The Hox genes encode a conserved family of homeodomain-containing transcription factors that specify tissue and cellular identities throughout the animal kingdom. As is typical for homeodomain proteins, they tend to bind a wide range of degenerate, TAAT-containing binding sites, raising the fundamental question of how these factors achieve specificity in vivo. We use a variety of approaches, including whole genome binding studies, in vitro DNA binding assays, X-ray crystallography, in vivo functional tests, and high-throughput DNA specificity measurements, to address this question. Our most recent work (Slattery et al., 2011) reveals that Hox cofactors reveal “latent specificity” that is present in the Hox homeodomain, but cannot be used in the absence of the cofactors. In one specific case (Scr; Joshi et al., 2007) we found that latent specificity allows normally unstructured residues in the Hox protein Scr to read a DNA shape: the width of the minor groove.
Current lab members working on this project: Siqian Feng and Rebecca Delker (collaborations with Barry Honig and Harmen Bussemaker).
Low affinity binding site clusters confer hox specificity and regulatory robustness. Crocker J, Abe N, Rinaldi L, McGregor AP, Frankel N, et al. Cell. 2015; 160(1-2):191-203. PMID: 25557079 PMCID: PMC4449256
Deconvolving the recognition of DNA shape from sequence. Abe N, Dror I, Yang L, Slattery M, Zhou T, et al. Cell. 2015; 161(2):307-18. PMID: 25843630 PMCID: PMC4422406
Quantitative modeling of transcription factor binding specificities using DNA shape. Zhou T, Shen N, Yang L, Abe N, Horton J, et al. Proceedings of the National Academy of Sciences of the United States of America. 2015; 112(15):4654-9. PMID: 25775564 PMCID: PMC4403198 101.
Specification of individual adult motor neuron morphologies by combinatorial transcription factor codes. Enriquez J, Venkatasubramanian L, Baek M, Peterson M, Aghayeva U, et al. Neuron. 2015; 86(4):955-70. PMID: 25959734 PMCID: PMC4441546
Illustrated above are the relative affinities for all of the Drosophila Hox-Exd heterodimers bound to the top ten binding sites identified by our SELEX-seq experiments. See Slattery et al., 2011 for details.
Shown is a space-filling model of the Hox protein Scr (blue) bound with it’s cofactor Exd (gray) to a specific binding site called fkh250 (magenta). In the presence of Exd, two basic Scr side chains, an Arg and a His (green) are positioned in such a manner that they can insert into the minor groove. This region of the minor groove is narrow, making it a poor binding site for most Hox or Hox-Exd heterodimers. See Joshi et al., 2007 for details.
Closeup side view of a narrow minor groove in the fkh250 binding site in which two basic side chains from Scr are inserting. See Mann, 2008 for details.
In collaboration with Barry Honig’s lab at Columbia, we generalized the concept of DNA shape recognition. Sequence-dependent differences in DNA structure, such as the examples illustrated here, can contribute to the recognition of specific DNA sequences by many DNA binding proteins. See Rohs et al., 2009.
Another interest of the lab related to Hox proteins is how transcription factors modify chromatin structures, perhaps in a tissue specific manner, to regulate gene expression. To address these questions, we recently described a novel method to analyze the local chromatin structure in specific cell types during embryogenesis (cgChIP). This figure illustrates a summary from this work, which shows that the local chromatin structure at the Dll gene differs in thoracic expressing cells compared to abdominal non-expressing cells, due to the action of the abdominal Hox proteins. See Agelopoulos et al., 2012, for details.
Slattery et al., Cofactor Binding Evokes Latent Differences in DNA binding Specificity between Hox Proteins. Cell (2011) 147: 1270–1282. PDF
Agelopoulos et al., Developmental Regulation of Chromatin Conformation by Hox Proteins in Drosophila. Cell Reports (2012) 1: 1-10. PDF
Joshi, R. Passner, J., Rohs, R., Jain, R. Sosinsky, A., Crickmore, M.A., Jacob, V., Aggarwal, A.K., Honig, B. and Mann, RS. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell. (2007) 131(3):530-43.
Affolter, M., Slattery, M., and Mann, R.S. A lexicon for homeodomain-DNA recognition. Cell (2008) 133:1133-1135.
Rohs, R., West, S., Sosinsky, A., Liu, P. Mann, RS, and Honig, B. The role of DNA shape in protein-DNA recognition. Nature (article) (2009) 461(7268):1248-53.
Mann RS, Lelli KM, Joshi R. Hox specificity: unique roles for cofactors and collaborators. Curr Top Dev Biol. 2009;88:63-101
West SM, Rohs R, Mann RS, Honig B. Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn. 2010 Jun;27(6):861-6.
Rohs, R., Jin, X., West, S. Joshi, R., Honig, B. and Mann, RS. Origins of Specificity in Protein-DNA Recognition. Annual Review of Biochemistry (2010), Volume 79:233-269.
Joshi, R., Sun, L. and Mann, RS. Dissecting the functional specificities of two Hox proteins. Genes Dev. 2010:24(14); 1533-1545.
PDF:Joshi et al G&D
Slattery, M. Négre, N. Ma, L., White, KP, and Mann, RS. Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila.