Roundtable Review

RNA: messenger, mediator, muter, and more
Posted 07 March '13

 

Pre-mRNA-1ysv.png-tubes

A hairpin loop from a pre-mRNA. Notice its bases (light green) and backbone (sky blue). Author: Vossman. Source: http://en.wikipedia.org/wiki/File:Pre-mRNA-1ysv.png-tubes.png. Under License: Creative Commons Attribution-Share Alike 3.0 Unported

While RNA is the less chemically stable and often less appreciated nucleic acid counterpart to the more famous DNA, RNA species are extraordinarily diverse in size, structure, and function. Though the roles of the most familiar RNA—messenger RNA—are well understood, several recent findings have opened up worlds of essential tasks carried out by RNA species of multiple families.

Making proteins straight from DNA would be akin to a contractor reading from the only copy of the blueprints to make a single wall.  Instead, to preserve the integrity of the genome, proteins are synthesized from intermediate transcripts of genes.

The central dogma of molecular biology holds that DNA is transcribed into messenger RNA (mRNA) and subsequently translated into a protein.  For many years, this three-step process dominated genetics. However, recent developments in gene regulation research have discovered several additional RNA species and highlighted their importance not only in gene expression but also in developing and sensing external signals.

RNA is an acronym for ribonucleic acid.  As its name implies, it is one “deoxy” away from deoxyribonucleic acid, or DNA.  The chemical difference between the two lies in the structure of the sugar-phosphate backbone- RNA has one more oxygen atom in each of its sugar groups.  This makes RNA more reactive and less stable than DNA.  RNA and DNA also employ a slightly different set of nucleotides; instead of thymine, RNA uses uracil.  A single-stranded RNA molecule is produced by a polymerase transcribing DNA nucleotides into their complementary RNA bases.  This single-strandedness is crucial for expanding the repertory of jobs performed by RNA species, as it exposes the information-carrying nucleotide sequence.

mRNA

Arguably, the most familiar form of RNA is messenger RNA (mRNA).  These are transcripts of genes made by an RNA polymerase and are used as templates for protein synthesis.

mRNAs do not simply vanish after their usefulness has passed.  On occasion, normal degradation fails, and mRNA can be reverse transcribed into DNA, with the potential of wreaking havoc on genomes.  Certain viruses use reverse transcriptases to reverse transcribe their mRNA genes for incorporation into the host genome.  These sequences are replicated during cell division and can be reactivated during disease flare-ups.

Similar non-viral products of reverse transcription called retrotransposons are host DNA elements that can copy and reintegrate themselves into the genome, using RNA transcription for their duplication. Retrotransposons are also stable indicators of evolutionary heritage.

mRNA is by no means the only RNA species, nor even the only one involved in gene or protein expression.  In fact, several RNA species are intimately involved in essentially all steps of the central dogma.

RNA splicing

Eukaryotic protein-coding genes exist in the genome as series of exons separated by introns.  Introns are not translated into protein and must be excised from the mRNA transcript.  This process is mediated by another RNA species that forms a complex called a small nucleolar ribo-nuclear protein (snRNP).  The RNA component of snRNPs recognizes sequence signals separating exons from introns in the pre-processed mRNA and mediates spliceosome excision of introns [1].

RNA Interference

Certain complementary dyads of nucleotides are paired across the Crick and Watson strands in the DNA double helix; in the case of RNA, complementary nucleotides on the same strand can pair in a common phenomenon known as self-complementarity.  Some RNAs are self-complementary for stretches of the RNA (i.e. several cytosines might pair with several guanines on the same strand) and can form complex secondary structures based on this pairing.

One such secondary structure, a stem-loop or hairpin, is formed by several complementary bases and an unpaired loop on one end.  Short hairpin RNAs (shRNAs) and primary microRNAs (pri-miRNAs) are substrates for the Dicer protein, which cleaves the loop, leaving a double-stranded short interfering RNA (siRNA).  One of the two strands of the siRNA is lost; the other targets complementary mRNAs and acts as a scaffold for translation-blocking and RNA-degrading enzymes.  Generally, the titles “micro RNA” (miRNA) and “short hairpin RNA” (shRNA) are used, to refer to a hairpin whose source is endogenous to the nucleus, or exogenous, respectively.

This powerful machinery has been used to incompletely prevent a gene from producing its protein.  For genes that are necessary for subject survival, interference using a viral vector to infect cells with shRNA has been used to test the result of reducing expression of a particular gene [2].

