Primary and Shadow Enhancers of Dorsal - Ventral Patterning Genes in Drosophila melanogaster
Keywords:Drosophila melanogaster, enhancers, transcription factors, in-silico, gene expression, activator, repressor, flanking sequence, cluster motifs
Recent studies have revealed that multiple enhancers can activate the transcription of a gene. They can be classified as primary or shadow enhancers. Earlier studies suggested that many dorsal target genes of Drosophila melanogaster might be regulated by these shadow enhancers. Therefore, primary and shadow enhancers of five different dorsal targeting genes viz., zen, sim, vnd, bun, and rho were predicted in this study. In addition, novel cluster motifs with high strand scores have been predicted and are referred to as primary enhancers, whereas similar sequences within 5kb are referred to as shadow enhancers. The information generated from this study may lead to the evolutionary innovation of enhancer mechanisms.
How to Cite
Cannavo E, Khoueiry P, Garfield D A, Geeleher P, Zichner T, Gustafson E H, Ciglar L, Korbel J O, Furlong E E M. 2016. Shadow enhancers are pervasive features of developmental regulatory networks. Current Biology 26 (1): 38-51.
Guerrero L, Cervera M. 2010. Secondary enhancers synergise with primary enhancers to guarantee fine- tuned muscle gene expression. Developmental Biology 337 (1): 16-28.
Hong J W, David A, Hendrix, Levine M. 2008. Shadow enhancers as a source of evolutionary novelty. Science 321(5894): 1314.
Ip Y T, Park R E, Kosman D, Yazdanbakhsh K, Levine M. 1992. Dorsal-twist interactions establish snail expression in the presumptive mesoderm of the Drosophila embryo. Genes and Development 6 (8): 1518-1530.
Jiang J, Kosman D, Tony Ip Y, Levine M. 1991. The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos. Genes and Development 5(10): 1881-1891.
Jiang J, Levine M. 1993. Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. Cell 72(5): 741-752.
Kapil S, Kaur T. 2021. Computational prediction and analysis of dorsal-ventral patterning gene enhancers in Drosophila melanogaster. Uttar Pradesh Journal of Zoology 42 (15): 83-89.
Khan A, Fornes O, Stigliani A, Gheorghe M, Mondrgon J, Vander-Lee R, Bessy A, et al. 2018. JASPAR update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research 6 (D1): D260-D266.
Kirschner M, Gerhart J. 1998. Evolvability. PNAS 95(15): 8420-8427.
Martin C F, Michael C Li, Zhiping W. 2003. Cluster-Buster: finding dense clusters of motifs in DNA sequences Nucleic Acids Research 31(13): 3666-3668.
Morel V, Schweisguth F. 2000. Repression by suppressor of hairless and activation by Notch are required to define a single row of single-minded expressing cells in the Drosophila embryo. Genes and Development 14(3): 377-388.
Ozdemir A, Ma L, White K P, Stathopoulos A. 2014. Su (H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos. Developmental Cell 31(1): 100-113.
Scholes C, Biette K M, Harden T T, DePace A H. 2019. Signal integration by shadow enhancers and enhancer duplications varies across the Drosophila embryo. Cell Reports 26: 2407-2418.
Small S, Arnosti D N. 2020. Transcriptional Enhancers in Drosophila. Genetics 216(1): 1–26.
Waymack R, Fletcher A, Enciso G, Wunderlich Z. 2020. Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic. eLife 9: e59351.
Zeitlinger J, Zinze R P, Stark A, Kellis M, Zhang H, Young R A, Levine M. 2007. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes and Development 21(4): 385-390.