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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Peter Cherbas

Photo of Peter Cherbas
Contact Information
By telephone: 812-855-6273
JH A317

FlyIU

Program
Genome, Cell & Developmental Biology
Research Areas
  • Chromatin, Chromosomes, and Genome Integrity
  • Developmental Mechanisms and Regulation in Eukaryotic Systems
  • Genomics and Bioinformatics
Education

Ph.D., Harvard University, 1973

Awards
Research Description

Nuclear receptors are present in every multicellular animal; some act as receptors for important hormones - estrogen, androgens, thyroid hormone, etc. - while we can only guess the functions of others. Transcriptional switches controlled by small molecules, the nuclear receptors are crucial regulators of development and have proven to be valuable tools for biotechnology.

The Cherbas lab uses genetics, biochemistry, functional genomics, and bioinformatics to study how one receptor cooperates with other transcription factors to induce tissue- and stage-specific changes during development. The ecdysone receptor synchronizes the spectacular transformations that occur during insect metamorphosis when virtually every cell responds to the hormone ecdysone by either initiating cell-type specific differentiation or dying. it consists of two proteins (EcR and USP) whose dimer binds to DNA all the time. When hormone is not present the dimer interacts with corepressor proteins to inhibit the transcription of nearby genes. When hormone is present the dimer interacts with coactivator proteins to stimulate nearby genes. The nature of these corepressor and coactivator complexes, how they are specified by regulatory DNA sequences, and how they impose target cell specificity are questions of wide interest.

The lab uses fly genetics to express modified receptors in specific target cells and to catalog the transcription factors that interact with receptor in those cells. It uses biochemical methods to test interacts between receptor and candidate interactors and to study the rates of assembly and disassembly of receptor complexes.

In conjunction with the Center for Genomics and Bioinformatics (http://cgb.indiana.edu) the lab is using computational methods and bioinformatics to study the properties of ecdysone regulatory elements and is using functional genomics (microarrays) to identify and study ecdysone-responsive genes.

In association with the Drosophila Genomics Research Center (http://dgrc.cgb.indiana.edu) we studying ecdysone-responsive genes using cell lines with different tissue origins.

And, in conjunction with the Center for Insect Genomics (a joint project with Notre Dame and Purdue) we are creating genomics tools for arthropods important in public health.

