Biomedical Engineering Reference
In-Depth Information
5.3 RNA: A Paradigm Shift from Messenger to Protagonist
RNA. is. highly. abundant. within. cells,. of. which. about. 5%. of. RNA. is. messenger. RNA.
(mRNA),. the. intermediate. for. protein. formation,. and. is. viewed. as. “coding”. RNA.. Most.
of. the. RNA. within. the. cell. is. noncoding,. such. as. ribosomal. (rRNA). and. transfer. RNA.
(tRNA),.which.are.essential.for.the.translation.of.proteins..However,.when.looking.at.the.
DNA.regions.coding.for.the.mRNA,.there.are.large.amounts.of.RNA.that.is.spliced.out.of.
the.inal.product,.becoming.introns..Since.these.noncoding.fragments.seemed.to.serve.no.
useful.purpose,.it.was.originally.thought.to.be.“junk.”.This.narrow.view.of.RNA's.function.
is.being.expanded.as.genomic.studies.have.revealed.greatly.increased.levels.of.noncoding.
RNA.(ncRNA).expression.with.possible.biological.activity..Many.of.these.molecules.have.
now.been.found.to.have.regulatory.functions.including.controlling.gene.expression..RNA.
regulatory.molecules.controlling.the.expression.of.genes.at.different.stages.of.development.
may.contribute.greatly.to.organism.complexity.
5.3.1 rNA: A Natural Nanomachine
The. past. decade. has. seen. a. rapid. growth. of. research. in. the. ield. of. post-transcriptional.
gene. regulation,. especially. in. the. rapidly. expanding. ield. of. ncRNAs.. Recently,. two.
additional. major. categories. of. ncRNAs. have. emerged:. silencing. or. short. interfering.
RNA.(siRNA).(Fire.et.al..1998).and.microRNA.(miRNA).(Bartel.2004),.both.small,.ncRNA.
molecules. involved. in. RNA. regulation.. siRNAs. are. double-stranded. RNA. that. inhibit.
gene.expression.by.binding.to.mRNA.with.complementary.sequence.and.having.a.protein.
cleave. the. mRNA.. miRNAs. are. single-stranded. ∼22. nucleotide. sequences. of. RNA. that.
inhibit.gene.expression.through.several.mechanisms,.but.do.not.destroy.the.bound.mRNA.
(Sontheimer. and. Carthew. 2005;. Wu. and. Belasco. 2008).. These. discoveries. have. focused.
more.attention.on.this.ield,.as.it.has.begun.to.compete.with.transcriptional.regulation.as.a.
major.focus.of.controlling.gene.expression..Technological.advances.in.both.genome-wide.
and. targeted. gene. expression. analysis. have. reinforced. and. enhanced. our. interpretation.
and.understanding.of.the.signiicance.that.post-transcriptional.mechanisms.play.in.several.
signiicant.cellular.systems.(Perou.et.al..1999;.Lockhart.and.Winzeler.2000;.Mata.et.al..2005;.
Sanchez-Diaz.and.Penalva.2006;.Townley-Tilson.et.al..2006).
Although. there. are. many. methods. for. mRNA. regulation. at. the. genetic. level,. post-
transcriptional. regulation. of. messenger. RNA. contributes. to. numerous. aspects. of. gene.
expression..The.key.component.to.this.level.of.regulation.is.the.interaction.of.RNA-binding.
proteins. (RBPs). and. their. associated. target. mRNAs.. Splicing,. stability,. localization,.
translational.eficiency,.and.alternate.codon.use.are.just.some.of.the.post-transcriptional.
processes.regulated.by.RBPs..Central.to.our.understanding.of.these.processes.is.the.need.
to.characterize.the.network.of.RBP-mRNA.associations.and.create.a.map.of.this.functional.
post-transcriptional. regulatory. system.. To. this. end,. RIP-Chip. or.
ribonomic
. proiling. has.
proven.to.be.a.versatile,.genomic,.
in vivo
.technique.widely.used.to.study.these.RBP-mRNA.
associations.
Immunoprecipitation. of. RBPs. followed. by. microarray. analysis,. known. as. RIP-Chip.
(
R
NA.
i
mmunopreci
p
itation. followed. by. microarray. (chip). analysis). (Tenenbaum. et. al..
2000;. Keene. et. al.. 2006),. can. be. a. powerful. endogenous,. high-throughput. technique. for.
identifying.speciic.associated.RBP.targets.from.cell.extracts..RIP-Chip.(and.more.recently.
RIP-Seq). complements. many. other. RNA. localization. and. characterization. methods. and.
is. widely. used. to. isolate. and. identify. mRNA. and. miRNA. targets. associated. with. RBPs.
