TRANSCRIPTION Student Edition 6/3/13 Version Dr. Brad Chazotte 213 Maddox Hall chazotte@campbell.edu Web Site: http://www.campbell.edu/faculty/chazotte Original material only ©2007-14 B. Chazotte Pharm. 304 Biochemistry Fall 2014 GOALS •Examine the different types of RNAs •Examine the mechanism of RNA replication. •Learn what steps are involved in transcribing DNA to RNA. •Examine which enzymes/proteins are involved in transcription. •Understand how RNA are modified post-transcriptionally •Understand how RNAi’s are involved in post-transcription regulation. •Examine the similarities and differences between prokaryotic and eukaryotic transcription. Types: RNA mRNA (messenger) – basic idea: the sequence of its nucleotides derived from a DNA sequence (gene) is converted (transcribed) by the ribosomes into a protein (sequence of amino acids). rRNA (ribosomal) – forms part of the structure, ribosome, that synthesizes proteins. tRNA (transfer) - small compact molecule that delivers specific amino acids to ribosome for protein synthesis. RNAi (interference) a class of small non coding RNAs that function in post transcription regulation as a silencing mechanism Long Noncoding RNA (lncRNA) extensively transcribed RNAs that do NOT code for proteins that form extensive networks of ribonucleoprotein complexes (RNPs) with numerous chromatin regulators that then target these enzymatic activities to appropriate locations in the genome RNA polymerase (RNAP) - enzyme that synthesizes RNA polymer. Selected Noncoding RNAs Voet, Voet & Pratt 2012 Table 26.1 Transcription The process by which a sequence of DNA nucleotides (gene) are copied (transcribed) to RNA. Major difference between Prokaryotes and Eukaryotes: Prokaryote (single cell organism) – almost all the DNA is “transcribed”. Eukaryote (multicellular & has nucleus) – most of the DNA is not transcribed. Therefore, control mechanisms need to regulate what is transcribed, e.g., consider liver vs brain cell’s structure/function and proteins Sequence for the Transcription Process Initiation, Elongation, & Termination •Find where to start – promoter sequence on DNA that RNA polymerase recognizes. •Get the DNA set – DNA strands must be temporarily unwound so RNA polymerase can read DNA. •Copy the DNA→RNA – RNA polymerase reads the DNA and synthesizes RNA. •Know when to stop - RNA polymerase comes to termination site (sequence). •Goodbye - RNA separates from the RNA polymerase. •Modify RNA – some RNAs may undergo posttranscriptional modification. RNA POLYMERASES (RNAP) Function: Synthesize RNA based on DNA template. Structure: Negative charges uniformly over enzyme outer surface, but inner walls of channel are positively charged. WHY? Prokaryote One enzyme synthesizes all RNAs Eukaryote Four to five different enzymes each synthesizing a different class of RNA Berg, Tymczko, & Stryer 2012 Fig 29.1 RNA POLYMERASES Prokaryote: E. Coli Holoenzyme: 2’σ “whole enzyme”, binds loosely to DNA but specifically to promoter sites. Core enzyme: 2’ Carries out RNA polymerization. It binds tightly but NON-SPECIFICALLY to DNA The sigma subunit, σ, helps the enzyme to bind loosely to DNA but specifically to promoter regions on DNA. Dissociates after initiation. Berg, Tymcko, & Stryer 2012 Table 29.1 Sense and Antisense DNA Strands Only one of two DNA strands transcribed by RNA Polymerase to make RNA strand Antisense (noncoding) strand: the DNA strand that is the template for RNA – it is complementary to the RNA Sense (coding) strand: the DNA strand that has the same sequence as the RNA differing only in thymine for RNA’s uracil. Voet, Voet & Pratt 2013 Fig 26.4 Lehninger (Nelson & Cox) 2005 Fig 26.3 Prokaryotes may have multiple genes controlled together E. Coli lac operon Prokaryotes: (above illustration) genes are frequently arranged in tandem so that they can be transcribed together. Lac operon codes 3 proteins (enzymes) for lactose metabolism. The separate regulatory gene codes for a repressor