Select Publications
Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. 2014. Diversity and dynamics of the Drosophila transcriptome. Nature 512: 393-399 [Mar 16 doi: 10.1038/nature 12962 Epub ahead of print]  
Zhen-Xia Chen, David Sturgill, Jiaxin Qu, Huaiyang Jiang, Soo Park, Nathan Boley,  Ana Maria Suzuki, Anthony R. Fletcher, David C. Plachetzki, Peter C. FitzGerald, Carlo G. Artieri, Joel Atallah, Olga Barmina, James B. Brown, Kerstin P. Blankenburg, Emily Clough, Abhijit Dasgupta, Sai Gubbala, Yi Han, Joy C. Jayaseelan, Divya Kalra, Yoo-Ah Kim, Christie L. Kovar, Sandra L. Lee, Mingmei Li, James D. Malley, John H. Malone, Tittu Mathew, Nicolas R. Mattiuzzo, Mala Munidasa, Donna M. Muzny, Fiona Ongeri, Lora Perales, Teresa M. Przytycka, Ling-Ling Pu, Garrett Robinson, Rebecca L. Thornton, Nehad Saada, Steven E. Scherer,  Harold E. Smith, Charles Vinson, Crystal B. Warner, Kim C. Worley, Yuan-Qing Wu,  Xiaoyan Zou, Peter Cherbas, Manolis Kellis, Michael B. Eisen, Fabio Piano, Karin Kionte, David H. Fitch, Paul W. Sternberg, Asher D. Cutter,  Michael O. Duff, Roger A. Hoskins, Brenton R. Graveley, Richard A. Gibbs, Peter J. Bickel, Artyom Kopp, Piero Carninci, Susan E. Celniker, Brian Oliver, and Stephen Richards. 2014. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research 24: 1209-1223.    
Jiayu Wen, Jaaved Mohammed, Diane Bortolamiol-Becet, Harrison Tsai, Nicolas Robine, Jakub O. Westholm, Erik Ladewig, Qi Dai, Katsutomo Okamura, Alex S. Flynt, Dayu Zhang, Justen Andrews, Lucy Cherbas, Thomas C. Kaufman, Peter Cherbas, Adam Siepel, and Eric C. Lai. 2014. Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Research 24:1236–1250.    
Lee H, McManus CJ, Cho D-Y, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, Przytycka TM, Gatti M, Oliver B, Graveley B, MacAlpine D. 2014. DNA copy number evolution in Drosophila modENCODE cell lines. Genome Biology 15:R70.    
Mark Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James Brown, Carrie Davis, LaDeana Hillier, Cristina Sisu, Jingyi Li, Baikang Pei, Arif Harmanci, Michael Duff, Sarah Djebali, Roger Alexander, Burak Alver, Raymond Auerbach, Kimberly Bell, Peter Bickel, Max Boech, Nathan Boley, Benjamin Booth, Lucy Cherbas, Peter Cherbas, Chao Di, Alex Dobin, Jorg Drenkow, Brent Ewing, Gang Fang, Meagan Fastuca, Elise Feingold, Adam Frankish, Guanjun Gao, Peter Good, Phil Green, Roderic Guigo, Ann Hammonds, Jennifer Harrow, Roger Hoskins, Cédric Howald, Long Hu, Haiyan Huang, Tim Hubbard, Chau Huynh, Sonali Jha, Dionna Kasper, Masaomi Kato, Thomas Kaufman, Robert Kitchen, Erik Ladewig, Julien Lagarde, Eric Lai, Jing Leng, Zhi Lu, Michael MacCoss, Gemma May, Rebecca McWhirter, Gennifer Merrihew, David Miller III, Ali Mortazavi, rabi Murad, Brian Oliver, Sara Olson, Peter Park, Michael Pazin, Norbert Perrimon, Dmitri Pervouchine, Valerie Reinke, Alexandre Reymond, Garrett Robinson, Anastasia Samsonova, Gary Saunders, Felix Schlesinger, Anurag Sethi, Frank Slack, William Spencer, Marcus Stoiber, Pnina Strasbourger, Andrea Tanzer, Owen Thompson, Kenneth Wan, Guilin Wang, Huaien Wang, Kathie Watkins, Jiayu Wen, Kejia Wen, Chenghai Xue, Li Yang, Kevin Yip, Christopher Zaleski, Yan Zhang, Henry Zheng, Steven Brenner, Brenton Graveley, Susan Celniker, Thomas Gingeras, and Robert Waterston. 2014. Comparative Analysis of the Transcriptome across Distant Species. Nature 512: 445-448.    
Smibert P,Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, and EC Lai. 2012. Cell Reports 1, 277–289. Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila.
Gauthier SA, VanHaaften E, Cherbas L, Cherbas P, Hewes RS. 2012. Cryptocephal, the Drosophila melanogaster ATF4, Is a Specific Coactivator for Ecdysone Receptor Isoform B2. PLoS Genet 8(8): e1002883. doi:10.1371/journal.pgen.1002883.
Hackney JF, Zolali-Meybodi O, Cherbas P. 2012. Tissue damage disrupts developmental progression and ecdysteroid biosynthesis in Drosophila. PLOS One 7(11):e49105. doi: 10.137/journal pone 0049105.    
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews  J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. [Epub 2010]    
Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P. 2011. The transcriptional diversity of 25 Drosophila cell ines. Genome Res. 21: 301-14. [Epub 2010]    
modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M, Comstock CL, Dobin A, Drenkow J, Dudoit S, Dumais J, Fagegaltier D, Ghosh S, Hansen KD, Jha S, Langton L, Lin W, Miller D, Tenney AE, Wang H, Willingham AT, Zaleski C, Zhang D, Acevedo D, Bishop EP, Gadel SE, Jung YL, Kennedy CD, Lee OK, Linder-Basso D, Marchetti SE, Shanower G, Auburn R, Bellen HJ, Chen J, Domanus MH, Hanley D, Heinz E, Li Z, Meyer F, Miller SW, Morrison CA, Scheftner DA, Senderowicz L, Shah PK, Suchy S, Tian F, Venken KJ, White R, Wilkening J, Zieba J, DeNapoli LC, Ding Q, Eng T, Kashevsky H, Li S, Prinz JA, Hannon GJ, Hirst M, Marra M, Rooks M, Zhao Y, Bryson TD, Barber G, Chateigner A,  Clawson H, Contrino S, Guillier F, Hinrichs AS, Kephart ET, Lloyd P, Lyne R, McKay S, Moore RA, Mungall C, Rutherford KM, Ruzanov P, Smith R, Stinson EO, Zha  Z, Jiang L, Mattiuzzo N. 2010.  Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-97. [Epub 2010]    
Cherbas, L., and P. Cherbas. 2006.  Transformation of Drosophila cell lines: An alternative approach to exogenous protein expression.  Ch. 16 in: Murhammer, D. (ed.): Baculovirus Expression Protocols, 2nd Edition. Humana Press. 
Badenhorst P, Xiao H, Cherbas L, Kwon SY, Voas M, Rebay I, Cherbas P, Wu C. 2005. The Drosophila nucleosome remodeling factor NURF is required for ecdysteroid signaling and metamorphosis. Genes & Development 19: 2540-2545.

Brown HLD, Cherbas L, Cherbas P, Truman JW. 2005. Use of time-lapse imaging and dominant negative receptors to dissect the steroid receptor control of neuronal remodeling in Drosophila. Development 133: 275-285.
Cherbas L, Hu X, Zhimulev I, Belyaeva E, Cherbas P. Development. 2003 Jan;130(2):271-84. EcR isoforms in Drosophila: testing tissue-specific requirements by targeted blockade and rescue. Myung S, Lee YJ, Moon MH, Taraszka J, Sowell R, Koeniger S, Hilderbrand AE, Valentine SJ, Cherbas L, Cherbas P, Kaufmann TC, Miller DF, Mechref Y, Novotny MV, Ewing MA, Sporleder CR, Clemmer DE. Anal Chem. 2003 Oct 1;75(19):5137-45. Development of high-sensitivity ion trap ion mobility spectrometry time-of-flight techniques: a high-throughput nano-LC-IMS-TOF separation of peptides arising from a Drosophila protein extract.
Hu X, Cherbas L, Cherbas P. Mol Endocrinol. 2003 Apr;17(4):716-31. Transcription activation by the ecdysone receptor (EcR/USP): identification of activation functions.
Sedkov, Y., E. Cho-Fertikh, S. Petruk, L. Cherbas, S. T. Smith, R. S. Jones, P. Cherbas, E. Canaani, J. B. Jaynes, and A. Mazo. 2003. Nature. 2003 Nov 6;426(6962):78-83. Role of histone H3-lysine 4 methylation in the ecdysone-dependent development of the Drosophila eye.
Riddiford, L.M., Cherbas, P., Truman, J.W. 2000. Vitamins and Hormones 60: 1-73. Ecdysone receptors and their biological actions.

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