I am working on an RNA-Seq project, and I am aware that some researchers use housekeeping genes as a method of normalization. My project has several different tissues, and I was wondering if housekeeping gene expression is generally invariant across tissue type?
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asked Sep 23, 2016 at 11:37
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1$\begingroup$ There is no such thing as a universal housekeeping gene. $\endgroup$– MattDMoSep 23, 2016 at 16:10
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2 Answers
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My experience is: Yes they can vary quite a lot (according to differences in the genetic profile of the cells) and you have to test this. As a primer I can recommend reading the articles listed below. These are mostly looking into this in the context of realtime PCR, but this should be valid for RNAseq as well. For some applications it is also a good idea to use more than one gene for normalization.
References:
- Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
- Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR
- Reference Genes / Housekeeping Genes
- Gene Ontology Based Housekeeping Gene Selection for RNA-seq Normalization
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It depends on the definition of housekeeping genes. ENCODE recently released RNA-seq of 17 tissues at 8 developmental stages.
A list of housekeeping genes was also provided.
They are not exactly constant. They just are less variable than other genes.
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1$\begingroup$ Your answer sounds as if it may be correct, however in order for the reader to find out he needs to go to an external site. It would be more useful, and more in keeping with our model if you could flesh out your statement "They are not exactly constant" with some representative examples, which would enable us to upvote your answer. The interested reader (the poster has presumably finished his project now) can follow your link for full details. $\endgroup$– DavidSep 4, 2020 at 16:20