1. microRNA
Cass Jabara

2. Exam Questions What are microRNAs, and what is their primary function?
Where are microRNAs commonly found in the human genome, and how does this correlate to disease?

3. Background

4. miRNA - miR - microRNA Eukaryotes S.S. RNA 19- to 25-nt Non-coding
Regulates gene expression
Evolutionary conserved
≠ mRNA!

5. Eukaryotic Genome
1/3 of genes
regulated
222
human
miRNAs

6. Exportin 5-induced export
Processing
DNA
RISC
transcription
pri-miRNA
mature
miRNA
Drosha processing
Dicer processing
pre-miRNA
Exportin 5-induced export
NUCLEUS CYTOPLASM

7. miRNA Function
AAAAAAAAAAA 5’ 3’
mRNA 3’ 5’
Translation

8. miRNA Functions Cellular division - coordination
Developmental apoptosis
Stress resistance
Fat metabolism
Positive or negative regulation

9. Primary Literature

10. Novel miRNA ID Bioinformatics Scan for conserved hairpin structure
Conserved, repetitive, protein coding
Thermodynamic stability
Expression of predicted miRNAs - microarrays
Validate microarray hits via cloning and sequencing, fish via capture biotinylated oligonucleotides
Placenta, testis, thymus, brain, prostate

11. Oligonucleotide Capture
Bentwich et. al, 2005

12. miRNA Clusters Cluster 1 - Chromosome 19 - placenta only
54 miRNAs - largest cluster discovered
Expression parallels human embryonic stem cells
Conserved in primates only
Cluster 2 - X Chromosome - testis only
10 miRNAs
10 conserved in primates only
7 conserved in dog
4 conserved in mouse and rat

13. Significance Human miRNA total >800
(vs current knowledge of 222)
Conserved only
Significant miRNA evolution unique to primates
89 Novel miRNAs discovered
53 not conserved under primates
Primate-specific developmental expression indicates important role in mammalian complexity

15. miRNA and Cancer Novel tumorigenesis gene class
e.g. 13q14 deletions - miR-15a, miR-16a
B cell chronic lymphocytic leukemia
Mantle cell lymphoma
Multiple myeloma
Prostate cancer

16. miRNA Locations HPV Integration Sites FRAs - Fragile Sites
oncogenes
HPV Integration Sites
FRAs - Fragile Sites
Loci prone to metaphase breakage
Rearrangement or deletions in cancer
CAGR - Cancer-associated genomic regions
LOH - loss of heterozygosity (e.g. p53, RB)
HOX - homeobox clusters
Developmental gene regulation

17. Calin et. al, 2003

18. Summary microRNAs - 19-25nt - regulates gene expression
Over 800 predicted, many primate conserved, may play role in complexity
Positive and negative regulation, novel tumorigenesis gene class

19. References
Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O., Barzilai, A., Einat, P., Einav., E., Meiri., E., Sharon, E., Spector, Y., Bentwich, Z. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nature 7:
Calin, G.A., Sevignani, C, Dumitru, C.D., Hyslop, T., Noch, E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, H., Negrini, M., Croce, C.M. (2003) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl. Acad. Sci. 101:
“microRNA (miRNA) Resource” Ambion.
“MicroRNA” Wikipedia.
“RNA-induced Silencing Complex” Wikipedia.