Housekeeping gene

Figure 1. Hierarchy of control of gene expression. A total of about 50,000 to 100,000 genes are necessary to encode a mammal, most of which encode housekeeping, structural component, or terminal differentiation gene products. Transcription factor genes regulate expression of the lower-level genes and are in turn controlled by other upper-level transcription factors.

Finke et al.54 BJAB cells (B-lymphocytic cell line) 1% SDS + proteinase K Housekeeping gene PBGD (porphobilinogen deaminase) Most routine FFPE tissues will be available for RNA analysis. 

Finke J, Fritzen R, Ternes P, et al. An improved strategy and a useful housekeeping gene for RNA analysis from formalin-fixed, paraffin-embedded tissues by PCR. BioTechniques 1993 14 448—453. 

Some investigators raised questions challenging housekeeping genes or proteins that were recommended as internal controls due to the variable gene/ protein expression that exists in various tissue or organs.35,36... 

In mammals there are four genes for the PMCA pump, two of which are expressed in all tissues (housekeeping enzymes), whereas the other two, which have a particularly high affinity for calmodulin, are restricted in their cellular distribution, notably to neurons. Additional variants of PMCAs are produced by alternative splicing of their primary RNA transcripts. 

Relationships between histone methylation and DNA methylation and histone acetyation and DNA methylation have been reported [191,314,315], A similar relationship may exist between poly(ADP ribosylated) HI and DNA methylation. Inhibition of poly(ADP-ribose) polymerase with 3-aminobenzamide increases the susceptibility of L929 mouse fibroblast nuclei to be methylated by endogenous DNA methyltransferases [316,317], Further, there is evidence that poly(ADP ribosylation) protects CpG islands located at the 5 end of housekeeping genes from methylation [318], Future studies will likely reveal an interesting dynamic relationship between histone methylation, histone acetylation, and histone poly(ADP-ribosylation). 

Designing an array is not a trivial task. In addition to the probes of interest, an array should include appropriate numbers of positive and negative control elements, such as housekeeping genes and controls that can be used to monitor the efficiency of important steps within the process. For example, you may wish to spike in internal standards that track recovery or labeling efficiency among different samples. It is also important to consider how you will print. How many replicates do you want Should these replicates be... 

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