/gkg540
Geserick, C., Meyer, H. A., & Haendler, B. (2005). The role of DNA response elements as allosteric modulators of steroid receptor function. Molecular and Cellular Endocrinology, 236, 1-7. https://doi.org/10.1016/j.mce.2005.03.007
Glass, C. K., & Rosenfeld, M. G. (2000). The coregulator exchange in transcriptional functions of nuclear receptors. Genes and Development, 14, 121-141.
Hah, N., Murakami, S., Nagari, A., Danko, C. G., & Kraus, W. L. (2013). Enhancer transcripts mark active estrogen receptor binding sites. Genome Research, 23, 1210-1223. https://doi.org/10.1101/gr.152306.112
Hazelett, D. J., Lakeland, D. L., & Weiss, J. B. (2009). Affinity Density: A novel genomic approach to the identification of transcription factor regulatory targets. Bioinformatics, 25(13), 1617-1624. https://doi.org/10.1093/bioinformatics/btp282
Jia, M., Dahlman-Wright, K., & Gustafsson, J.-A. (2015). Estrogen receptor alpha and beta in health and disease. Best Practice and Research Clinical Endocrinology and Metabolism, 29, 557-568. https://doi.org/10.1016/j.beem.2015.04.008
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007). Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502. https://doi.org/10.1126/science.1141319
Kato, K., & Standley, D. M. (2013). MAFFT Multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772-780. https://doi.org/10.1093/molbev/mst010
Kato, S., Tora, L., Yamauchi, J., Masushige, S., Bellard, M., & Chambon, P. (1992). A Far upstream estrogen response element of the ovalbumin gene contains several half-palindromic 5'-TGACC-3' motifs acting synergistically. Cell, 68, 731-742. https://doi.org/10.1016/0092-8674(92)90148-6
Kel, A. E., GoBling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O. V., & Wingender, E. (2003). MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Research, 31(13), 3576-3579.
Klein-Hitpass, L., Ryffel, G. U., Heitlinger, E., & Cato, A. C. B. (1988). A 13bp palindrome is a functional estrogen responsive element and interacts specifically with estrogen receptor. Nucleic Acids Research, 16(2), 647-663. https://doi.org/10.1093/nar/16.2.647
Klinge, C. M., Jernigan, S. C., Smith, S. L., Tyulmenkov, V. V., & Kulakosky, P. C. (2000). Estrogen response element sequence impacts the conformation and transcriptional activity of estrogen receptor alpha. Molecular and Cellular Endocrinology, 174, 151-166.
Lin, C.-Y., Vega, V. B., Zhang, T., Kong, S. L., Xie, M., Chiu, K. P., … Liu, E. T. (2007). Whole-genome carography of estrogen receptor alpha binding sites. PLoS Genetics, 3(6), 867-885.
Man, T.-K., & Stormo, G. D. (2001). Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Research, 29(12), 2471-2478. https://doi.org/10.1093/nar/29.12.2471
Martinez, E., & Wahli, W. (1989). Cooperative binding of estroge nreceptor to imperfect estrogen-responsive DNA elements correlates with their synergistic hormone-dependent enhancer activity. The EMBO Journal, 8(12), 3781-3791. https://doi.org/10.1002/j.1460-2075.1989.tb08555.x
Matthews, J., & Gustafsson, J.-A. (2003). Estrogen signaling: A subtle balance between ERalpha ERbeta. Molecular Interventions, 3(5), 281-292.
McDonnell, D. P., & Norris, J. D. (2002). Connections and regulation of the human estrogen receptor. Science, 296, 1642-1644. https://doi.org/10.1126/science.1071884
Mukherjee, S., Berger, M. F., Jona, G., Wang, X. S., Muzzey, D., Snyder, M., … Bulyk, M. L. (2004). Rapid analysis of the DNA-binding specficities of transcription factors with DNA microarrays. Nature Genetics, 36(12), 1331-1339.