protein that inhibits lac operon transcription. Eukaryotes: are different – most genes coding proteinsare individually transcribed Voet, Voet & Pratt 2013 Fig 26.5 RNAP Binds to Promoters for Initiation Sense Strand Sequences of selected E. Coli Promoters upstream TATA box Promoter: sequence on 5’ side of initiation site to which RNAP holoenzyme tightly binds. One is TATA box ~ -10 upstream of initiation. Important: The rate of gene transcription depends on the rates at which promoter forms a stable initiation complex with RNAP holoenzyme. The closer to consensus sequence the stronger the promoter. Consensus sequence: an “average” sequence found for many promoters Voet, Voet & Pratt 2013 Fig 26.6 Different Promoter Sequences & Sigmas Bacteria have different sigmas that recognize different promoters. Determines which genes are transcribed Sigma recognizes two sequences – give greater specificity, more precise control, less chance of error ( a good thing). Second centered ~ -35 σ70 σ32 Berg, Tymoczko & Stryer 2012 Fig. 29.11 Transcription Initiation & Elongation by E. Coli RNA Polymerase Multiple transcriptions can occur along DNA molecule RNAP is processive – once the open complex is formed the enzyme proceeds along the template without dissociating. Voet, Voet & Pratt 2013 Fig 26.9 Lehninger (Nelson & Cox) 2005 Fig 26.6 DNA Supercoiling during Transcription ~17 bp Voet, Voet & Pratt 2013Fig 26.8 Transcription Frequency •Transcription frequency is different for different genes Constitutive Enzymes – synthesized at a ~ constant rate. Typically involved in basic cellular functions Inducible Enzymes – synthesis depends on cell’s needs. •Gene expression is found to be significantly controlled via mechanisms that regulate the rate of transcription. •Control can also result from the stability of transcription products. mRNA are much shorter lived than rRNA. Why? Termination of Transcription In E. Coli many gene transcription (spontaneous) termination sequences have: •AT base pairs – series of 4-10 consecutive bases pairs with A’s on template strand. Termination in or just past this sequence. Voet, Voet & Pratt 2008 Fig 26.9a •G+C-rich region with a palindromic sequence immediately before the series of A-T’s. Voet, Voet & Pratt 2008 Fig 26.9b Rho Factor Terminates Transcription A protein hexamer; a helicase catalyzing the unwinding of DNA-RNA or RNA-RNA double helices. •Induces termination of non-spontaneous terminating sequences •Enhances efficiency of spontaneously terminating sequences. Rho binds to an RNA recognition site and slide in 5’3’ direction till encountering RNAP paused at termination site. Rho unwinds DNA-RNA at transcription bubble which releases the RNA. (Rho-RNA Complex) Voet, Voet & Pratt 2008 Fig 26.10 Eukaroytic Transcription Some key differences with prokaryotes: • Multiple RNA polymerases (differ in RNAs they synthesize) • Relatively complex control sequences • More complex process involving > 100 polypeptides In eukaryotes transcription and translation are separated in space. Transcription of the genome occurs in the nucleus. Berg, Tymoczko & Stryer 2012 Fig. 29.21 Eukaryotic RNA Polymerases •RNAP I - synthesizes most rRNA precursors, located in nucleoli •RNAP II - synthesizes mRNA precursors, located in nucleoplasm •RNAP III - synthesizes 5S rRNA precursors, tRNAs & variety of other small nuclear and cytosolic RNAs, located in nucleoplasm Do not have a σ factor like prokaryotes, but the RNAP is recruited to the initiation site by accessory proteins that recognize promoters. Each RNAP recognizes a different promoter. Yeast RNA Polymerase II Structure Voet, Voet & Pratt 2013 Fig 25.12 RNA Polymerase II RNA Elongation Voet, Voet & Pratt 2013 Fig 26.13b Eukaroytic Promoters Some key differences with prokaryotes: • Each RNA Polymerase has it’s own promoters. • Eukaryotes also have ENHANCERS: DNA sequences that can enormously increase the effectiveness of promoters. Play a key role in gene expression in a