Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless

Genome Research
Edwin J OstrinRui Chen

Abstract

The discovery of direct downstream targets of transcription factors (TFs) is necessary for understanding the genetic mechanisms underlying complex, highly regulated processes such as development. In this report, we have used a combinatorial strategy to conduct a genome-wide search for novel direct targets of Eyeless (Ey), a key transcription factor controlling early eye development in Drosophila. To overcome the lack of high-quality consensus binding site sequences, phylogenetic shadowing of known Ey binding sites in sine oculis (so) was used to construct a position weight matrix (PWM) of the Ey protein. This PWM was then used for in silico prediction of potential binding sites in the Drosophila melanogaster genome. To reduce the false positive rate, conservation of these potential binding sites was assessed by comparing the genomic sequences from seven Drosophila species. In parallel, microarray analysis of wild-type versus ectopic ey-expressing tissue, followed by microarray-based epistasis experiments in an atonal (ato) mutant background, identified 188 genes induced by ey. Intersection of in silico predicted conserved Ey binding sites with the candidate gene list produced through expression profiling yields a list of 20 put...Continue Reading

References

Oct 15, 1976·Developmental Biology·D F ReadyS Benzer
Jan 1, 1969·The Journal of Experimental Zoology·A Garcia-Bellido, J R Merriam
May 11, 1982·Nucleic Acids Research·G D StormoA Ehrenfeucht
Sep 23, 1997·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·E DahlR Balling
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·J ToyO H Sundin
Jan 20, 1999·Proceedings of the National Academy of Sciences of the United States of America·B HauckU Walldorf
May 26, 1999·Journal of Bioenergetics and Biomembranes·J A Dow
Jul 3, 1999·Nature Genetics·S TavazoieG M Church
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Benjamin P BermanMichael B Eisen
Aug 30, 2002·Current Opinion in Genetics & Development·Michele Markstein, Michael Levine
Nov 1, 2002·Developmental Cell·Angelike Stathopoulos, Michael Levine
Dec 5, 2002·Mechanisms of Development·Olivier Renaud, Pat Simpson
Jan 17, 2003·Genome Research·Laura ElnitskiFrancesca Chiaromonte
Mar 26, 2003·Proceedings of the National Academy of Sciences of the United States of America·Lydia MichautWalter J Gehring
Jun 10, 2003·Nature Biotechnology·Li ZhangKenneth D Aldape
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Sep 2, 2003·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Nov 25, 2003·Nature·Jayanagendra P RayapureddiRashmi S Hegde
Nov 25, 2003·Nature·Tina L TootleIlaria Rebay
Jul 16, 2004·Development·Claudio PunzoWalter J Gehring
Sep 2, 2004·PLoS Biology·Mark D SchroederUlrike Gaul
Nov 24, 2004·The International Journal of Developmental Biology·Kartik S Pappu, Graeme Mardon

❮ Previous
Next ❯

Citations

Jun 22, 2011·Nucleic Acids Research·Natascha BushatiChristopher Watkins
Aug 2, 2006·Genome Biology·Jennifer Jemc, Ilaria Rebay
Jul 25, 2014·PloS One·Umesh C KarandikarGraeme Mardon
Oct 2, 2012·Briefings in Functional Genomics·Matthew SlatteryKevin P White
Dec 20, 2007·Arthropod Structure & Development·Patrick CallaertsKorneel Hens
Mar 17, 2016·Scientific Reports·Meng Jin, Graeme Mardon
Aug 30, 2008·Current Opinion in Genetics & Development·Lynn M Powell, Andrew P Jarman
Dec 9, 2008·Developmental Biology·Claire L Salzer, Justin P Kumar
Mar 19, 2014·Developmental Biology·Jessica A BlaquiereEsther M Verheyen
Feb 20, 2015·PLoS Genetics·Carla S Lopes, Fernando Casares
Apr 30, 2016·Experimental Eye Research·Ales Cvekl, Patrick Callaerts
Sep 29, 2009·Developmental Biology·Nicolas A D ChristophorouAndrea Streit
Mar 2, 2017·Development·Jannik VollmerDagmar Iber
Sep 10, 2013·Wiley Interdisciplinary Reviews. Developmental Biology·Jessica E Treisman

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.