Lecture 22 - Regulatory non-coding RNAs Flashcards
What type of RNA are non coding RNAs?
Transcripts that do not code for protein
- housekeeping ncRNAs (rRNA, tRNA, snRNA)
- regulatory ncRNAs (control gene expression)
- ncRNAs of unknown function
What are the two types of regulatory non-codingRNAs?
Long non-coding RNAs (100s of kb)
Short non-coding RNAs
Give an example of a long non-coding RNAs?
e. g. Xist ncRNA involved in dosage compensation (X-inactivation) in mammals
- switch of one X early in expression
- produced from the activated X chromosome
- often act as scaffolds to recruit epigenetic modifiers (histone modifications and DNA methylation) to the inactive chromosome
What are the features of small ncRNAs?
- act as sequence specificity guides for effector complexes
- can influence gene expression at the transcriptional and post-transcriptional level (RNA level)
- MicroRNAs are a major class
- 1000s of sRNAs in higher eukaryotes
- produced by the RNA silencing/RNA interference pathway
What is the process by which sRNAs are produced in the RNA silencing/RNA interference pathway?
- dsRNA is processed into sRNAs (21-25nts) by the DICER class of enzymes (RNAse III class)
- forms small dsRNAs with overhangs
- these then form into effector complexes, RNA-Inducde Silencing Complex (RISC), which is a nucleprotein, including:
- small RNA component (sequence specificty determinant)
- effector component (Argonaute class of proteins, endonuclease activity)
- Accessory proteins
Who discovered RNA interference? And how?
Fire and Mello
- looked at gene expression in c.elegans
- Made GPT transgenic c.elegans
- injected with GFP dsRNA
- no fluorescence
What is the trigger for targeted RNA degradation?
Double-stranded RNA triggers targeted RNA degradation of complementary transcripts
=RNA interferance
What is RNA interference?
Mechanism that allows switching off of any gene through interaction with complementary sRNAs
-triggered by double stranded RNAs
How do sRNAs result in surpression of gene expression?
small RNAs can direct mRNA cleavage or translational inhibition dependeing on the degree of complimentarity with its target (if high or almost exactly complimentary)
- if near perfect complimentarity with a coding region or UTR -> mRNA cleavage
- if have short complementary segment in 3’-UTR -> mRNA tranlational attenuation
How can we identify the biological role of RNA silencing?
- how well conserved
- identify the phenotypic mutnats
- which regions of the genome produce small RNAs
- natural sources of sRNAs
- sequences of the small RNAs and what do they target
What are the mutant phenotypes of RNAi in Arabiposis thaliana?
argonaute1 mutants -effector complex mutated -small, stunted growth, fail to develop properly argonaute2 mutants -hyper-susceptible to virus infection
Therefore role of RNAi:
- control of endogenous gene expression
- defense against invasive nucleic acids
What are the biological role of RNAi?
- control of endogenous gene expression
- defense against invasive nucleic acids
What are the sources of dsRNA?
- read through transcription of inverted repeats e.g. from transposon elements, result in a fold back to form a ds structure
- replicating viruses
- via the copying action of RNA-dependent RNA polymerases (RDRs) (copy RNA into dsRNA)
- ‘Structured loci’ transcrirpts that have the potential to form secondary structures (e.g. miRNA)
What two categories have cloning and sequencing of sRNAs of 21-24nts identifide?
- small interfering RNAs (derived from perfect dsRNA e.g. transposons, viruses, copying action)
- miRNAs (derived from imperfect hairpin structures)
Where can animal miRNAs be derived from?
- mainly from RNA pol III transcripts
- a range of transcript forms that share the imperfect bulge hairpin structure
e. g. miR-21 (1 hairpin)
What is the process of miRNA biogenesis in animals?
- transcription of primary miRNA transcripts (pri-mRNAs) by RNA pol II (have long 5’ and 3’ ends)
- processing of the pri-miRNA to pre-miRNA by the Drosh enzymes
- export of the pre-miRNA into the cytoplams by the specific transporter complex (Exportin5)
- processing of the pre-miRNA by dicer to form the miRNA duplex
- unwinding of the duplex and loading into the RISC effector complex
- target mRNA cleavage or inhibition of translation
Give an example of how miRNAs control developmental transitions?
- miR156 targets SPL3 mRNA
- SPL3 is a transcription factor that promotes the juvenile to adult transition in arabidopsis (no flowers -> flowers)
- miR156 supresses SPL3, consequentially supressing the juvenile to adult transition
Tested by increasing/decreasing miR156 activity
- over expression of miR156 by conjugating the sRNA to a strong promoter e.g. 35s promoter results in a delay in flowering
- expression of miR156 resistant form of SPL3 (by changing the nucleotide sequence by keeping the aa sequence the same) rsuls in an early flowering and a short juvenile phase
- expression of an mRNA that sequesters miR156 (dilutes the effect) results in early flowering and a short juvenile phase
How are miRNAs involved in human disease?
- high percentage of human genes are targets of miRNAs
- any mis-regulation of miRNA expression can have far reaching consequences
- mis-regulation of miRNAs has been associated with many diseases (and proposed as biomarkers)
e. g. Lin28 and let-7, miR200, miRNAs involved in cardiac disase
Outline the involvement of Lin28 and let-7 miRNAs in cancer
- let-7 is an evolutionarily conserved class of miRNAs, negatively regulated by the RNA binding protein Lin28
- Lin28 is a pluripotency factor
- let-7 has important targets including oncogenes
- Lin28 levels are normally low in developing cells, leading to high Let-7 levels, allowing the supression of onco genes
- Lin28 level are elevated in cancer, supressing Let-7, leading to less supression of oncogenes (c-MYC, K-Ras and cyclin D1)
How is miR200 involved in cancer?
- cancer progression has similarities with the epithelial-to-mesenchymal transition found during embryonic development in which E-cadherin (CDH1) is downregulated
- miR200 usually down regulates ZEB transcription repressors (which repress the expression of CDH1)
- in cancers expression of miR200 is often found to be switched off by DNA methylation
- reduction of miR200 rsults in increased levels of ZEB1 and ZEB2 and consequently reduced levels of CDH1 - increased cancer mestasis
How are miRNAs involved in cardiac disease?
- cardiac myocytes respond to stress by undergoing hypertrophy
- miR133 is downregulated in diseased tissue
- miR133 normally supresses genes that promote hypertrophy
- hypertrophy like symptoms can be induced by supressing miR133
What technique can be used to loook at miRNA levels?
Northern blot
