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Literature DB >> 12876199

Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila.

Ling V Sun¹, Liang Chen, Frauke Greil, Nicolas Negre, Tong-Ruei Li, Giacomo Cavalli, Hongyu Zhao, Bas Van Steensel, Kevin P White.

Abstract

We demonstrate the use of a chromosomal walk (or "tiling path") printed as DNA microarrays for mapping protein-DNA interactions across large regions of contiguous genomic DNA in Drosophila melanogaster. Microarrays were constructed with genomic DNA fragments 430-920 bp in length, covering 2.9 million base pairs of the Adh-cactus region of chromosome 2 and 85,000 base pairs of the 82F region of chromosome 3. We performed DNA localization mapping for the heterochromatin protein HP1 and for the sequence-specific GAGA transcription factor, producing a comprehensive, high-resolution map of in vivo protein-DNA interactions throughout these regions of the Drosophila genome.

Entities: Gene Species

Mesh：

Substances：

Year: 2003 PMID： 12876199 PMCID： PMC170935 DOI： 10.1073/pnas.1533393100

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

26 in total

1. Genome-wide location and function of DNA binding proteins.

Authors: B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal: Science Date: 2000-12-22 Impact factor: 47.728

2. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase.

Authors: B van Steensel; S Henikoff
Journal: Nat Biotechnol Date: 2000-04 Impact factor: 54.908

3. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.

Authors: V R Iyer; C E Horak; C S Scafe; D Botstein; M Snyder; P O Brown
Journal: Nature Date: 2001-01-25 Impact factor: 49.962

4. A global profile of germline gene expression in C. elegans.

Authors: V Reinke; H E Smith; J Nance; J Wang; C Van Doren; R Begley; S J Jones; E B Davis; S Scherer; S Ward; S K Kim
Journal: Mol Cell Date: 2000-09 Impact factor: 17.970

5. Microarray analysis of Drosophila development during metamorphosis.

Authors: K P White; S A Rifkin; P Hurban; D S Hogness
Journal: Science Date: 1999-12-10 Impact factor: 47.728

6. Genome annotation assessment in Drosophila melanogaster.

Authors: M G Reese; G Hartzell; N L Harris; U Ohler; J F Abril; S E Lewis
Journal: Genome Res Date: 2000-04 Impact factor: 9.043

7. Genomic analysis of gene expression in C. elegans.

Authors: A A Hill; C P Hunter; B T Tsung; G Tucker-Kellogg; E L Brown
Journal: Science Date: 2000-10-27 Impact factor: 47.728

8. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints.

Authors: Bing Ren; Hieu Cam; Yasuhiko Takahashi; Thomas Volkert; Jolyon Terragni; Richard A Young; Brian David Dynlacht
Journal: Genes Dev Date: 2002-01-15 Impact factor: 11.361

9. GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.

Authors: Christine E Horak; Milind C Mahajan; Nicholas M Luscombe; Mark Gerstein; Sherman M Weissman; Michael Snyder
Journal: Proc Natl Acad Sci U S A Date: 2002-02-26 Impact factor: 11.205

10. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans.

Authors: M Jiang; J Ryu; M Kiraly; K Duke; V Reinke; S K Kim
Journal: Proc Natl Acad Sci U S A Date: 2001-01-02 Impact factor: 11.205

30 in total

Review 1. Charting gene regulatory networks: strategies, challenges and perspectives.

Authors: Gong-Hong Wei; De-Pei Liu; Chih-Chuan Liang
Journal: Biochem J Date: 2004-07-01 Impact factor: 3.857

2. Identification and analysis of vnd/NK-2 homeodomain binding sites in genomic DNA.

Authors: Lan-Hsiang Wang; Rebecca Chmelik; Derek Tang; Marshall Nirenberg
Journal: Proc Natl Acad Sci U S A Date: 2005-05-03 Impact factor: 11.205

Review 3. Drosophila dosage compensation: a complex voyage to the X chromosome.

Authors: Marnie E Gelbart; Mitzi I Kuroda
Journal: Development Date: 2009-05 Impact factor: 6.868

4. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.

Authors: Celine Moorman; Ling V Sun; Junbai Wang; Elzo de Wit; Wendy Talhout; Lucas D Ward; Frauke Greil; Xiang-Jun Lu; Kevin P White; Harmen J Bussemaker; Bas van Steensel
Journal: Proc Natl Acad Sci U S A Date: 2006-07-31 Impact factor: 11.205

5. A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.

Authors: Yuling Jiao; Peixin Jia; Xiangfeng Wang; Ning Su; Shuliang Yu; Dongfen Zhang; Ligeng Ma; Qi Feng; Zhaoqing Jin; Lei Li; Yongbiao Xue; Zhukuan Cheng; Hongyu Zhao; Bin Han; Xing Wang Deng
Journal: Plant Cell Date: 2005-04-29 Impact factor: 11.277