Ogawa, N., & Biggin, M. D. (2012). High-throughput SELEX determination of DNa sequences bound by transcription factors in vitro. Methods Molecular Biology, 786, 51-63.
Omidi, S., Zavolan, M., Pachkov, M., Breda, J., Berger, S., & van Nimwegen, E. (2017). Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13(7), e1005176. https://doi.org/10.1371/journal.pcbi.1005176
Pages, H., Aboyoun, P., Gentleman, R., & DebRoy, S. (2018). Biostrings: Efficient manipulation of biological strings. R package version 2.48.0.
Shang, Y., Hu, X., DiRenzo, J., Lazar, M. A., & Brown, M. (2000). Cofactor dynamcs and sufficiency in estrogen receptor-regulated transcription. Cell, 103, 843-852.
Stormo, G. D. (2000). DNA binding sites: Representation and discovery. Bioinformatics, 16(1), 16-23. https://doi.org/10.1093/bioinformatics/16.1.16
Suryamohan, K., & Halfon, M. S. (2015). Identifying transcriptional cis-regulatory modules in animal genomes. Wires Developmental Biology, 4, 59-84.
Tan, G., & Lenhard, B. (2016). TFBSTools: An R/Bioconductor package for transcription factor binding site analysis. Bioinformatics, 32(10), 1555-1556. https://doi.org/10.1093/bioinformatics/btw024
Teytelman, L., Thurtle, D. M., Rine, J., & van Oudenaarden, A. (2013). Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. PNAS, 110(46), 18602-18607. https://doi.org/10.1073/pnas.1316064110
Thornton, J. W., Need, E., & Crews, D. (2003). Resurrecting the ancestral steroid receptor: Ancient origin of estrogen signaling. Science, 301, 1714-1717. https://doi.org/10.1126/science.1086185
Tohyama, S., Miyagawa, S., Lange, A., Ogino, Y., Mizutani, T., Ihara, M., … Iguchi, T. (2016). Evolution of estrogen receptors in ray-finned fish and their comparative responses to estrogenic substances. Journal of Steroid Biochemistry and Molecular Biology, 158, 189-197. https://doi.org/10.1016/j.jsbmb.2015.12.009
Tyulmenkov, V. V., & Klinge, C. M. (2001). A mathematical approach to predict the affinity of estrogen receptors alpha and beta binding to DNA. Molecular and Cellular Endocrinology, 182, 109-119.
Wang, Z., Martins, A. L., & Danko, C. G. (2016). RTFBSDB: An integrated framework for transcription factor binding site analysis. Bioinformatics, 32(19), 3024-3026. https://doi.org/10.1093/bioinformatics/btw338
Wasserman, W. W., & Sandelin, A. (2004). Applied bioinformatics for the identification of regulatory elements. Nature Reviews Genetics, 5, 276-287. https://doi.org/10.1038/nrg1315
Welboren, W., van Driel, M. A., Janssen-Megens, E. M., van Heeringen, S. J., Sweep, F. C. G. J., Span, P. N., & Stunnenberg, H. G. (2009). ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands. The EMBO Journal, 28(10), 1418-1428. https://doi.org/10.1038/emboj.2009.88
Yang, J., & Ramsey, S. A. (2015). A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites. Bioinformatics, 31(21), 3445-3450. https://doi.org/10.1093/bioinformatics/btv391
Young, L. J., & Crews, D. (1995). Comparative neuroendocrinology of steroid receptor gene expression and regulation: Relationship to physiology and behavior. Trends in Endocrinology and Metabolism, 6, 317-323. https://doi.org/10.1016/1043-2760(95)00175-1
Zheng, Y., Shao, X., Huang, Y., Shi, L., Chen, B. O., Wang, X., … Zhang, X. (2016). Role of estrogen receptor in breast cancer cell gene expression. Molecular Medicine Reports, 13, 4046-4050. https://doi.org/10.3892/mmr.2016.5018