HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

HOT (highly occupied target) regions bound by many transcription factors are considered to be one of the most intriguing findings of the recent modENCODE reports, yet their functions have remained unclear. We tested 108 Drosophila melanogaster HOT regions in transgenic embryos with site-specifically integrated transcriptional reporters. In contrast to prior expectations, we found 102 (94%) to be active enhancers during embryogenesis and to display diverse spatial and temporal patterns, reminiscent of expression patterns for important developmental genes. Remarkably, HOT regions strongly activate nearby genes and are required for endogenous gene expression, as we show using bacterial artificial chromosome (BAC) transgenesis. HOT enhancers have a distinct cis-regulatory signature with enriched sequence motifs for the global activators Vielfaltig, also known as Zelda, and Trithorax-like, also known as GAGA. This signature allows the prediction of HOT versus control regions from the DNA sequence alone

Fly Light Split-GAL4 Driver Collection

<p>The data presented on this site are the work of the <a href="http://janelia.org/team-project/fly-light" target="_blank">Janelia FlyLight Project Team</a> and the laboratories of <a href="http://www.janelia.org/lab/rubin-lab" target="_blank">Gerald M. Rubin</a>. </p><p>The split-GAL4 lines can be requested from the Janelia fly facility by performing a search and adding the desired lines to your cart. You will then be able to use the FlyBank website to tell us where to send them. For additional help ordering lines, please contact us at <a href="mailto:flybank.janelia.org">flybank.janelia.org</a></p><p>In publications, please attribute the data presented on this site to one of the following papers, as follows: <br><br>For the overall strategy and methods used to produce the split-GAL4 lines for the mushroom body neurons: <br>Aso, Y., Hattori, D., Yu, Y., Johnston, R. M., Iyer, N., Ngo, T. B., Dionne, H., Abbott, L. F., Axel, R., Tanimoto, H. & Rubin, G. M. . The neuronal architecture of the mushroom body provides a logic for associative learning. <a href="http://elifesciences.org/content/3/e04577" target="_blank">eLife (2014) 3:e04577</a><br><br>For split-GAL4 lines for the Lobula Columnar (LC) visual projection neurons:<br>Wu, M., Nern, A., Williamson, W. R., Morimoto, M. M., Reiser, M. B., Card, G. M. & Rubin, G. M. Visual projection neurons in the Drosophila lobula link feature detection to distinct behavioral programs. under review<br><br>For refinement of the split-GAL4 vectors and methodology: <br>Pfeiffer, B. D., Ngo, T. T., Hibbard, K. L., Murphy, C., Jenett, A., Truman, J. W. & Rubin, G. M. Refinement of tools for targeted gene expression in Drosophila. <a href="http://www.genetics.org/content/186/2/735.long" target="_blank">Genetics (2010) 186: 735-55</a>. <br><br>For Multicolor Flp-out (MCFO) technique and single cell labeling:<br>Nern, A., Pfeiffer, B.D., and Rubin, G.M. Optimized tools for multicolor stochastic labeling reveal diverse stereotyped cell arrangements in the fly visual system. <a href="http://www.pnas.org/content/112/22/E2967.long" target="_blank">Proc Natl Acad Sci USA (2015) 112: E2967-2976</a>. <br><br>Split-GAL4 lines were designed based on the expression patterns of GAL4 driver lines in the adult nervous system: <br>The Janelia collection of lines is described in Jenett, A., Rubin, G.M., Ngo, T.-T. B., Shepherd, D., Murphy, C., Dionne, H., Pfeiffer, B.D., Cavallaro, A., Hall, D., Jeter, J., Iyer, N., Fetter, D., Hausenfluck, J.H., Peng, H., Trautman, E., Svirskas, R., Myers, G.W., Iwinski, Z.R., Aso, Y., DePasquale, G.M., Enos, A., Hulamm, P., Lam, S.C.B., Li, H-H., Laverty, T., Long, F., Qu, L., Murphy, S.D., Rokicki, K., Safford, T., Shaw, K., Simpson, J.H., Sowell, A., Tae, S., Yu, Y., Zugates, C.T. A GAL4-Driver Line Resource for Drosophila Neurobiology. <a href="http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00292-6" target="_blank">Cell Reports (2012) 2: 991-1001</a> <br><br>The VT collection of lines is described in Kvon, E.Z., Kazmar, T., Stampfel, G., Yanez-Cuna, J.O., Pagani, M., Schernhuber, K., Dickson, B.J., and Stark, A. Genome-scale functional characterization of Drosophila developmental enhancers in vivo. <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13395.html" target="_blank">Nature (2014) 512: 91-95</a> and Barry J. Dickson, unpublished data. <br><br>For opening and viewing h5j and LSM stacks:<br>Use <a href="http://fiji.sc/" target="_blank">Fiji</a> (<a href="http://fiji.sc/" target="_blank">http://fiji.sc</a>). Fiji has a built-in plugin (H5J_Loader_Plugin-1.0.4) for opening stack in h5j format, a "visually lossless" compression format.</p