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microRNA sponges

Marta Puerto Plasencia

Introduction microRNA CircularRNA Publications Conclusions

The most well-studied regions in the human genome belong to protein-

coding genes.

Coding exons are 1.5% of the genome.

Non-protein-coding portion of the genome has shown to have functional consequences in development, physiology and human disease (cancer, neurodegenerative diseases…)

microRNAs.

4. Manel Esteller. Non-coding RNAs in human disease. Nature Reviews Genetics 12, 861-874 (2011).

In humans, microRNAs regulate expression of mRNAs. microRNAs guide the effector protein Argonaute complex (AGO) to

mRNAs of coding genes to repress their protein production. AGO proteins interact with microRNAs and are involved in cytoplasmic

post-transcriptional gene-silencing processes

Discovered in plants.

circRNA molecules stable in the cytoplasm: single-stranded viruses,

such as hepatitis 6 virus or the plant viroids and virusoids.

The first best known circRNA is antisense to the mRNA transcribed

from the SRY gene highly expressed in testes.

In animals are an enigmatic class of RNA with unknown function.

circRNA contains miRNA target sites and seems to be

regulating the miRNA activity. cirRNA acts like miRNA sponge.

CircRNA Micro RNA Micro RNA mRNA mRNA Protein Expression Protein Expression

8.Jeremy E et al. A Circuitous Route to Noncoding RNA Vol. 340 no. 6131 pp. 440-44. (2013).

They sequence total RNA from a human cell retaining the spliced reads.

Next, the mapp spiced reads to the reference genome.

They detect circularization splicing from the reversed (head-to-tail)

orientation of exons (ANTISENSE).

2. Memczak S, lens M, Elefsinioti A et al.Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 21;495(7441):333-8. (2013).

Combining data from cell line HEK 293 and human leukocyte data they identifie 1950 cirRNAs IN HUMANS.

1903 cirRNAs in mouse, 81 of mapped to human

circRNAs. To explore if circRNAs exist in other animal they

used sequencing data from various C. Elegans developmental detecting 724 circRNAs

82,15% Inside coding transcripts 2. Memczak S, lens M, Elefsinioti A et al.Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 21;495(7441):333-8. (2013).

2. Memczak S, lens M, Elefsinioti A et al.Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 21;495(7441):333-8. (2013).

They intersect their catalogue of circRNAs with transcript

annotations and then look for conserved matches to miRNA families. They found that circRNA antisense to the cerebellar degeneration-

related protein 1 transcript was densely bound by microRNA. ciRS-7 has 74 conserved microR-7 seed matches. 63 conserved in at

least one other species indicating that microR-7 binding sites are probably functional

ciRS-7 functions as a microR-7 suppressor.

microR-7 disruption increase levels of miR-7 targets.

ciRS-7 microR-7 mRNA Protein Expression

They knockdown ciRS-7 in HEK293 cells and

monitor expression of published miR-7 targets. All miR-7 targets were low expressed.

In humans miR-7 is highly expressed in neuronal tissues, pancreas and pituitary gland.

They quantified levels of ciRS-7 and mir-7

across mouse tissues.

Evidence: ciRS-7 is exclusively for adult and embryonic mouse brain.

ciRS-7 and miR-7 seem to interact specifically in neuronal

tissues.

Mir-7 Control Control CiRS-7 Scrambled

2. Memczak S, lens M, Elefsinioti A et al.Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 21;495(7441):333-8. (2013).

In zebrafish, knockdown of miR-7 or expression of ciR-7 causes midbrain defects.

Evidence: miR-7 loss-of-function causes a specific reduction of midbrain size.

2.Memczak S, lens M, Elefsinioti A et al.Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 21;495(7441):333-8. (2013).

Control Knockdown miR-7 or ciR-7 expression

ciRS-7 post-transcriptional regulator by binding miR-7 in brain ciRS-7 harbours 74 miR-7 seed matches, often deeply

conserved. ciRS-7 and miR-7 share specific expression domains in

mouse embryonic brain

ciRS-7 suppress miR-7 activity resulting in increased levels of miR-7 targets and size brain decreases.

miR-7 is a key regulator of various cancer pathways (Thomas B.

Hansen et al). miR-7 is involved in Parkinson’s disease by direct targeting of a-

synuclein protein expression (Junn E et al). ciRS-7 probably serves as a crucial factor in the functioning of

neurons as well as a responsible candidate in neurological disorders and brain tumor development.

CircularRNAs are imortant post-transcriptional regulators of

gene expression acting by direct base pairing to microRNA.

microRNAs regulates the expression of mRNA usually by

suppression.

1. Gunter Meister. Argonaute proteins: functional insights and emerging roles.Nature Reviews Genetics 14, 447–459 (2013).

2. Memczak S, lens M, Elefsinioti A et al.Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 21;495(7441):333-8. (2013).

3. Thomas B. Hansen, Trine I. Jensen, Bettina H. Clausen et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013).

4. Manel Esteller. Non-coding RNAs in human disease. Nature Reviews Genetics 12, 861-874 (2011). 5. Capel, B. et al. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell 73,

1019–1030 (1993).

6. Junn E, Lee KW, Leong BS. Repression of alpha-synuclein expression and toxicity by microRNA-7. Proc Natl Acad Sci U S A. 4;106(31):13052-7. (2009).

7. Thomas B. Hansen, Jørgen Kjems and Christian K. Damgaard. Circular RNA and miR-7 in Cancer.

Cancer Res 2013;73:5609-5612. (2013).

8. Jeremy E et al. A Circuitous Route to Noncoding RNA Vol. 340 no. 6131 pp. 440-44. (2013).