Basic Cycle: large RNA gets chopped up into small RNAs (siRNAs) RNA use by category:
Protists: RNA is used as a template to splice out DNA (RNA-dependent DNA elimination and splicing)
mRNA and DNA in nucleus: DNA chopped and recombined based on gaps in mRNA (“quirky phenom- ena”)
Plants: RNA-dependent RNA polymerase, where the polymerase takes template of RNA and make a copy of it, is available in plants but not humans, and can make small RNAs. Mammals have at most one copies. Very different than RNA polymerase and DNA polymerase in structure. From this, we know that plants do DNA methylation with noncoding RNA.
Flies: use RNAs for an RNA switch; coordinated regulation of hox gene requires noncoding RNA. Mammals: Non-coding RNAs can form triple helices, guide proteins to them; chromatin-modifying complexes; involved in germ line; guide behaviour of transcription factors.
For the rest of this talk, we focus on specifically lincRNA, which we will define as RNA larger than 200 nucleotides.
Long non-coding RNAs
There are a number of different mechanisms and biological devices by which epigenetic regulation occurs. One of these is long non-coding RNAs which can be thought of as fulfilling an air traffic control function within the cell.
Long non-coding RNAs share many similar characteristics with microRNAs. They are spliced, contain multiple exons, are capped, and poly-adenuated. However, they do not have open reading frames. They look just like protein coding genes, but cannot.
They are better classified by their anatomical position:
Antisense: These are encoded on the opposite strand of a protein coding gene.
Intronic: Entirely contained with an intron of a protein coding gene.
Bidirectional: These share the same promoter as a protein coding gene, but are on the opposite side.
Intergenic: These do not overlap with any protein coding genes. Think of them as sitting blindly out in the open. They are much easier targets and will be the focus of this chapter.