Non Coding RNAs and Disease Flashcards
2006
In 2006, Andrew Fie and Craig Mello won the Nobel prize for medicine for their work on “RNA interference- gene silencing by double stranded RNA”
RNA interference pathway is an Epigenetic method where gene silenced by small RNA’s binding to them, blocking their transcription or translation
-RNA now has function
ncRNAs are involved in disease
Pathogenesis: development and progression of disease
Therapeutics: treatment of disease
Biomarkers: diagnosis and prognosis of disease
-drug and protein serum tests
Central Dogma of molecular Biology
1958 Francis Crick, one of the discoverers of the DNA double helix structure, described that genetic info flows from DNA –> RNA –> protein in a simple linear manner
Specialised Mechanisms:
1. RNA –> DNA. Reverse Transcription. seen in virus
2. RNA –> RNA
mRNA encode proteins
Translation RNA’s= Non-coding RNA’s = rRNAs and tRNAs = ribosomal and transfer RNAs
RNA importance in the future
Total RNA
1) Coding RNA 1.5%–> mRNA
2) Noncoding RNA 98.5% (has regulatory roles)—>
a) Long ncRNAs (>200nt)
- Signal, Decoy, Guide, Scaffold IncRNA
b) Small ncRNAs (
Organism Complexity
Can judge the increasing organism complexity, by the amount of transcribing RNA that it makes
- same number of protein coding genes as other species
- huge amount of Non-coding RNA, that allows for complexity
e. g Bacteria vs Yeast vs Worms vs Humans
Non-coding RNA publications
Rapid increase in the number of publications due to increase in mRNA interest
What are Non-coding RNAs?
Classified into many subtypes within two major groups, defined by size (not function)
-200nt “long”ncRNAs
All forms have varied regulatory roles within the cell, some well characterised (tRNA), some not
Examples of Small ncRNAs
70-100 nt trasnfer RNAs (tRNA)
-carry a/acids for building growing peptide chain during translation
70-120 nt small nucleolar RNAs (snoRNA)
-involved in translation. modify ribosome. involved in direct splicing of mRNAs (can make different protein isoforms). associated with many different disease types
18-26 nt microRNAs (niRNA)
-distinctive hairpin structure
-work v similarily with siRNA (the F and M won nobel prize for)
tRNAs general
Identified in 1958
-well characterised non-coding RNA
-clover leaf structure
-bind to read mRNA, identify in triplets which a/acids should come to the growing peptide
Vital for correct translation of proteins
-error in tRNA = problems with protein production
tRNA in human disase
MELAS syndrome:
Mitochondrial myopathy, Encephalomyopathy, Lactic Acidosis and Stroke-like episodes
-Maternal Mitochondrial inheritance
-tRNA normally encoded on mitochondrial DNA that is 12 kilobases, inherited through mother
-this extra piece of DNA/mitcohondrial genome encodes quite alot of these tRNAs
-A3243G mutation tRNALeu ^UUR causes a/acid misincorporation
-A–>G switch
-effects mutiple organs
-errors in mitochondria genome tRNAs results in a single nucleotide mutation
How are tRNA’s mutated
tRNA are a gene
can be mutated in the same way as any other protein coding mRNA
snoRNA general
snoRNAs act as a guide for RNAs for modification of ribosomal RNA and tRNA’s
are crucial in ribosome biogenesis = translation of RNA into protein
-names in 1981
-discovered in late 60s
2x forms:
-C/D box, methylation (modify ribosomal RNA so they function properly) (if they dont function properly there will be translation problems)
-H/ACA box, pseudouridylation
snoRNA transcription
snoRNA sit within protein coding genes
- snoRNA host gene
1. Primary RNA transcription (including all exons and introns with their snoRNAs)
2. RNA processing (splicing of exons and removal of introns) –> - highlights that the “junk” discarded proteins actually contain regulatory RNAs
- ensures youre not wasting anything
a) Cytoplasm (mRNA used for protein)
b) Further processing–> snoRNAs - -> nucleolus
snoRNA and human disease
Prader-Willi and Angelman syndromes
-Loss of imprinted(methyl groups) region C15q11-13 (long arm), paternally expressed, included six snoRNAs (chromosome 15 long arm has methyl groups expressed only from father’s copy)
-SNORD116 mice show a defect in growth and feeding regulation (have different roles in different syndromes. losing more than one gene, and more than one function, changing the effect on more than one gene ==> get an effect on more than one organ)
