@article{c2f0bb6060fd4773b2608e6226b589c0,
title = "Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites",
abstract = "We describe the comprehensive characterization of homeodomain DNA-binding specificities from a metazoan genome. The analysis of all 84 independent homeodomains from D. melanogaster reveals the breadth of DNA sequences that can be specified by this recognition motif. The majority of these factors can be organized into 11 different specificity groups, where the preferred recognition sequence between these groups can differ at up to four of the six core recognition positions. Analysis of the recognition motifs within these groups led to a catalog of common specificity determinants that may cooperate or compete to define the binding site preference. With these recognition principles, a homeodomain can be reengineered to create factors where its specificity is altered at the majority of recognition positions. This resource also allows prediction of homeodomain specificities from other organisms, which is demonstrated by the prediction and analysis of human homeodomain specificities.",
keywords = "DNA",
author = "Noyes, {Marcus B.} and Christensen, {Ryan G.} and Atsuya Wakabayashi and Stormo, {Gary D.} and Brodsky, {Michael H.} and Wolfe, {Scot A.}",
note = "Funding Information: We would like to thank Xiangdong Meng for his valuable advice and technical support. We would like to thank the Berkeley Drosophila Genome Project (BDGP) for producing the cDNA clones used in this study, the Drosophila Genomics Resource Center (DGRC) for distributing the clones, and Mark Stapleton and Susan Celniker for sharing unpublished results. Some of these ORFs were obtained from clones produced by BDGP under a National Institutes of Health (NIH) grant (HG002673 to S.E. Celniker). We would like to thank Adam Richards for technical support. S.A.W. and M.B.N. were supported by NIH grant 1R21HG003721 from the National Human Genome Research Institute (NHGRI. A.W. was supported in part by NIH grant 1R21HG003721 from the NHGRI. M.H.B. and A.W. were supported in part by a New Scholar in Aging Award from the Ellison Medical Foundation and American Cancer Society grant RSG-05-026-01-CCG. R.G.C. was supported by training grant T32 GM08802. G.D.S. was supported by NIH grant HG00249 from NHGRI. ",
year = "2008",
month = jun,
day = "27",
doi = "10.1016/j.cell.2008.05.023",
language = "English",
volume = "133",
pages = "1277--1289",
journal = "Cell",
issn = "0092-8674",
number = "7",
}