18.01.11 Regulatory non-coding RNA Flashcards Preview

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Give three examples of regulatory non-coding RNA species.

1. miRNA
2. siRNA
3. piwiRNA
4. lncRNA


What is the typical structure of a miRNA?

Small, naturally occurring ncRNAs ~21-22 nt long, highly conserved in eukaryotic organisms.


What is the role of miRNAs?

Regulate gene expression by post-transcriptional gene silencing (>60% protein coding genes)

Some regulate specific individual targets

Others are master regulators of a process (regulate expression of 100’s genes simultaneously)

Some regulate targets cooperatively.

Involved in regulating many processes e.g. proliferation, differentiation, apoptosis and development


How many miRNA molecules have been identified in humans?

In humans, 1881 precursors (pre-miRNAs) and over 25,000 mature miRNA molecules have now been identified (). A recent study identified a further 3,700 new miRNA many with tissue specific expression (Londin E (2015) Proc Natl Acad Sci U S A. 112: E1106-15.).


How do miRNAs enact their function?

Function by binding complementary sequences within the 3’ UTR of target mRNA then

(1) Inhibiting translation by preventing binding of the translation machinery or

(2) Promote mRNA degradation (e.g. through deadenylation of the PolyA tail)


Where are the majority of miRNAs encoded?

Majority encoded by introns of non-coding or coding transcripts, some found in exonic regions. Many miRNAs are known to reside in introns of their pre-mRNA host genes and are transcribed in the same direction as the pre-mRNA – leading to hypothesis that these miRNAs share their regulatory elements.

~70% of human miRNAs are found in defined poly-cistronic transcription units– generally co-transcribed - with a large proportion located in sense orientation within the introns of protein coding genes.


What is the seed region of miRNA?

In mature miRNAs there is strong conservation of nt 2-7 (from 5’ end), known as the seed region (crucial for recognition of target mRNA).

miRNAs with identical sequences at nt 2-8 belong to same ‘miRNA family’. miRNAs in a cluster are often related to each other suggesting that clusters may have arisen by gene duplication.


How can mature miRNAs function as developmental regulators?

Due to transcription of the miRNA genes by RNA polymerase II, mature miRNAs can function as developmental regulators by blocking expression of specific genes in specific tissues, and at specific times.


Where does miRNA maturation occur?

Unlike mRNAs, miRNA maturation begins in the nucleus and finishes in the cytoplasm.


Where are miRNA response elements found?

miRNA response elements (MREs) are found in coding and non-coding RNA. Other non-coding RNA species have roles in regulating (and being regulated by) miRNAs that bind to their MREs (eg CDR1as and miR-7, see Circular RNA section below).


What is the pathway involved in the regulation of mRNA by miRNAs?

Pathway by which miRNAs regulate mRNA translation involves mechanism used by cells as a defence against exogenous mRNA e.g. viral infection called: Post Transcriptional Gene Silencing (PTGS pathway)


How are miRNA molecules formed?

miRNA genes transcribed by RNA pol II into long primary miRNA (pri-miRNA) transcripts (typically over 1 kb) contains stem loop structure, a 5’ cap & a polyA tail (similar to mRNAs).

Maturation initiated by the RNASEN/ Drosher microprocessor complex - contains DGCR8 essential cofactor (RNA binding activity) and Drosher (RNAse III type endonuclease). Drosher crops the stem loop structure from pri-miRNA to produce ~65nts length pre-miRNA within the nucleus. Deletion of DGCR8 gene implicated in DiGeorge syndrome.

Hairpin precursor miRNAs (pre-miRNAs) are transported to the cytoplasm by exportin 5 (XPO5)

The Dicer-TARBP2 complex (RNAse III type endonuclease Dicer and argonaute protein TAR RNA-binding protein 2) removes the loop region from pre-miRNAs to create an miRNA duplex.

Duplex RNA is loaded into the RNA induced Silencing Complex (RISC)/ Argonaute complex, the helix is unwound and the passenger strand is degraded.

