I presented the CAGE technology and the paper "Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE" by A.Sandelin et.al. during the Next Generation Sequencing course at Karolinska Insitutet.
- RNA Pol II - H3K4me1 - H3K27ac - p300 Active promoters Shen et al, 2012. Nature Antibody specificity and quality Lower resolution Computational peak-calling ENCODE Consortium provides • ChIP-seq analysis • Dnase hypersensitive site analysis • DNA methylation analysis Used as validation methods for DeepCAGE Rapid Amplification of cDNA ends (RACE) Capping of specific transcripts RT-PCR and PCR needed to amplify the ends of the transcripts (mRNA and cDNA, respectively) Difficult to validate (designing primers) new core promoters if the exon structure of the downstream protein is not known. Great sensitivity for lowly expressed transcripts
in different tissues, or in different cell types within the tissue. Restore the unfunctional PEP or inhibit the activity of an alternatively activated promoter - antigene RNAs (agRNA) - peptide nucleic acids (agPNA) - locked nucleic acids (LNA) in vitro (Janowski et al. 2005. Nat Chem Biol) General overview of the PEP (Preferentially Expressed Promoters) in a tissue- or cell- specific manner Biological relevance of CAGE Compare the PEP in normal and disease condition (cancer or other diseases).