DbSUPER: A database of Super-enhancers in mouse and human genome

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D164-D171

  Khan, Aziz ^a   Zhang, Xuegong ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; COMPUTER INTERFACE; CONTROLLED STUDY; EMBRYO; ENHANCER REGION; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; HUMAN; HUMAN CELL; HUMAN TISSUE; MOUSE; NONHUMAN; PRIORITY JOURNAL; SUPER ENHANCER; WEB BROWSER; ANIMAL; GENOMICS; HUMAN GENOME; INTERNET; NUCLEIC ACID DATABASE; SOFTWARE;

ANIMALS; DATABASES, NUCLEIC ACID; ENHANCER ELEMENTS, GENETIC; GENOME, HUMAN; GENOMICS; HUMANS; INTERNET; MICE; SOFTWARE;

EID: 84976872373     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1002     Document Type: Article

References (51)

1. Levine, M., Cattoglio, C. and Tjian, R. (2014) Looping back to leap forward: transcription enters a new era. Cell, 157, 13-25.
2. Shlyueva, D., Stampfel, G. and Stark, A. (2014) Transcriptional enhancers: from properties to genome-wide predictions. Nat. Rev. Genet., 15, 272-286.
3. Wamstad, J. A., Wang, X., Demuren, O. O. and Boyer, L. A. (2013) Distal enhancers: new insights into heart development and disease. Trends Cell Biol., 24, 294-302.
4. Kolovos, P., Knoch, T. A., Grosveld, F. G., Cook, P. R. and Papantonis, A. (2012) Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin, 5, 1.
5. Pennacchio, L. A., Bickmore, W., Dean, A., Nobrega, M. A. and Bejerano, G. (2013) Enhancers: five essential questions. Nat. Rev. Genet., 14, 288-295.
6. Plank, J. L. and Dean, A. (2014) Enhancer function: mechanistic and genome-wide insights come together. Mol. Cell, 55, 5-14.
7. Banerji, J., Rusconi, S. and Schaffner, W. (1981) Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell, 27, 299-308.
8. Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C. A., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
9. Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
10. Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F. et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature, 457, 854-858.
11. Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
12. Rivera, C. M. and Ren, B. (2013) Mapping human epigenomes. Cell, 155, 39-55.
13. Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A. and Wysocka, J. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature, 470, 279-283.
14. Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A. et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. U. S. A., 107, 21931-21936.
15. Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I. and Young, R. A. (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153, 307-319.
16. Lovén, J., Hoke, H. A., Lin, C. Y., Lau, A., Orlando, D. A., Vakoc, C. R., Bradner, J. E., Lee, T. I. and Young, R. A. (2013) Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell, 153, 320-334.
17. Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A. and Young, R. A. (2013) Super-enhancers in the control of cell identity and disease. Cell, 155, 934-947.
18. Parker, S. C. J., Stitzel, M. L., Taylor, D. L., Orozco, J. M., Erdos, M. R., Akiyama, J. A., van Bueren, K. L., Chines, P. S., Narisu, N., Black, B. L. et al. (2013) Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc. Natl. Acad. Sci. U. S. A., 110, 17921-17926.
19. Gröschel, S., Sanders, M. A., Hoogenboezem, R., De Wit, E., Bouwman, B. A. M., Erpelinck, C., Van Der Velden, V. H. J., Havermans, M., Avellino, R., Van Lom, K. et al. (2014) A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in Leukemia. Cell, 157, 369-381.
20. Li, Y., Rivera, C. M., Ishii, H., Jin, F., Selvaraj, S., Lee, A. Y., Dixon, J. R. and Ren, B. (2014) CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. PLoS One, 9, e114485.
21. Hnisz, D., Schuijers, J., Lin, C. Y., Weintraub, A. S., Abraham, B. J., Lee, T. I., Bradner, J. E. and Young, R. A. (2015) Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Mol. Cell, 58, 362-370.
22. Siersbæk, R., Rabiee, A., Nielsen, R., Sidoli, S., Traynor, S., Loft, A., Poulsen, L. L. C., Rogowska-Wrzesinska, A., Jensen, O. N. and Mandrup, S. (2014) Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. Cell Rep., 7, 1443-1455.
23. Wang, H., Zang, C., Taing, L., Arnett, K. L., Wong, Y. J., Pear, W. S., Blacklow, S. C., Liu, X. S. and Aster, J. C. (2014) NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers. Proc. Natl. Acad. Sci. U. S. A., 111, 705-710.
24. Chapuy, B., McKeown, M. R., Lin, C. Y., Monti, S., Roemer, M. G. M., Qi, J., Rahl, P. B., Sun, H. H., Yeda, K. T., Doench, J. G. et al. (2013) Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. Cancer Cell, 24, 777-790.