-SNORD115 also causes alternative splicing of seratonin receptor 2C so loss of the sno causes different isoforms of 5-HC2cR –> growth retardation, increased energy expenditure
Illustrates how snoRNAs are directly associated with the development of disease
microRNAs
• Initially identified in C. elegans in 1993 and found conserved in animals in 2000
Mutations (knocked out) in the C. elegans let-7 (lethal) miRNA gene result in developmental abnormalities that often lead to rupturing of the worms (leak out of insides/burst of vulvo) and lethality
• First associated with human disease in 2002, miR-15/-16 deleted in chronic lymphocytic leukemia (Calin GA et al PNAS 2002, 99(24):15524-9) (pair of microRNA in region, and their loss was directly associated wiht the development of the leukemia)
• So well studied now – online database (inks different microRNAs with different disease states)
• In miRBase V21 (June 2014) contains 2588 miRNAs
Pathway of miRNA (microRNA)
RNA pathway miRNA binds to a Target mRNA (messenger RNA)
a) blocks translation of that protein
b) causes RNA to be degraded
-overall decreasing the expression of the target RNA
Is an Epigenetic mechanism
-expression of miRNA is regulated like most other genes
-can be inherited with disease states
microRNAs and Cancer
Cancer: miRNAs repress the translation of oncogenes and tumour suppressors
(miRNA itself is working as an oncogene or a tumour surpressor gene)
-many of the hall marks of cancer are regulated directly by micro RNAs (Cell adhesion and invasion. Apoptosis. Epigenome. Cell Proliferation cycle. Genomic Stability. Differentiation)
microRNAs and Down syndrome
Down syndrome: Gain of C21 DNA
– C21 carries 5 miRNAs, (all tumour supressor genes)
–two of which repress the production/translation of protein MeCP2.
– (Lower levels of MeCP2 may lead to) abnormal brain development (also lost in neurodevelopmental disorder Rei syndrome)
– Decreased risk of solid tumours in DS, all the miRNAs are known tumour suppressor genes.
Increased expression of C21 miRNAs in hippocampus from DS pa)ent. Kuhn DE et al, BBRC 2008, 370(3).
microRNAs and human disease (Neurodegeneration)
NEUROdegeration: -Huntington's Disease -Parkinson's Disease -Alzhiemers Disease -Amyotrophin Lateral Sclerosis MiRNA regulate mRNAs (transcription factors) which directly regulate cell functions --> phenotypes
microRNA and Sporadic Alzheimer’s disase
Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer’s disease correlates with increased BACE1/ b-secretase expression
BACE1 is the protein which nibbles off Alzheimer’s protein –> Senile Plaque development
-lose the regulatory microRNA, lose ability to control/repress this gene –> increased Senile Plaque development
Long non-coding RNAs
Harder to classify into groups. know less about them.
• >200nt in size
• Can look like mRNAs (protein-coding genes) with introns and exons and a poly-adenylated tail
-main different is that they DONT encode protein (as is Non-coding RNA)
-really varied in their functions
• Functions are highly varied
-lncRNAs cannot easily be grouped into functional families like ‘miRNAs’ and ‘snoRNAs’
lncRNA mapping
The Human Genome Project has identified transcribed regions in our DNA that do not encode for proteins.(non doing regions)
-can identify which genes sit within this region
UCSC (University of California, Santa Cruz) genome browser with ENCODE (Encyclopedia of DNA elements) data
-try to identify new non-coding RNA and new mCRA
-identify genes that sit within the region
-XIST gene
How the Landscape has changed having Long non-coding RNA
Increased Techniques + Increased knowledge
= allowed increased information. more able to answer questions
1999-2002 Identification of Tumour Suppressor genes on C11p15 in Ovarian Cancer
-UCSC Genome Browser on Human July 2003 Assembly
-gives so much more information that before (more known genes)
—->2009
-more genes identified
-more tracks on UCSC browser identifying and annotating mRNA
—-> 2010
miR-210 links hypoxia with cell cycle regulation and is deleted in human epithelial ovarian cancer
-functions like a Tumour surpressor gene
lncRNAs and disease
– XIST and X-inacOvaOon
– HOTAIR and Cancer
– H19 on chromosome 11, many diseases
– lncRNA and Prader-Willi syndrome
