Regulatory elements analysis handouts
- 1. 5/19/202 0 PROMOTER SEQUENCEANALYSI S Isabella BS biochemistry Learning objectives ◦ Introduction ◦ Types of promoter elements ◦ Databases of Promoter elements 2 1
- 2. 5/19/202 0 Two languages in our genes ◦ Protein coding information - indirect reading ◦ DNA transcription pre-mRNA splicing mRNA translation protein ◦ Less than 2% of the human genome ◦ Regulatory information - direct reading ◦ DNA binding of TF gene activation Indirect read-out through transcription/translationDirect read-out by TFs Cis Trans 3 cis-elements = Templates for assembly The function of cis-elements is being templates for the assembly of multiprotein complexes 4 2
- 3. 5/19/202 0 Types of promoter elements ◦ Core Promoter elements ◦ Elements required to initiate the transcription e.g TATA box ◦ Regulatory promoter elements ◦ Responsive elements ◦ CRE, HSE, GRE - mediates response to cAMP, heat shock, glucocorticoids ◦ Cell type specific elements ◦ Location-- mixed with Upstream regulatory elements (UPEs) 5 Three RNA polymerases - three groups of promoters ◦RNA polymerase I ◦ rRNA (28S, 18S and 5.8S ) ◦ RNA polymerase III ◦tRNAs and 5S rRNA ◦RNA polymerase II ◦ Protein-coding genes 80% of total RNAsynthesis from these ”Oddpols” 6 3
- 4. 5/19/202 0 7 Transcription factors Sequence- specific DNA binding Non-DNA binding TF1 TF 2 TF 3 TF 4 adapter HA T DNA Layer I Layer III Co-activator Layer II 8 4
- 5. 5/19/202 0 Transcription factors recognition sites ◦ Typically 6-10 positions very selective and several others show bias ◦ Often selectivity profile summarized by ‘motif’ 9 Eukaryotic promoter databases ◦ TRANSFAC ◦ JASPAR ◦ PLANT CARE ◦ PLACE ◦ Consite 10 5
- 12. 5/19/202 0 Class work ◦ Scan the following sequence in JASPAR and Plant CARE for identification of putative cis-acting elements ◦ Save the results as pdf and email me today ◦ CTGGTCTACTTGGCATTGTAGAAACCATTGAAACTTAACCTGCCAACCTATGTGACCTCTTCCTTTTAG AAACTTGGCTTACGATGCTACATCCCTAGTGGATGCTGATGCATACCTCTTACCCTTCTGGTCAGACT GGTTATCCTTCAACATGTTAGCTGAAAAAAGTACTATGTTGCATGCCATCAATCTCAATAAAAGTTTTGA TGACTTCCACCGACCCGGCAAAAAAAAAAAACAGATATATAGAATTGGCCTTATTAATAACAAGCC TTATTAAGCTAATCGATCGACAGGACTAGCGTTCGGGACAGCCTGCATAAGTGTCCGTACCAGTA CGGTCAGAGTGACATATGGGAAAACCAGTACAGTTAAACTGTATTTATTCTCCAGAAAAAAAAATTG TAGTCTTTGTTACGCCTGTAATATTGCCAGTGAAAGTAATTAACCACTCCCCAGAAAAATGCATGGC GTGTGACCAAGTAAATTTTTGACTAGTCTGCAGAGTGATCAGTGACAAAATTAATGATATGCTAAAAG GTAGCAAAAGCTGCTCGTAATGTCCTTCTCATAATCCTTAATTACCGGCCGGTTCGAAACAATTTGATT TGATCCCAAGATAATGGCGACCAAGTAAATGAAAAAGGTTGGAAACAATAGTTCTTTCGATCGATG ACTTAGCATGCAGGTCATTGATTGATGATGCACGCTCGTTGGCCCTTTCTGCAGATCCGAACATAAC TACTGCTATCCTTAATTTCCTTCAAAAAGAGATAAAAGATAACTACTCTATGCCATCGTCAAAATGTGT GAAAACACAATCGACCACGTCAGGTTAGTTAGTAGTGCCGATACATATATTTTTAAGCTGAAAAGTTC AACCTGCAGGCAGCAAATTGCAGACCATTTCAGTCTACTAGCTGACATCAGTTCAGATTAATTGACT TGTTCAGTTGTTCACAAGTTCACGCTGCCGCGCCCCTGCGGCTATATAAGCACATTAATCCTCCAC AGCCAAAGCATCACCCAACGATAACACAAGCAGTTAGCTAGCAGCTAGCTAGCTTCTCAGCCA CCAGAGAAACAGCAAATAATTCAGCAGAGAAG 23 12