I want to construct a vector to drive shRNA expression by U6 promoter. However, due to limited genetic space I would like to use minimum possible nucleotides of U6 promoter. Do anybody know whether we can reduce the size of U6 promoter and still get efficient shRNA expression ? Reported size of U6 promoter is 241 bp.
I too was wondering this, and the papers below provide the clearest annotation & characterization of the U6 promoter that I found. They show that an OCT1 binding site ~220bp upstream from the TTS is needed for efficient transcription. Other papers by Kunkel may indicate whether one can shorten the intervening sequences between the PSE and OCT1 site.
"Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used."
https://www.ncbi.nlm.nih.gov/pubmed/3360322
"Functional characterization of elements in a human U6 small nuclear RNA gene distal control region."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC360093/
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