1. Chen yonggang Transcription Zhejiang Univ. School of Medicine

2. What you should already know: DNA RNA protein transcription translation nucleotides amino acids

3. DNA is the carrier of genetic information from one cell to all of its progeny. DNA is comprised of nitrogen-containing bases (A, T, G, C) connected to deoxyribose sugars, linked by a phosphate backbone. DNA is transcribed into RNA upon the basis of complementary base formation by RNA polymerase. RNA is comprised of nitrogen-containing bases (A, U, G, C) connected to ribose sugars, linked by a phosphate backbone. The “T” of DNA codes the same as the “U” of RNA. The only difference is that T has a methyl group in the 5-position. The RNA molecule, which contains both coding regions (exons) and intervening, noncoding sequences (introns) is processed by splicing to yield a mature mRNA containing a 3’ polyA tail. The mature mRNA is then translated into a sequence of amino acids on the ribosome using three letter codons that direct the utilization of a specific tRNA charged with a specific amino acid. There are a total of 64 possible unique 3-base codons that can be generated from four bases. There are only about 20 structural amino acids needed for protein synthesis, therefore multiple codons can encode the same amino acids. Some codons provide “punctuation”, serving as either initiation or termination signals. Some proteins carry additional amino acid sequences (signals) that aid in the delivery of proteins to the correct cellular location. Proteins can serve as structural elements, provide physiological functions, and serve as enzymes in the catalysis of biochemical reactions.

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5. Additional complexities: DNA RNA protein transcription translation Transcription is controlled at multiple levels including regulation of/by transcription factors, and chromatin structure (next lectures-Dr. Neidigh) Additional levels of complexity have been discovered with respect to RNA processing and turnover. degradation It was previously thought that once formed, most proteins existed for the life of the cell. It is now known that degradation and protein turnover occur regularly and that human disease can result from defects in protein turnover.

6. Comparison of prokaryotic and Eukaryotic mRNA molecules: Mol. Biol. Of the Cell, Alberts et al., 2002.

7. initiation Capping and elongation polyadenylation splicing nuclear export Overview of mRNA synthesis

11. RNA factory concept: Mol. Biol. Of the Cell, Alberts et al., 2002.

13. The number of “factors” involved in elongation is growing: you can’t keep up with it

15. DNA Supercoiling:

17. RNA splicing The average human gene contains a mean of 8.8 exons with a mean size of 145 nucleotides. The mean intron length is 3365 nucleotides and the 5’ and 3’ untranslated regions (UTR’s) are 770 and 300 nucleotides, respectively. More than 90% of the pre-mRNA is removed as introns. Though this seems wasteful, this removal enables eukaryotes to increase the coding potential of their genomes. The introns are removed through a process called splicing. The 5’ spice site in higher eukaryotes conforms to the consensus sequence AG/GURAGU where “/” is the cut site, R = purine and Y = pyrimidine. The 3’ splice site is characterized by the sequence YAG/ and is preceded by a stretch of pyrimidine residues in most vertebrate introns. Another sequence element, the branch site is usually located at a distance of 18 to 40 nucleotides upstream from the 3’ splice site.

19. Trans-esterification: R-C- OR’ + R”O-H = O R-C- OR” + R’O-H = O H + or OR” - In the esterification of an acid, an alcohol acts as a nucleophilic reagent; in hydrolysis of an ester, an alcohol is displaced by a nucleophilic reagent. Also one alcohol is capable of displacing another from an ester. This alcoholysis (cleavage by an alcohol) of an ester is called transesterification. Morrison & Boyd, 1987

21. Spliceosome U1 SF1 U2AF 65 U2AF 35 Complex E A B C pGU A (Py)n - AGp U1 U2 U2AF 65 U2AF 35 pGU A (Py)n - AGp U1 U2 U4 U6 U5 Rearrangement to C complex and Catalysis: U1 snRNP is replaced with U6 and U1 &4 are lost from complex pGU A (Py)n - AGp

22. The mammalian consensus sequences at the 5 ’ splice site and the 3 ’ splice site in the pre-mRNA The 5 ’ splice site is defined by the consensus sequence - MAG/GURAGU (M = A or C; R = A or G and the / indicates the exon - intron junction). The 3 ’ splice site is defined by three sequence elements going 5 ’ to 3 ’ : the branch site (YNYURAC, where A indicates the adenosine used to form the lariat intermediate structure during splicing; Y = U or C; N = A or G or U or C) the polypyrimidine tract, and the 3 ’ splice site consensus (YAG/G; Y = U or C). The branchpoint consensus sequence is usually located 18 to 38 nucleotides upstream of the 3 ’ splice site.

26. Alternative splicing can occur in any region of the nascent messenger RNA, in the 3 ’ or 5 ’ untranslated regions (UTRs) or in the protein coding sequence.

30. Complications ! Errors in these processes are known to result in human disease. Familial isolated growth hormone deficiency type II The Wilm’s tumor suppressor gene (WT1) undergoes extensive alternative splicing. Frontotemporal dementia Atypical cystic fibrosis. Spinal muscular atrophy Myotonic dystrophy

34. double-stranded RNA (dsRNA) Dicer (ATP dependent) 19-26 nt siRNA siRNA/protein (RISC) complex formation Gemin3 Gemin4 eIF2C OH-3’ 5’-p target recognition Gemin3 Gemin4 eIF2C p-5’ AAA…A n 7 mGpppG 3’-HO base pairing target cleavage helicase unwinding (?) mRNA AAA…A n 7 mGpppG Modified from Wall NR and Shi Y, LANCET, 2003. OH-3’ 3’-OH 5’-p p-5’ Gemin3 Gemin4 eIF2C OH-3’ 3’-OH 5’-p p-5’

35. G C GXXX XXXXX XXXXX XXXXX X TTC A CXXX XXXXX XXXXX XXXXX X AAG T TCGA AGCTT X XXXXX XXXXX XXXXX XXXC TTTTT G A X XXXXX XXXXX XXXXX XXXG AAAAA CTTAA U6/H1 Promoter 5’ 3’ 3’ 5’ 5’ 3’ 3’ 5’ for HindIII for HindIII for EcoRI Oligo 1a Oligo 1b Oligo 2a Oligo 2b Transcripted siRNA: GXX XXXXX XXXXX XXXXX XX C XX XXXXX XXXXX XXXXX XX 5’ 3’ (U) n C A A G C U U * * ‘ ‘ U U * ‘ pBS/U6/siRNA 3.4 kb U6 KpnI BamHI HindIII EcoRI BamHI

37. A final step in the synthesis of the mRNA molecule is the ligation of the Poly-A tail. The mRNA sequence itself provides the signals that determine the site of polyadenylation. The AAUAAA element 20-30 nucleotides upstream of the cleavage site is where the poly-A is added. Addition of the poly-A tail (approximately 200 A nucleotides) is essential to protect the RNA from 3’ hydrolytic enzymes. Why would a poly-T column be used in an experiment to look at the effects of a drug on gene expression? Polyadenylation

38. PolyA binding proteins (PABP): protecting the ends and directing traffic