RISC directs regulation of mRNA by recognizing and binding to the complementary sequences on the targeted mRNA transcript. If the pairing is 100% complementary between miRNA and mRNA the mRNA will be degraded, if only partially complementary this results in translational inhibition of the mRNA.


Give two examples of AD genetic disorders associated with miRNA mutations.

1. Hereditary progressive hearing loss due to a heterozygous mutation in the seed region of miR-96 (Mencia et al 2009 Nat Genet 41: 609-613), and a mutation in miR-96 outside of the seed region that hinders precursor processing, probably by interfering with Dicer cleavage (Solda et al 2012 Hum Mol Genet 21: 577-585).

2. Hereditary keratoconus with cataracts due to a heterozygous mutation in the seed region of miR-184 (Hughes et al 2011 Am J Hum Genet 89: 628-33). The mutant form fails to compete with miR-205 for overlapping target sites on the 3' UTRs of INPPL1 and ITGB4 genes. Although these target genes and miR-205 are expressed widely, the phenotype is restricted to the cornea and lens because of the very high expression of miR-184 in these tissues.

3. Germline hemizygous microdeletions at 13q31.3 encompassing the MIR17HG gene result in a syndrome of microcephaly, short stature and digit abnormalities (de Pontual et al 2011 Nat Genet 43: 1026-30). The MIR17HG locus encodes for miR-17-92, a polycistronic miRNA cluster from which six distinct miRNAs are produced. Mutations in the Human MYCN transcription factor result in a similar phenotype likely due in part to MYCN’s regulation of MIR17HG gene expression.

4. Mutations affecting miRNA processing machinery
- Mutations in Drosha microprocessor complexes Fus and TDP-43 are responsible for ~50% of familial ALS
- Mutations in RISC complex component Fragile X mental retardation 1 protein (FMRP) cause fragile X syndrome.


How are miRNAs involved in cancer?

miRNAs involved in Cancer via:

1) Direct disruption of miRNA loci

2) Disruption miRNA-target genes regulation

3) Inhibition of global miRNA processing.


Give examples of how miRNA can be involved in cancer.

miR15 and miR16 dysregulation in most B cell chronic lymphocytic leukaemias as a result of chromosome 13q14 deletion.

Dysregulation of the miR-21 identified as one of the most consistently overexpressed miRNA in a variety of different cancers including lung and colorectal cancer. Controls a wide range of biological processes and has role in carcinogenesis, recurrence, metastasis and resistance. Could be used as a diagnostic and prognostic marker of malignant tumours and may promote radioresistance of cancers.

Higher expression of miR-21 in serum of lung cancer patients is associated with lymph node mestatases and lymph node staging – could be used as a diagnostic marker for early stage lung cancer. Overexpression of miR-21 decreases the sensitivity of Gastric Cancer cells to Trastuzumab, significantly suppresses Trastuzumab induced apoptosis.


Which miRNA is associated with Li-Fraumeni syndrome?

The G allele of a polymorphism (rs2043556) within the miRNA miR-605 has been shown to accelerate the age of on-set of Li-Fraumeni syndrome by 10 years. May help to explain some of the intra-family heterogeneity of symptoms in LPS. The G allele appears to cause a defect in the processing efficiency of its host miRNA thus reducing expression of the mature miRNA, leading to dysregulation of MDM2, higher expression of which has been associated with younger ages of onset


What is the structure of siRNAs?

Small, double stranded ncRNA molecules ~21-22nt long

Endogenous short interfering RNAs arise as a result of production of limited amount of natural double-stranded RNA in the cell and occasional transcription of some pseudogenes.


How are siRNAs formed?

The enzyme catalyzes the production of siRNAs from the degradation of long double-stranded RNA (dsRNA) and from the processing of small hairpin RNA (shRNA).


What are the precursors of siRNAs?

siRNA precursors include: exogenous dsRNA and shRNA, centromeres, transposons and other repetitive sequences, convergent mRNA transcripts and other natural sense-antisense pairs, duplexes involving pseudogene-derived antisense transcripts and the sense mRNAs from their cognate genes.


