Cap-Seq
CXXC Affinity Purification Plus Deep Sequencing
CAP-seq maps the 5′ end of RNAs anchored to RNAPII (Illingworth et al., 2010). In this method, RNA transcripts are treated sequentially with Terminator exonuclease, CIP, and TAP, followed by linker ligation and RT to cDNA. Deep sequencing of the cDNA provides high-resolution sequences of RNAPII transcripts.
Advantages:
- Maps RNAs anchored to RNAPII
Disadvantages:
- Multiple steps and treatments can lead to loss of material
Reagents:
Illumina Library prep and Array Kit Selector
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References:
Illingworth R. S., Gruenewald-Schneider U., Webb S., et al. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 2010;6:e1001134