specific tissue or during development. Position on DNA relative to promoters is NOT fixed. • Transcription factors (coded by gene elsewhere) enable RNA polymerase to find it’s specific initiation site, e.g. Class I TF for RNAP I, Class II for RNAP II . Cis-acting : control elements on the same DNA strand. Trans-acting: control elements from a gene on a different DNA strand, e.g. transcription factors. Eukaryotic Genes Promoter Sequences CCAAT box located upstream of many structural genes Constituently transcribed genes expressed in all tissues have the GC box upstream of transcription start site Structural genes selectively transcribed in one or a few cell types lack GC box but have ATrich sequence resembling the TATA box Eukaryotic RNA polymerases do NOT bind to actual promoter. Berg, Tymoczko & Stryer 2012 Fig. 29.23 Berg, Tymoczko & Stryer 2012 Fig. 29.24 start Voet, Voet & Pratt 2013 Fig 26.15 Voet, Voet & Pratt 2006 Fig 25.13 Eukaryotic General Transcription Factors Similar to the function of prokaryotic σ-factor’s function, eukaryotes utilize a complex of six or more general transcription factors to bind to the promoter region and initiate transcription. TFs, polymerase, and promoter DNA combine to form a PREINIATION COMPLEX (PIC). Voet, Voet & Pratt 2013 Table 26.2 PIC Assembly on a TATA Box Promoter Protein-protein and protein-DNA interactions by transcription factors alter conformations causing changes in structure/function. Note: TF induced kink in DNA (white molecule) Voet, Voet & Pratt 2013 Fig 26.19 Voet, Voet & Pratt 2013 Fig 26.17 Transcription Inhibition & Antibiotics Many antibiotics are highly specific inhibitors of biological processes. A wide variety of compounds can inhibit transcription in prokaryotes and eukaryotes. Rifamycin B specifically inhibits prokaryotic but not eukaryotic transcription by preventing elongation. Actinomycin D tightly binds to double helical DNA and prevents it from being an effective template for RNA Actinomycin D phenoxazone ring intercalates between DNA base pairs unwinding the DNA 23˚and separating neighboring base pairs 7Å Voet, Voet, & Pratt 2013 Box 26.2 Posttranscriptional Processing Primary transcript: the immediate product of transcription RNAs are modified in a number of ways after transcription: • Appending of nucleotide sequences to 3’ & 5’ ends • Exo and endonucleolytic removal of polynucleotide sequences • Modification of specific nucleotide residues mRNA Processing Prokaryote Most mRNAs undergo no modification after transcription. Eukaryote mRNAs are transported out of the nucleus where they are synthesized - can undergo extensive posttranscription processing before leaving the nucleus. Eukaryotic 5’ Cap & Poly(A) Tail on mRNA CAP TAIL Cap protects mRNA from degradation; enhances translation 7-methylguanosine residue joined via a 5’5’ bridge to transcript’s initial 5’nucleotide Voet, Voet & Pratt 2013 Fig 26.20 Poly(A) tail thought to protect mRNA from Mature mRNAs have ~250 nt Poly(A) tail, degradation. The i.e., on their 3’ end. older the mRNA the shorter the tail. Berg, Tymoczko & Stryer 2012 Fig. 29.31 Eukaryotic Genes Contain Exons & Introns Primary Transcripts must be Edited Introns: Nonexpressed intervening sequences are excised from pre-mRNAs Exons: Expressed sequences of mRNA. Edited (spliced ) together after intron excisions. Production of mature mRNAs Voet, Voet & Pratt 2013 Fig 26.22 How are Eukaryotic Exon-Intron Junctions Marked in mRNAs? •High sequence homology at exon-intron boundary – note percentages next to base symbols. •The 3’ splice is preceded by a sequence of 11 predominately pyrimidine nucleotides. •Invariant GU at intron 5’ boundary •Invariant AG at intron 3’ boundary Consensus Sequences at Exon-Intron Junction GU AG Voet, Voet & Pratt 2013 Fig 26.23 Eukaryotic mRNA Splicing Two transesterification reactions involved: 1. Form LARIAT structure from 2’5’ phosphodiester bond between intron’s 5’ terminal phosphate & intron adenosine residue (20-50 residues upstream of 3’ end). 