Müller et al. Genome Biology 2010, 11:304
http://genomebiology.com/2010/11/5/304

MEETING REPORTmRNA: a complex(ed) life
Michaela Müller, Karla M Neugebauer* and Christian Eckmann

Abstract
A report of the EMBL conference ‘The Complex Life ofmRNA: From Synthesis to Decay’, Heidelberg, Germany,
18-21 March 2010.

An EMBL conference held recently in Heidelberg took on
the daunting task of examining the life of mRNAs fromstart to finish. The assumption of the ‘central dogma’ isthat mRNA production leads to protein expression. Yet
cellular mRNA levels reflect a balance between the ratesof gene transcription and mRNA degradation andtranslation is highly regulated. Therefore, the level ofgene transcription in the cell does not necessarily corre­late with encoded protein level. Throughout their
lifetimes, all mRNAs exist in complexes with numerous
proteins that regulate mRNA at the level of maturation,
export, translation and decay. Thus, the life of eachmRNA is complex(ed), enabling modulation of gene
expression programs beyond promoters. This meetingprovided a rare occasion to discuss both mRNA proces­sing and translation regulation in one forum, thereby
addressing the central tenets of gene expression in aholistic way. Here we present some of the highlights ofthe meeting.

The centrality of the poly(A) tailDuring processing in the nucleus, all eukaryotic mRNAs
are modified at their 5’ ends by the addition of a 7-methyl
guanosine cap and are extended at their 3’ ends byaddition of a poly(A) tail. These features of mRNAtermini are added by enzymatic reactions that are tightly
coupled to transcription, ensuring the near universalityof these signals, which are crucial for the life of mRNAs
in the cytoplasm. Mechanisms of post-transcriptional
mRNA regulation exploit the cap and poly(A) tail tocontrol the mRNA’s half-life and translational efficiency.
Novel cytoplasmic regulatory mechanisms that operate*Correspondence: neugebau@mpi-cbg.de
Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse
108, 01307 Dresden, Germany© 2010 BioMed Central Ltd© 2010 BioMed Central Ltd