25. Trabucco, S. E., Gerstein, R. M., Evens, A. M., Bradner, J. E., Shultz, L. D., Greiner, D. L. and Zhang, H. (2014) Inhibition of bromodomain proteins for the treatment of human diffuse large B-cell lymphoma. Clin. Cancer Res., 21, 113-122.
26. Brown, J. D., Lin, C. Y., Duan, Q., Griffin, G., Federation, A. J., Paranal, R. M., Bair, S., Newton, G., Lichtman, A. H., Kung, A. L. et al. (2014) NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis. Mol. Cell, 56, 219-231.
27. Amaral, P. P. and Bannister, A. J. (2014) Re-place your BETs: the dynamics of super enhancers. Mol. Cell, 56, 187-189.
28. Kwiatkowski, N., Zhang, T., Rahl, P. B., Abraham, B. J., Reddy, J., Ficarro, S. B., Dastur, A., Amzallag, A., Ramaswamy, S., Tesar, B. et al. (2014) Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature, 511, 616-620.
29. Christensen, C. L., Kwiatkowski, N., Abraham, B. J., Carretero, J., Al-Shahrour, F., Zhang, T., Chipumuro, E., Herter-Sprie, G. S., Akbay, E. A., Altabef, A. et al. (2014) Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor. Cancer Cell, 26, 909-922.
30. Augert, A. and MacPherson, D. (2014) Treating transcriptional addiction in small cell lung cancer. Cancer Cell, 26, 783-784.
31. Mansour, M. R., Abraham, B. J., Anders, L., Berezovskaya, A., Gutierrez, A., Durbin, A. D., Etchin, J., Lawton, L., Sallan, S. E., Silverman, L. B. et al. (2014) An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science, 346, 1371-1377.
32. Vähärautio, A. and Taipale, J. (2014) Cancer by super-enhancer. Science, 346, 1291-1292.
33. Meng, F. L., Du, Z., Federation, A., Hu, J., Wang, Q., Kieffer-Kwon, K. R., Meyers, R. M., Amor, C., Wasserman, C. R., Neuberg, D. et al. (2014) Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell, 159, 1538-1548.
34. Qian, J., Wang, Q., Dose, M., Pruett, N., Kieffer-Kwon, K. R., Resch, W., Liang, G., Tang, Z., Mathé, E., Benner, C. et al. (2014) B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell, 159, 1524-1537.
35. Vahedi, G., Kanno, Y., Furumoto, Y., Jiang, K., Parker, S. C. J., Erdos, M. R., Davis, S. R., Roychoudhuri, R., Restifo, N. P., Gadina, M. et al. (2015) Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature, 520, 558-562.
36. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
37. Zhang, Y., Liu, T., Meyer, C.a, Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
38. Pott, S. and Lieb, J. D. (2014) What are super-enhancers? Nat. Genet., 47, 8-12.
39. Kuhn, R. M., Haussler, D. and Kent, W. J. (2012) The UCSC genome browser and associated tools. Brief. Bioinform., 14, 144-161.
40. Ong, C. T. and Corces, V. G. (2011) Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat. Rev. Genet., 12, 283-293.
41. Chepelev, I., Wei, G., Wangsa, D., Tang, Q. and Zhao, K. (2012) Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res., 22, 490-503.
42. Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S. and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
43. Rosenbloom, K. R., Armstrong, J., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M. et al. (2014) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res., 43, D670-D681.
44. Pruitt, K. D., Brown, G. R., Hiatt, S. M., Thibaud-Nissen, F., Astashyn, A., Ermolaeva, O., Farrell, C. M., Hart, J., Landrum, M. J., McGarvey, K. M. et al. (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res., 42, D756-D763.
45. Maglott, D., Ostell, J., Pruitt, K. D. and Tatusova, T. (2011) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 39, D52-D57.
46. Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny Stein, T., Shmoish, M., Nativ, N., Bahir, I., Doniger, T., Krug, H. et al. (2010) GeneCards Version 3: the human gene integrator. Database (Oxford)., 2011, baq020.
47. UniProt Consortium. (2014) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
48. Blankenberg, D., Coraor, N., Von Kuster, G., Taylor, J. and Nekrutenko, A. (2011) Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database (Oxford)., 2011, bar011.
49. McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M. and Bejerano, G. (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol., 28, 495-501.
50. Liu, T., Ortiz, J. A., Taing, L., Meyer, C. A., Lee, B., Zhang, Y., Shin, H., Wong, S. S., Ma, J., Lei, Y. et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol., 12, R83.
51. Quinlan, A. R. and Hall, I. M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.