2. The 5’ exon’s free 3’OH displaces 3’ end of intron to form a phosphodiester bond with 5’ terminal phosphate of 3’exon Voet, Voet & Pratt 2013 Fig 26.24 Spliceosome and snRNAs (“snurps”) Spliceosome Spliceosome: 45S particle where splicing occurs. Forms complex with pre-mRNA, snRNPs, & pre-mRNA binding proteins. •Preassembled spliceosome binds to pre-mRNA •Spliceosome undergoes conformational changes as it carriers out the two esterification reactions to excise intron and join adjacent exons. Structure of U1-snRNP small nuclear riboproteins U1-snRNP recognizes complementary consensus sequence at 5’ intron boundary Lehninger (Nelson & Cox) 2005 Fig 26.16c Berg, Tymoczko & Stryer 2012 p. 876 Voet, Voet & Pratt 2008 Fig 25.25b What are the Advantages of Gene Splicing? •Can promote rapid evolution of proteins Noted that many eukaryotic proteins have a modular design. Likely that the genes encoding these modular proteins have arisen via the stepwise collection of exons assembled by recombination between their neighboring introns. •Can provide a means from a single gene to encode multiple proteins via Alternative Splicing. The expression of numerous cellular genes can be modulated by the selection of alternative splice sites. As such one may have exons in one cell type be introns in another cell type. Gives greater protein diversity in fewer completely separate genes. Alternative Splicing •Occurs in all multicellular organisms. •Especially prevalent in vertebrates •Some 60% of human structural genes are subject to it. Exons can be retained or skipped Alternative Splice Site Selection in Drosophila Sex Determination Pathway Introns may be excised or retained 5’ or 3’ splice sites can be shifted to make exons longer or shorter Transcription start site or polyadenylation site can be altered to further diversify of a gene’s product Voet, Voet & Pratt 2006 Fig 25.26 mRNA Stability/Half-Life •Most mRNAs have limited stability •In Eukaryotes half-life ~ 30min or less •Shortest half-life for coding for regulatory proteins •Long sequence of AU-rich nucleotides can code for enhanced degradation by stimulating removal of poly(A) tail. •(Compared to Prokaryotes typical half-life ~ 3 min.) ALberts, Bray et al 1994 p 464 RNAi – Post-transcriptional Regulation of mRNA (Gene Silencing) Roles of Small ncRNAs in Cells Group 1: the siRNAs - target mRNAs for destruction Group 2: the miRNAs – generally regulate protein translation from mRNAs Group 3: the short siRNAs which target chromatin for modification Elliot & Ladomery “Molecular Biology of RNA” 2011 Table 18.1 Important RNAi Definitions •RNAi Ribonucleic Acid interference (see Fire et al 1998) •siRNA Short interfering RNA. These are dsRNA 21-25bp in length with a 3’ overhang that are processed from longer RNAs by the enzyme “Dicer”. Synthetic siRNA can be introduced in mammalian cells to produce interference. •miRNA microRNA. ssRNA 19-23nt long that originate from ss precursor transcripts characterized by imperfectly base-paired hairpins. Function as a silencing complex. •piRNA PIWI-interacting RNAs 24 -32 nt long involved in germ line cells. Function: Block transposons •shRNA Short (interfering) hairpin RNA. Used to supply siRNAs with vector-based approaches to produce stable gene silencing ( a research, experimental approach to add exogenous RNAs) •RISC RNA-induced silencing complex. A nuclease complex of proteins and siRNA, miRNA, etc. that targets and cleaves mRNAs complementary to the siRNA, miRNA, in the RISCRNAi complex. & Epigentics Sourcebook, Invitrogen 2010 How RNA interference (RNAi) works This illustration is based on in vitro approaches to using RNAi in research RNAi & Epigentics Sourcebook, Invitrogen 2010 1 In this process the antisense strand of the siRNA duplex becomes part of a multi-protein complex, or RNAinduced silencing complex (RISC), 2 RISC identifies the corresponding mRNA and cleaves it at a specific site. 3 