Research Description

Mapping the regulatory wiring diagrams encoded in genomes is key to understanding development, disease and evolution. The White lab studies the coordinated action of networks of genes that control developmental and evolutionary processes. We have particular focus on building genome-wide models of transcriptional networks, and we use an integrated approach that makes use of gene expression microarrays, large-scale protein-protein and protein-DNA interaction analyses, systematic RNAi analysis and high throughput polymorphism detection. By applying our methods to both closely and distantly related species, we are investigating how conserved molecular networks control basic developmental processes and how variation in molecular networks translates into variation in organismal phenotypes. We are particularly interested in the transcriptional networks controlled by nuclear receptor proteins in development and disease. We also are studying the transcriptional mechanisms involved in patterning early embryos. We make use of the compact Drosophila genome and the genomes of related species as model systems for many of our studies, and recently we have also begun to apply these genomics and computational approaches to investigations of the human genome.

Selected Publications

CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia.

McNerney ME, Brown CD, Wang X, Bartom ET, Karmakar S, Bandlamudi C, Yu S, Ko J, Sandall BP, Stricker T, Anastasi J, Grossman RL, Cunningham JM, Le Beau MM, White KP

(Feb 2013) Blood 121(6):975-83 PMID:23212519 (Full Text)

A comprehensive nuclear receptor network for breast cancer cells.

Kittler R, Zhou J, Hua S, Ma L, Liu Y, Pendleton E, Cheng C, Gerstein M, White KP

(Feb 2013) Cell reports 3(2):538-51 PMID:23375374

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome.

Ni X, Zhang YE, Nègre N, Chen S, Long M, White KP

(2012) PLoS biology 10(11):e1001420 PMID:23139640 (Full Text)

A cis-regulatory map of the Drosophila genome.

Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP

(Mar 2011) Nature 471(7339):527-31 PMID:21430782 (Full Text)

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

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

(Dec 2010) Science (New York, N.Y.) 330(6012):1787-97 PMID:21177974 (Full Text)

Genomic antagonism between retinoic acid and estrogen signaling in breast cancer.

Hua S, Kittler R, White KP

(Jun 2009) Cell 137(7):1259-71 PMID:19563758 (Full Text)

Unlocking the secrets of the genome.

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH

(Jun 2009) Nature 459(7249):927-30 PMID:19536255 (Full Text)

Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.

Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP

(Feb 2009) Science (New York, N.Y.) 323(5918):1218-22 PMID:19164706 (Full Text)

Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression.

Hua S, Kallen CB, Dhar R, Baquero MT, Mason CE, Russell BA, Shah PK, Liu J, Khramtsov A, Tretiakova MS, Krausz TN, Olopade OI, Rimm DL, White KP

(2008) Molecular systems biology 4:188 PMID:18414489 (Full Text)

Expression profiling in primates reveals a rapid evolution of human transcription factors.

Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP

(Mar 2006) Nature 440(7081):242-5 PMID:16525476

A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression.

Rifkin SA, Houle D, Kim J, White KP

(Nov 2005) Nature 438(7065):220-3 PMID:16281035

A gene expression map for the euchromatic genome of Drosophila melanogaster.

Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP

(Oct 2004) Science (New York, N.Y.) 306(5696):655-60 PMID:15499012

A protein interaction map of Drosophila melanogaster.

Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM

(Dec 2003) Science (New York, N.Y.) 302(5651):1727-36 PMID:14605208

Evolution of gene expression in the Drosophila melanogaster subgroup.

Rifkin SA, Kim J, White KP

(Feb 2003) Nature genetics 33(2):138-44 PMID:12548287

Gene expression during the life cycle of Drosophila melanogaster.

Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP

(Sep 2002) Science (New York, N.Y.) 297(5590):2270-5 PMID:12351791