Synthesis and processing of RNA

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Synthesis and processing of RNA

• Speaker ???

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The Central Dogma
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(No Transcript)
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Possible Model for DNA Replication
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DNA Replicating Itself
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Structure of DNA
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DNA (deoxyribonucleic acid)

• 4 Bases
• A, G, C, T

Base
Base
- phosphate deoxyribose phosphate
deoxyribose phosphate -
DNA polyribonucleotide
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DNA - A More Detailed Description
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Base Pairing Double Helix
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Schematic View
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RNA Ribonucleic Acid
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RNA (ribonucleic acid)

• 4 Bases
• A, G, C, U

Base
Base
- phosphate ribose phosphate ribose
phosphate -
RNA polyribonucleotide
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RNA Ribonucleic Acid - A More Detailed Description
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RNA

• Several different kinds of RNA
• mRNA messenger RNA
• A copy of gene. The genetic code of protein
• tRNA transfer RNA
• Bind amino acid and mRNA. To carry the amino acid
  elements of a protein to the appropriate place.
• rRNA ribosomal RNA
• Structural components of the ribosome.

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The Central Dogma
DNA
Transcription
Expression
RNA
Translation
Protein
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Synthesis of bacterial mRNAs
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The elongation phase of bacterial transcription

• 3---AACTGTAG---5
• UUGACAUC
• 5---TTGACATC---3

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Transcription (??)

• Transcriptional regulation
• Splicing

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Transcription

• Polymerase
• Transcription Factors

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Initiation of Transcription
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Initiation of Transcription by RNA Polymerase

• TATA box -25 region
• TBP TATA binding protein

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Transcription Factor
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Induction of the Lac Operon
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Repressor
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Termination
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RNA structural motifs
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Example of RNA structure
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Iron response elements (IRE)

• IRE structure

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Post-transcription Modifications
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RNA Synthesis and Processing
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Exon - A More Detailed Description
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Intron splicing

• The existence of introns was not suspected until
  1977.
• We now recognize seven distinct type of intron in
  eukaryotes, and additional forms in the archaea.

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Two competing hypotheses for the evolution of
introns

• When the same gene is compared in related
  species, we usually find that some of the introns
  are in identical positions but that each species
  has one or more unique introns.
• Tow competing hypotheses for the evolution of
  introns
• Introns late
• Introns evolved relatively recently and are
  gradually accumulating in eukaryotic genomes
• Introns early
• Introns are very ancient and are gradually
  being lost from eukaryotic genomes

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Introns in human genes

• These introns must be excised and exons joined
  together in the correct order before the
  transcript can function as a mature mRNA

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Conserves sequence motifs indicate the key sites
in GU-AG introns

• With the vast bulk of pre-mRNA introns, the first
  two nucleotides of the introns are 5-GU-3 and
  the last two 5-AG-3. They are therefore called
  GU-AG introns and all all members of this class
  are spliced in the same way

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Conserved sequence elements (Motifs) at or near
the intron ends
Cartegni et. al. Nature, 2002
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Conserved sequence motifs indicate the key sites
in GU-AG introns

• 5 splice site donor site
• 5-AG?GUAAGU-3
• 3 splice site acceptor site
• 5-PyPyPyPyPyPyNCAG ?-3
• Py U or C
• N A/C/G/U
• ? The exon-intron boundary

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Conserved sequence motifs indicate the key sites
in GU-AG introns
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Outline of the splicing pathway for GU-AC introns

• The splicing pathway can be divided into tow
  step
• Cleavage of the 5 splice site
• Cleavage of the 3 splice site and joining of the
  exons.

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Splicing in outline
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Two aberrant forms of splicing

• Exon skipping
• All splice sites are similar, so if a pre-mRNA
  contains two or more introns then there is the
  possibility that the wrong splice sites could be
  joined
• Cryptic splice site
• A site within an intron or exon that has
  sequence similarity with the consensus motifs of
  real splice sites

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Two aberrant forms of splicing
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The central components of the splicing apparatus

• snRNAs (U1,U2,U4,U5,U6) associate with proteins
  to form small nuclear ribonucleoproteins (snRNPs)

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The roles of snRNPs and associated proteins
during splicing
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Alternative splicing
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Alternative splicing
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Alternative Splicing
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Five Common Types of Alternative Splicing
Cartegni et. al. Nature, 2002
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Steps Leading from Gene to Protein
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Control of Gene Expression
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Introduction to RNA related Databases and Tools

• Non-coding RNA DB
• Rfam http//www.sanger.ac.uk/Software/Rfam/index.s
  html
• mRNA DB
• GenBank http//www.ncbi.nlm.nih.gov/entrez/query.f
  cgi?dbnucleotidecmdindextermsrcdbddbj/embl/g
  enbankprop
• RNA secondary structure prediction tool
• mFold http//www.bioinfo.rpi.edu/applications/mfol
  d/old/rna/form1.cgi