This cleaved message is targeted for degradation -results in the loss of protein expression.” Can induce RNAi as: • synthetic molecules • RNAi vectors In vitro dicing of RNA (Figureleft). In mammalian cells, short pieces of dsRNA, short interfering RNA (siRNA), initiate the specific degradation of a targeted cellular mRNA. RNAi & Epigentics Sourcebook, Invitrogen 2010 miRNAs •Are small noncoding RNAs that play important roles in posttranscriptional gene regulation. •May comprise a new layer of regulatory control over gene expression programs in many organisms. •In animal cells miRNAs regulate their targets by translational inhibition and mRNA destabilization Ann Rev Cell Biol 23 175-205 2007 miRNA Naturally occurring and evolutionarily conserved Effect gene expression Most miRNAs transcribed by RNA Polymerase II –form stem-loop structures Located either within mammalian introns or exons of protein-coding genes (70%) or intergenic areas (30%). Found to downregulate gene expression by base-pairing with the 3’ untranslated regions (3’UTRs) of target mRNAs. Annu Rev Cell Biol 23 175-205 2007 Annu Rev Med 60 167 2009 miRNA Biogenesis Pri - Primary transcript •miRNA gene transcribed by Pol II. •Drosha an RNase III endounclease & DGR8/Pasha protein in nucleus cleave PrimiRNA to give 2nt overhang •Exportin-5 transports pre-miRNA into cytoplasm •Cleaved by the Rnase III endonuclease, Dicer, and TRBP/loquacious protein •Release 2-nt 3 overhang containing 21nt miRNA:miRNaA*duplex •miRNA strand loaded into an Argonaute containing RISC •(miRNA* typically degraded) Annu Rev Cell Biol 23 175-205 2007 Fig. 1 siRNA Differ from miRNAs mainly in their origin. siRNA derive from endogenous or exogenous dsRNAs and are processed into smaller siRNAs by Dicer siRNAs usually induce cleavage of their targets when loaded onto an Ago2-containing RISC (RNA-induced silencing complex). Can also act like miRNAs on targets with imperfect complementarity and induce translational repression Ann Rev Cell Biol 23 175-205 2007 piRNA •Small non-coding RNAs involved in gamateogenesis (Mammals generate huge numbers of pachytene piRNAs {pachytene a stage in meiosis} that do not match transposon sequence – function currently unknown) •Interact with piwi proteins and Argonaute proteins. •Contain partial and complete (complementary) transposon sequences that serve as memory banks for the pi system analogous to how the immune system defends an organism. (Think of it as a “genome immune system”. •piRNAs track down a transposon and Piwi proteins slice up the rogue DNA. •Some scientists postulate that they adjust gene expression viz. siRNAs and miRNAs. •piRNAs have recently been found in central nervous system – maybe involved in memory [Thompson & Liu Annu. Rev. Cell Dev. Biol. 25:355-376 2009 Leslie Science 339:25-27 2013] RNA-Induced Silencing Complex (RISC) •Complex with an RNAi, Argonaute protein and other proteins. •Uses the RNAi (miRNA, siRNA, etc.) to target a mRNA in the 3’ UTR region and bind to it. •The complex proceeds to degrade the mRNA so the gene product is not expressed. RNAi in Research “RNAi is a specific, potent, and highly successful approach for loss-of-function studies in virtually all eukaryotic organisms. Several appropriate tools to induce RNAi: •Chemically synthesized siRNA and shRNA •miR RNAi-encoding plasmid and viral vectors Select one of the above depending on the model system, the length of time required for knockdown, and other experimental parameters Invitrogen web site need reference miRNAs in Cancer, Viral Infection, & Disease •CANCERS miRNA levels are altered in primary human tumors. Loss of miRNAs in cancer tissues may suggest a role for miRNAs as tumor suppressors. •Significantly different miRNA profiles can be assigned to various tumor types – may be of diagnostic use. •VIRUS INFECTION Viruses use miRNAs in their effort to control their host cell, while reciprocally host cells use miRNAs to target essential viral