How can siRNAs mediate transcriptional gene silencing?

siRNAs can mediate transcriptional gene silencing by direct heterochromatin formatio


What is RNA interference (RNAi)?

a cellular defence mechanism triggered by the presence of dsRNA and shRNA resulting in degradation of specific gene transcripts (hence potent and long lasting silencing of expression).


What is the role of siRNAs in RNAi?

siRNA produced as the first stage in the process of RNA interference

long dsRNAs and shRNAs are processed in the cytoplasm by the RNase Dicer into siRNAs.

The resulting siRNAs containing the characteristic 19-nt duplexed region with 2-nt 3’ overhangs and 5’-terminal phosphate groups are taken up by the Argonaute multi-subunit RNA-induced silencing complex (RISC).

The duplexed siRNA bound to the Ago2 protein, the central component of siRISC, is unwound and the passenger strand rapidly dissociates.

Once unwound, the antisense RNA strand guides siRISC to the complementary site in the target mRNA which engages the endonucleolytic (slicer) activity of Ago2, resulting in mRNA cleavage.

The siRNA-loaded RISC is recycled for several rounds of mRNA cleavage.


What is the stucture of piwiRNA?

Small ncRNAs ~23-36 nt long

Most diverse class of ncRNA molecules; over 15,000 human piRNAs have been identified.


What is the function of piwiRNAs?

Function with AGO and PIWI proteins to regulate transposon activity and chromatin states. PIWI proteins expressed mainly in germline but piRNAs expressed in many adult differentiated cells.

Role: Limit transposition by retrotransposons (LINE-1) in mammalian germ cells.

piRNAs associate with PIWI proteins to create an active piRNA-induced silencing complex (piRISC) that recognises complementary targets.

piRNAs recently reported to play an important role in the control of gene expression – can share post-transcriptional activities by interacting with other Argonaute proteins and silencing mRNAs in cytoplasm


How do piwiRNAs differ from miRNAs and siRNAs?

Differ from miRNA/siRNA: they are longer, produced from single strand precursor up to 200kb (Dicer-independent mechanism), associate with the Piwi-class Argonaute proteins, expressed only in germline cells.


Where in the genome are piwiRNAs located?

89 large clusters distributed across the genome; individual clusters span 10 kb - 75 kb with an average of 170 piRNAs per cluster. Cleaved from large multigenic transcripts. (


What are the three groups of piwiRNAs?

(1) transposon derived - transcribed from both strands to produce sense and antisense piRNAs,

(2) mRNA derived piRNAs – found in 3’UTR of mRNA from which they originate (sense strand),

(3) lncRNA-derived piRNAs – produce piRNAs from entire transcript.


Give disease examples associated with piwiRNAs.

piRNA and infertility - Loss of function mutations in piRNAs derepress transposons allowing them to insert copies of themselves or relocate within the genome - activates Chk2 DNA damage checkpoint resulting in defects of microtubule organization and axis specification during gonadal development, which often lead to infertility.

piRNA and cancer - potential biomarker in human cancer e.g. piR-651 upregulated in gastric, colon, lung and breast cancer and in several cell lines. Growth of gastric cancer cells inhibited by piR-651 inhibition – arrest in G2/M phase.

piR-823 expression lower in gastric cancer tissues. Increasing the level of piR-823 inhibits cell growth


What is the structure of long ncRNAs (lncRNA)?

ncRNAs over 200 nt long

~20, 000 lncRNA transcripts have been identified; Little evolutionary conservation of lncRNA between species ie only small regions of lncRNA are functional.

Many similarities to mRNA: Often transcribed by RNA Pol II, may be polyadenylated, can show complex splicing patterns


What different types of lncRNAs exist?

Several types: antisense lncRNAs (that overlap known protein coding genes), intronic lncRNAs (that are encoded within introns of protein coding genes), overlapping transcripts lncRNA (that overlap protein coding genes) and intergenic lncRNAs (that are encoded completely within intergenic genomic space between protein coding loci).