The Elgin lab has pioneered, within the lab or through collaboration, a number of methods exploiting the unique capabilities of Drosophila: immunofluorescent staining of the polytene chromosomes to determine the distribution of chromosomal proteins; chromatin cleavage by nucleases or chemical reagents followed by Southern blot to map hypersensitive sites and nucleosome arrays; using P elements carrying reporter genes to map euchromatin/heterochromatin status as shown by PEV phenotype. More recently we have utilized high-throughput assays such as ChIP-chip and ChIP-seq (as part of the modENCODE project) to obtain genome-wide determinations of chromosomal protein and histone modification patterns at higher resolution. Others have built on these methods to expand the range and sensitivity of the assays for obtaining genome-wide information; often these newer assays are faster and cheaper than those we developed. However, there are still circumstances under which the older assays are appropriate. Therefore we have grouped here selected papers that discuss these methods. These are generally the last major review of the method, not the first instance (see research publications), but the reviews do provide those references.
More recently, we have collaborated with Jeremy Goecks and Luke Sargent from the Galaxy project to develop a workflow, G-OnRamp, that enables one to create a genome browser for a recently sequenced genome to facilitate collaborative annotation (Liu et al 2019; see http://gonramp.wustl.edu ).
Shaffer, C.D., Wuller, J.M,. and Elgin, S.C.R. (1994) “Raising large quantities of Drosophila for biochemical experiments,” Meth. Cell Biol. 44, 99-108.
Shaffer, C.D., Wuller, J.M., and Elgin, S.C.R. (1994) “Preparations of Drosophila nuclei,” Meth. Cell Biol. 44, 185-189.
Cartwright, I.L., Cryderman, D.E., Gilmour, D.S., Pile, L.A., Wallrath, L.L., Weber, J.A., and Elgin, S.C.R. (1999) “Analysis of Drosophila chromatin structure in vivo,” Meth. Enz. 304, 462-496.
Stephens, G.E., Craig, C.A., Li, Y., Wallrath, L.L., and Elgin, S.C.R. (2003) “Immunofluorescent Staining of Polytene Chromosomes: Exploiting Genetic Tools,” Meth. Enz 376B, 372-393. Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SCR, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD. (2011) “An assessment of histone modification antibody quality,” Nature Struct Mol Biol 18:91-93. Epub. PMID: 21131980.
Liu, Y, L Sargent, W Leung, SCR Elgin, J Goecks (2019) G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation.
Submitted for publication; preprint available at https://www.biorxiv.org/content/early/2018/12/18/499558.