Non-coding RNAs

What percentage of the genome is made up of repeat sequences, what is majority of this made of?

50% is repeated sequences, a large amount of this is transposons.

What can provide evidence of function in transcipts?

High expression levels.

High degree of conservation.

Experimental evidence that ncRNA is required for biological processes.

What are the most abundant types of RNA?

rRNA 80-90%.

tRNA 10-15%.

mRNA 3-7%

What is snRNA?

Small nuclear RNA. Variety of nuclear processes, including splicing.

What is snoRNA?

Small nucleolar RNA. Processing and chemical modifications of rRNA.

What is miRNA?

Micro RNA. Regulates gene expression by preventing translation of mRNA

What is siRNA?

Small interfering RNA. Direct degradation of selective mRNAs.

What is piRNA?

Piwi-interacting RNA. Bind to piwi proteins and protect from transposable elements

What is lncRNA?

Long non-coding RNA. Regulate diverse cell processes

What are sncRNA fragments?

Newly discovered, many roles

What are the roles of circular RNAs, vault RNAs, and YRNAs?

Multiple roles in translation and protein homeostasis

What are the applications of RNA sequencing?

Abundance estimation, alternative splicing, RNA editing, finding novel transcripts

How is RNA sequencing done?

RNA captured and converted into cDNA.

Adapter ligation and DNA sequencing.

Reads are aligned to an existing gene framework.

Counts per gene determined.

How has RNA sequencing determined regulation of RNA processing?

Fragments of RNA produced align with specific, distinct regions of the RNA.

If random, unregulated degradation took place the fragments would align at random points along RNA sequences

What RNA fragments can be formed from the cleavage of tRNA?

5'-tiRNA and 3'-tiRNA due to cleavage by angiogenin (ANG) at the anticodon loop.

Can then be cleaved further into 5'-tRF and 3'-tRF.

How can 5'-tRF be formed?

Cleavage of the 5' end of tRNA by endonucleolytic cleavage and exonuclease digestion of the D-loop.

How can 3'-tRF be formed?

Cleavage of the 3' end of tRNA at the T-loop

How can tRNA fragments be used to regulate translation?

Inhibition of translation by sequestration of initiation factors.

Trapping of initiation factors.

How can tsRNA cause sequestration of initiation factors?

tsRNA with terminal oligo-G motifs form an RNA G-quadruplex (RG4) structure, which then interacts with initiation factors.

How can tsRNAs trap initiation factors?

Short (18 nt) tsRNAs can bind with different affinities to initiation factors based in modifications at C8 position (U to C).

18nt C8 tsRNA inhibits translation, which 18nt U8 tsRNAs do not.

How can tsRNA target mRNA sequences?

5'-tsRNA targets by 7-mer match to mRNA, inhibits translation in an AGO-dependent manner.

How can tsRNA increase translation?

Formation of a duplexed structure in mRNA can impede translation, binding of tsRNA-LEuCAG unfolding the duplex increasing ribosome biogenesis and global translation

How can tsRNA impede mRNA loading in archaea/yeast?

5'-tsRNA-Val competes with 16S rRNA of the small subunit of the ribosome and impedes mRNA loading, inhibiting translation.

How can the region of RNA responsible for a fragment be determined?

RNA-sequencing can identify the location of a fragment of RNA on a full sequence of RNA

What are circular RNAs?

Covalently closed, endogenous biomolecules in eukaryotes with tissue and cell-specific expression patterns.

Biogenesis is dependent on the canonical splicing machinery

What are some functions of circRNAs?

miRNA sponges/decoys, Protein sponges/decoys, protein recruitment, protein scaffolding

How can circRNAs be produced?

Produced from splice sites after transcription and splicing. Highly expressed and often expressed in tandem with specific transcripts.