Somewhat mysterious Piwi-interacting RNAs (piRNA) show similar silencing effects as miRNA and siRNA but appear to be larger and less conserved.  Their function is essential for germline development and suppression of transposons but their mechanism of action is poorly understood.  Recent work demonstrates that piRNA targets transposable elements via weak complementarity and recruits a similar silencing complex as miRNA [3].

Another recent finding indicates that interfering RNAs may not be restricted to linear fragments.  Current research is focusing on novel circular RNAs that show sequence similarities to miRNAs and function as inhibitors of gene expression [4]. 

RNA Editing

Some recent research has focused on RNA editing, rare post-mRNA processing modifications made to specific nucleotides.  Insertions, deletions or modifications of specific bases can be mediated by guide RNAs (gRNAs), which recognize specific sequences in the mRNA to be modified [5].

Translation

Several RNAs are essential components of mRNA-to-protein translation.  In fact, the protein machines used for translation are themselves at least partially comprised of RNA.  Ribosomal RNAs (rRNA) assemble ribosome complexes of rRNA and protein on chemically modified mRNA molecules.  Upon discovery of a translation start site on the mRNA, the ribosome recruits a transfer RNA (tRNA) molecule that recognizes the first three bases (codon) of the mRNA.  This tRNA is comprised of several hairpins arranged in a cloverleaf fashion.  One end of each tRNA recognizes a specific codon and the other attaches itself to the cognate amino acid.  Ribosomes incorporate this amino acid into its nascent protein chain when the tRNA recognizes its codon.  Traditionally, Marshal Nirenberg’s term “genetic code” has referred to the relationship of codons to amino acids as mediated by tRNAs.

Chromosome Inactivation

An example of a non-messenger RNA critical for development is Xist. Mammalian females inherit two X chromosomes.  To prevent doubled expression resulting from genes on both copies, one of the two X chromosomes in each cell is silenced.  The non-coding RNA called Xist is expressed by the X chromosome to be inactivated.  This RNA proceeds to coat the inactivated chromosome, causing a cascade of signals that prevents transcription of its genes.  Thus, only one X chromosome remains active.

Divergent Transcription

Not even basic eukaryotic transcription is simple.  Recent advances have shown that most transcription diverges from start sites and is the source of most of the long non-coding RNAs (lncRNAs) in the nucleus [6]. Other studies implicate these lncRNAs in development [7]. Their molecular function may correlate with their complementarity to RNA or single-stranded DNA; lncRNAs have been proposed to target specific nucleotide sequences and recruit large chromatin-related complexes such as Polycomb to these regions [8].

Extracellular Signaling

In addition to intracellular signaling, some RNAs are secreted from cells in an apparent inter-cellular signaling mechanism [9].  It is hypothesized that these extracellular RNAs (exRNA) allow cells to communicate nucleic acid sequences of specific importance and thus influence cell behavior.  NIH has established significant funding for work on these molecules, as there is hope for exRNA treatments of diseased cells or for use as biomarkers of disease [10].  Much work is still needed to assess the mechanism of exRNA function and the extent to which they can be therapeutic.

Ribozymes

Some RNAs can even exhibit the functional traits of proteins.  In fact, tRNAs are one example of these so-called ribozymes.  Another example is RNase P which is comprised of, and cleaves RNAs.

This extreme versatility of RNA as information carrier, processor, and independent machinery has led some to hypothesize that RNA was the foundation of early life.  This “RNA world” hypothesis is supported by the finding that most components used for information storage and processing are made at least partially of RNAs.  In fact, recent work has started to elucidate potential first evolutionary steps toward spontaneous RNA formation in pre-life conditions [11].  The extraordinary diversity of structure and function of RNAs attest that they are crucial components of nearly all parts of molecular biology and even life itself.  

 References 

[1] McGraw Hill. How Spliceosomes Process RNA.

[2] Kagey MH, et al. (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature.

[3] Bagijn MP, et al (2012) Functions, Targets and Evolution of Caenorhabditis elegans piRNAs. F1000 Developmental Biology.

[4] Ledford H. (2013) Circular RNAs throw genetics for a loop. Nature News.

[5] McManus M. (2012) Guide RNA. 

[6] Sigova A, et al. (2012) Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. PNAS.

[7] Klattenhoff C, et al. (2013) Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment. Cell.

[8] Banasio R. (2010) Molecular Signals of Epigenetic States. Science.

[9] Dinger M, et al. (2008) RNAs as extracellular signaling molecules. Journal of Molecular Endocrinology.

[10] NIH. (2012) Extracellular RNA Communication.

[11] Service RF. (2013) Self-Assembling Molecules Offer New Clues on Life’s Possible Origin. Science News.

 

 

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