BCH3031 Lecture Notes - Lecture 13: Noncoding Dna, H3K4Me3, Epistasis

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25 May 2018
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Lecture 13 The Emerging Role of Long NonCoding RNAs in Cells
Versatility of RNA
Junk DNA
o Number of genes is not correlated to genome size or with organismal
complexity
o Vertebrate genomes can produce more than one polypeptide per gene
because of alternative splicing of RNA transcripts
o Controversial: if its not coding it must be junk
Diversity of RNA functions
Can encode information
Or be substrate for producing proteins
Binds on base pairing efficient at finding its targets
Can form 3D structures (RNA aptamers) interact with specific substrates
Can be direct non coding RNAs allows it to produce a transcript can be
functional straight away after decapping or degraded
Flexible in mismatching base pairing
o Provide flexibility in system mutant RNA retains ability to recognise
its target
Complexity of interactions: 4 nucleic acid and protein interactions
o RNA-protein
Gene regulated by RNA and protein
RNA binding on specific sequences on genome transcription
factors (activator or suppressor)
o DNA-RNA
o Protein-DNA
o RNA-RNA
Characteristics of long non-coding RNAs
E.g. lncRNAs
o Mostly RNA polymerase II (RNA Pol II)
o Can sequence it
o Promoter can identify
H3K4me3 (promoter): Histone 3, lysine 4 and trimethylated
H3K36me3 (gene body): histone 3, lysine 36, trimethylated
region of gene that is going to be transcribed
o >200 nt long
o May undergo splicing or comprise of single exon
o Most are processed just like mRNAs (cap and polyA tail)
o Dynamic and diverse in function
How long non-coding RNAs were identified
Identifications of lncRNAs
o Tiling arrays
cDNA is hybridized to microarray slides
o SAGE
Short stretches of unbiased cDNA sequence (SAGE tags) by
restriction digests
o CAGE
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