functions. •e.g. Tourette’s Syndrome miRNA may be involved due to a mutation. Replacement of a GU pair with UA pairing in 3’UTR region of SLITRK1 causes stronger miRNA regulation. Ann Rev Cell Biol 23 175-205 2007 Long Noncoding RNAs (lncRNA) Are key regulatory layers in global gene expression There are now numerous examples of lncRNAs in controlling access or dismissal of regulatory proteins from chromatin. Epigenetics - lncRNAs affect packing of DNA – which, in turn, affects gene expression. Common emerging theme: “they form ribonucleic acid-protein interactions to carry our their functions by modulating chromatinmodifying complexes, by interactions with transcription factors, and likely by many additional mechanisms.” Enhancers transcribe RNA. “Two classes of enhancer RNAs have been identified that are by-products of transcription and lncRNAs that play a role in forming enhancer contacts to promote gene expression” Rinn & Chang Annu. Rev. Biochem 81:145-166 2012 Long Noncoding RNAs: Structure & Function lncRNAs adopt 2° and 3° structures that relate to function. Being able to bind to protein partners facilitates their regulatory capacities in gene expression (facilitating or silencing). •Decoys: At simplest level lncRNAs can serves as decoys that preclude access of regulatory proteins to DNA, i.e. prevent DNA-biding proteins from binding to DNA •Scaffold: lncRNAs can serves as adaptors to bring two or more proteins into discrete complexes. Hundreds of lncRNAs have been identified that form ribonucleic-protein interactions with multiple protein partners. •Guides: Many lncRNAs are individually required for the proper localization of specific protein complexes. Can serve to target gene silencing in an allele-specific fashion. These lncRNAs combine two basic molecular functions – (a) binding a protein partner, (b) a mechanism to interface with selective regions of the genome. Rinn & Chang Annu. Rev. Biochem 81:145-166 2012 lncRNAs & Disease lncRNAs have emerged as key role-players in the etiology of several disease states. •Cancer: Dozens of lncRNAs have been documented to have altered expression in human cancers and are regulated by specific oncogenic and tumor suppression pathways, e.g. P53, MYC and NF-κB •Other: Currently hypothesized that lncRNAs are involved in the pathogenesis of many other diseases. Hundreds of genomic regions that do not contain proteincoding genes are strongly associated with a wide spectrum of human diseases. Rinn & Chang Annu. Rev. Biochem 81:145-166 2012 rRNA Processing Prokaryote In E. Coli, e.g., 5S, 16S, & 23 S rRNA on a primary polycistronic transcript that undergo processing. Eukaryote Genes transcribed and processed in the nucleolus. Primary transcript includes 18S, 5.8S & 28S rRNA. Some eukaryotic rRNAs are self-splicing, i.e. act as own enzyme! Posttranscriptional Processing of E. Coli rRNA Primary Processing : Separate polycistronic primary transcript into separate rRNAs (and 4 tRNAs). Secondary Processing: Trim 5’ & 3’ ends of pre-rRNAs. Methylation (for protection?) of specific residues during ribosome assembly. Voet, Voet & Pratt 2013 Fig 26.29 Eukaryotic rRNA Processing Primary 45S transcript is methylated then cleaved into 5.8S, 18S & 28S. Self-Splicing of Tetrahymena pre-rRNA Methylation sites targeted by small nucleolar (snoRNA) encoded by introns(!) of structural genes. Methyltransferase enzyme does methylation Some rRNAs (group I introns) are self-splicing carrying out transesterification reactions. Occur in nuclei, mitochondria, and chloroplasts, but NOT in VERTEBRATES., Voet, Voet & Pratt 2013Fig 26.30 tRNA Processing •tRNAs are initially made longer and processing shortens them. •RNase P cleaves 5’ and RNase D cleaves 3’ ends •CCA added to 3’ end of all tRNAs •Specific bases are modified (methylation, deamination, or reduction) (some eukaryotic tRNAs have introns that must be excised) Lehninger (Nelson & Cox) 2005 Fig 26.23 Lehninger (Nelson & Cox) 2005 Fig 26.24 End of Lectures