What genes can be used to validate H3K27me3-ChIP - (Jun/29/2009 )

I am going to do a ChIP against H3K27me3 in a cell type hasn't been studied for this histone modification before. Is there any well recognized common H3K27me3 target. So that I can validate the ChIP assay itself before jumping into the following seqencing step?

-TracyDuke-

Hi Tracy,

One reply in this forum or other ChIP place did mention that in -2007 nature
papers addressed H3K27me3 as Mark;
Sorry, for the moment , I cannot remember these papers (authors/ titles);
maybe later. But Just for as neg control withH3K27me3 (i.e. silencing ) ,
for sure , one guy used H3K27me3 on GAPDH promoter.

Bus

-BioBus-

Thank you BioBus. If you, by any chance, recall the information about that paper later, would you pls let know? A million thanks!

-TracyDuke-

TracyDuke on Jun 29 2009, 12:45 PM said:

Thank you BioBus. If you, by any chance, recall the information about that paper later, would you pls let know? A million thanks!

I am not sure , but have a look at , Tarjei S. Mikkelsen1,2, ....Bradley E. Bernstein1,4,6* , 2007 nature

http://www.nature.com.ezp-prod1.hul.harvar...ature06008.html

-BioBus-

TracyDuke on Jun 29 2009, 07:27 PM said:

We use Gsx2 (a gene involved in the brain) as our positive control. What cells are you using?
Clare

-Clare-

Thank you Clare. We are using B cells.
Say, CD2 is silent in B cells. Can I just use CD2 as a positive control in the validation of H3K27me3-ChIP? If yes, shall I just amplify the core promoter region (spanning the transcriptional start site) of CD2 gene?

-TracyDuke-

TracyDuke on Jun 29 2009, 11:27 AM said:

Rhodopsin has worked well for us in multiple cell types.

-KPDE-

TracyDuke on Jun 29 2009, 11:27 AM said:

I use SFRP4 - I used it first in a primary cell which hasn't been studied before and it worked really well, it is from:

Schlesinger, Y., et al., Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genetics, 2007. 39(2): p. 232-236 and Sen, G., D. Webster, and D. Barragan, Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. Genes and Development, 2008. 22: p. 1865-1870.

Think the supplemental data from Sen has primer sequence.

Good luck

-orlatron-

If I plan to use B.actin promoter to see H3K4me3 and H3K27me3 marks, how are the marks suposed to be seen. Should I see no K27 marks??

thanks

-kika-