The best way could be to design two to three pairs of primers for each gene of interest. But before performing the PCR first verify the primers bioinformatically that they detect your gene of interest. doing BLAST in NCBI.

Now the primer designing depends on the type of marks for instance if you are doing ChIP for H3k4me3 then usually this mark is present at the transcription start site (TSS) so try to restrict your primer pairs in between 500 -1000 bp upstream or 500 bp downstream of TSS of the gene.

or if you are doing ChIP for H3K27me3 then this mark can be present on the whole gene body also so you can design within the gene and some 500 to 1000 bp upstream of the TSS. Like wise try to see first what kind of marks and where they are usually present and then design your primers.

Control gene is again a question depends on what system you are working with usually GAPDH or RPLs are used but first check if there is any report of these house keeping genes to be regulated in that system. Or try to check some expression datasets in the GEO or other microarray study databases to confirm if they are not regulated in your system.

And important thing is you can check for the TSS in the ENCODE or DBTSS databases.

hope my answer gives some help in your research

Best of luck

Prasoon

The best way could be to design two to three pairs of primers for each gene of interest. But before performing the PCR first verify the primers bioinformatically that they detect your gene of interest. doing BLAST in NCBI.

Now the primer designing depends on the type of marks for instance if you are doing ChIP for H3k4me3 then usually this mark is present at the transcription start site (TSS) so try to restrict your primer pairs in between 500 -1000 bp upstream or 500 bp downstream of TSS of the gene.

or if you are doing ChIP for H3K27me3 then this mark can be present on the whole gene body also so you can design within the gene and some 500 to 1000 bp upstream of the TSS. Like wise try to see first what kind of marks and where they are usually present and then design your primers.

Control gene is again a question depends on what system you are working with usually GAPDH or RPLs are used but first check if there is any report of these house keeping genes to be regulated in that system. Or try to check some expression datasets in the GEO or other microarray study databases to confirm if they are not regulated in your system.

And important thing is you can check for the TSS in the ENCODE or DBTSS databases.

hope my answer gives some help in your research

Best of luck

Prasoon

In addition to the suggestions given above, you could also find ChIP-seq data of relevant histone modifications in any relevant tissues you are supposed to use. So look for the histone modification patterns on your candidate gene and draw an average conclusion on the basis of different data as each gene could be an exception to general norms. This could be tedious but it pays if your conditions are rigorous Likewise, choice of internal control very much depend upon whether it is affected by any treatment you may wish to give to your sample.

Secondly, since the region to design primer from is restricted, you could choose to loosen the Tm restriction and adjust QPCR reaction protocol on the QPCR machine by switching from two step run method to three step run method.