Literature DB >> 19308935

Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time.

Benjamin P Berman1, Baruch Frenkel, Gerhard A Coetzee.   

Abstract

A small fraction of the typical animal genome (<5% in humans) codes for the organism's collection of proteins, yet the study of protein coding sequences dominated the early years of genomics research. In the decade since the sequencing of complete eukaryotic genomes, however, genomic techniques have shed a great deal of light on the non-coding DNA making up the remainder. A single molecular technique, Chromatin Immuno-Precipitation (ChIP) location analysis, has had a profound impact and has made possible the study of an incredible range of biology. This issue of The Journal of Cellular Biochemistry aims to put into context advancements made possible by the ChIP-location revolution, while at the same time highlighting some of the most important technical aspects and challenges along with some of the work yet to come.

Entities:  

Mesh:

Year:  2009        PMID: 19308935      PMCID: PMC2748114          DOI: 10.1002/jcb.22133

Source DB:  PubMed          Journal:  J Cell Biochem        ISSN: 0730-2312            Impact factor:   4.429


  46 in total

1.  Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Authors:  David S Johnson; Wei Li; D Benjamin Gordon; Arindam Bhattacharjee; Bo Curry; Jayati Ghosh; Leonardo Brizuela; Jason S Carroll; Myles Brown; Paul Flicek; Christoph M Koch; Ian Dunham; Mark Bieda; Xiaoqin Xu; Peggy J Farnham; Philipp Kapranov; David A Nix; Thomas R Gingeras; Xinmin Zhang; Heather Holster; Nan Jiang; Roland D Green; Jun S Song; Scott A McCuine; Elizabeth Anton; Loan Nguyen; Nathan D Trinklein; Zhen Ye; Keith Ching; David Hawkins; Bing Ren; Peter C Scacheri; Joel Rozowsky; Alexander Karpikov; Ghia Euskirchen; Sherman Weissman; Mark Gerstein; Michael Snyder; Annie Yang; Zarmik Moqtaderi; Heather Hirsch; Hennady P Shulha; Yutao Fu; Zhiping Weng; Kevin Struhl; Richard M Myers; Jason D Lieb; X Shirley Liu
Journal:  Genome Res       Date:  2008-02-07       Impact factor: 9.043

2.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.

Authors:  Lars Guelen; Ludo Pagie; Emilie Brasset; Wouter Meuleman; Marius B Faza; Wendy Talhout; Bert H Eussen; Annelies de Klein; Lodewyk Wessels; Wouter de Laat; Bas van Steensel
Journal:  Nature       Date:  2008-05-07       Impact factor: 49.962

3.  SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis.

Authors:  Hye-Jung Han; Jose Russo; Yoshinori Kohwi; Terumi Kohwi-Shigematsu
Journal:  Nature       Date:  2008-03-13       Impact factor: 49.962

4.  Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome.

Authors:  Jing Zhao; Bryan K Sun; Jennifer A Erwin; Ji-Joon Song; Jeannie T Lee
Journal:  Science       Date:  2008-10-31       Impact factor: 47.728

5.  The ENCODE Project at UC Santa Cruz.

Authors:  Daryl J Thomas; Kate R Rosenbloom; Hiram Clawson; Angie S Hinrichs; Heather Trumbower; Brian J Raney; Donna Karolchik; Galt P Barber; Rachel A Harte; Jennifer Hillman-Jackson; Robert M Kuhn; Brooke L Rhead; Kayla E Smith; Archana Thakkapallayil; Ann S Zweig; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2006-12-13       Impact factor: 16.971

6.  Species-specific transcription in mice carrying human chromosome 21.

Authors:  Michael D Wilson; Nuno L Barbosa-Morais; Dominic Schmidt; Caitlin M Conboy; Lesley Vanes; Victor L J Tybulewicz; Elizabeth M C Fisher; Simon Tavaré; Duncan T Odom
Journal:  Science       Date:  2008-09-11       Impact factor: 47.728

7.  Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Authors:  Raja Jothi; Suresh Cuddapah; Artem Barski; Kairong Cui; Keji Zhao
Journal:  Nucleic Acids Res       Date:  2008-08-06       Impact factor: 16.971

8.  Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation.

Authors:  Emily E Hare; Brant K Peterson; Venky N Iyer; Rudolf Meier; Michael B Eisen
Journal:  PLoS Genet       Date:  2008-06-27       Impact factor: 5.917

9.  Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer.

Authors:  Kerstin B Meyer; Ana-Teresa Maia; Martin O'Reilly; Andrew E Teschendorff; Suet-Feung Chin; Carlos Caldas; Bruce A J Ponder
Journal:  PLoS Biol       Date:  2008-05-06       Impact factor: 8.029

Review 10.  RNA polymerase II stalling: loading at the start prepares genes for a sprint.

Authors:  Jia Qian Wu; Michael Snyder
Journal:  Genome Biol       Date:  2008-05-02       Impact factor: 13.583

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