June 09, 2017

Multiple Challenges in ChIP (Adam Blattler)

35 minutes

Chromatin Immunoprecipitation (ChIP) was first developed in Drosophila, where interactions of RNA Pol II with genes were investigated (Mol. Cell. Biol. August 1985 vol. 5 no. 8 2009-2018). Then, in a 1993 publication, (Genes & Dev. 1993 7:592-604), the group of James Broach described the association of histone acetylation state with transcriptional gene silencing in yeast. The technique was first used successfully in mammalian cells by Richard Treisman's group, published in 1998 (Cell (1998) 92:475-87).

Chromatin Immunoprecipitation is used to link specific states of chromatin to individual loci in a cell, to understand how genes are regulated, and to decipher the Histone Code. In this Episode, we discuss the multiple challenges of ChIP experiments and the difficulties that can arise during different steps of the process.

References for this episode

Epigenetics News:

Chung-Chau Hon, Jordan A. Ramilowski, … Alistair R. R. Forrest. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature. March 2017. doi:10.1038/nature21374

Jennifer L. Guerriero, Alaba Sotayo, … Anthony Letai. Class IIa HDAC inhibition reduces breast tumours and metastases through anti-tumour macrophages. Nature. March 2017. doi:10.1038/nature21409

Nitika Taneja, Martin Zofall, … Shiv I. S. Grewal. SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication. Molecular Cell. April 2017. DOI:10.1016/j.molcel.2017.02.006

Multiple Challenges in ChIP

D. S. Gilmour, J. T. Lis. In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Molecular and Cellular Biology. August 1985. doi:10.1128/MCB.5.8.2009

M. Braunstein, A. B. Rose, … J. R. Broach. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes & Development. 1993. doi:10.1101/gad.7.4.592

Arthur S. Alberts, Olivier Geneste, Richard Treisman. Activation of SRF-Regulated Chromosomal Templates by Rho-Family GTPases Requires a Signal that Also Induces H4 Hyperacetylation. Cell. February 1986. doi:10.1016/S0092-8674(00)80941-1

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