through the poly(A) tail are now coming to light.
Numerous microRNAs (miRNAs) repress translation in
the context of Argonaute-containing RNA-silencing
complexes. The conserved protein GW182 interacts withthese RNA-silencing complexes and can trigger trans­
lational repression upon tethering to the mRNA. A
mechanistic model of how GW182 elicits this response
was proposed by Nahum Sonenberg (McGill University,Montreal, Canada). He and colleagues have found thatthe silencing domain in the human GW182 ortholog
TNRC6C interacts with poly(A)-binding protein (PABP),
revealing an unexpected role for cytoplasmic PABP as anegative regulator of RNA translation. This model wasreinforced and extended by Elisa Izaurralde (Max Planck
Institute for Developmental Biology, Tübingen, Germany),
who showed that Drosophila GW182 interacts with
PABPC1 and may inhibit the closed-loop configurationof the translation initiation factor eIF4G and PABPC1,
which stimulate translation synergistically. Importantly,
both speakers reported a structural conservation in theGW182/TNRC6C silencing domain that resembles theinteraction platform of the well-known PABP inhibitor
PAIP2 (PABP-interacting protein 2). Interestingly,
although GW182 proteins possess an evolutionarily
conserved RNA-silencing function, the molecular details
that confer these roles differ. Thus, GW182 is a key player
in miRNA-mediated translational repression, which acts
by interfering with the stimulatory roles of the 5’ and 3’ends of mRNA.
The poly(A) tail also has a role in regulating the decayof mRNA. Decay is initiated when the poly(A) tail shrinks
below a critical length and the 5’ cap is removed bydecapping machinery. Deadenylases shorten the poly(A)tail and can directly promote decapping. Bertrand
Seraphin (IGBMC, Illkirch, France) revealed the impor­tance of BTG/TOB proteins as a novel class of conservedmRNA decay regulators in metazoans. BTG/TOB proteinsbind directly to the CAF1 subunit of the CCR4/CAF1/Not complex, an assembly that contains multiple de­adeny­lases. BTG/TOB proteins regulate the generaldeadeny­lation of mRNAs and thereby contribute toseveral post-transcriptional control mechanisms, includ­ing development and the control of cell proliferation. A
second example of such post-transcriptional regulation
was provided through Seraphin’s analysis of the role ofMüller et al. Genome Biology 2010, 11:304
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yeast AU-rich element binding proteins, which were,
surprisingly, shown to control alternative polyadenylationin addition to mRNA decay.
All classes of RNA are subject to mechanisms ofsurveil­lance, which remove aberrant or nonfunctional
RNAs. David Tollervey (Wellcome Trust Centre for Cell
Biology, University of Edinburgh, UK) presented work on
the yeast Nrd1/Nab3 surveillance complex, which may
recognize cryptic noncoding RNAs and cryptic unstabletranscripts via a short poly(A) tail of four adenosines andtarget them for rapid decay mediated by the TRAMP
complex. Tollervey introduced cross-linking and analysis
of cDNAs (CRAC) as a tool for identifying ribonucleo­
proteins (RNPs) at the whole-transcriptome level. He
reported that long antisense noncoding RNAs andnascent rRNA transcripts of stalled RNA polymerase Icomplexes are also targets of the Nrd1/Nab3-TRAMP
surveillance complex. With the advance of RNA sequenc­
ing technologies, we have only begun to understand theworld of nonproductive RNA synthesis and the duties ofRNA surveillance machineries.
Poly(A) tail elongation by noncanonical poly(A) poly­merase complexes is known to stimulate RNA translation.
Raúl Méndez (CRG, Barcelona, Spain) presented exciting
work on the expanding biological roles of the cytoplasmic
polyadenylation element binding proteins (CPEBs).
CPEBs are important for cytoplasmic polyadenylation,
regulate translation, and have now been found to also
control the progression of the mitotic cell cycle. Mendez
described how cell-cycle-specific changes in poly(A) taillength are important for cell division. Deregulation ofthis process may occur in tumors and result in abnormal
expression of factors involved in tumor progression.
Originally, regulation of poly(A) tail length was shown tobe heavily used by female germ cells undergoingprogram­med developmental arrest in their normal
meiotic program. This new work shows the versatility ofcytoplasmic polyadenylation as an important regulatory
mechanism in health and disease.

Binding sites for small RNAs: the importance oflocation
In general, miRNAs interact with binding sites localized
in the 3’ UTR of target mRNAs. Matthias Hentze (EMBL,Heidelberg, Germany) reported that the mechanism oftranslational repression by Drosophila miR-2 is princi­
pally independent of the position of miRNA-bindingsites. When a reporter mRNA with six neighboring miR2-binding sites was used, miRNA targeting to the 5’ UTR,
coding sequence or 3’ UTR was equally effective atrepressing translation. Interestingly, when the miR-2binding sites were progressively reduced to one or two,
reflecting the most common physiological settings,
translational repression became sensitive to position;

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miRNA-mediated regulation was only observed when thesingle binding site was located in the 3’ UTR. In contrast,
the liver-specific miR-122 binds to two adjacent sites
close to the 5’ end of the hepatitis C virus (HCV) RNA
genome; miR-122 binding results in upregulation of viral
RNA levels and propagation of the virus. Peter Sarnow(Stanford University, Stanford, USA) reported that inser­
tion of the viral miR-122 binding site into the 3’
noncoding region of a reporter mRNA led to a decrease
in mRNA expression in human tissue culture cells. Bothexamples illustrate how the location of miRNA bindingsites dictates their effects on gene regulation.
In contrast to the eukaryotic miRNAs, the binding sitesof small bacterial RNAs (sRNAs) that repress translation
are mainly localized in the 5’ UTR of the mRNA in close
proximity to the Shine-Dalgarno (SD) sequence. This isconsistent with the known role of sRNAs in regulation ofloading of mRNAs onto ribosomes. However, Jörg Vogel(Max Planck Institute for Infection Biology, Berlin,
Germany) described how sRNA-binding sites arecommon outside the canonical SD region, even far
upstream in the 5’ UTR or within the coding sequence.
He revealed that target sites in the coding sequencesuggest that sRNAs can silence genes downstream oftranslational initiation, probably by promoting mRNAdegradation.

Regulating the regulators
Diverse Argonaute (Ago) proteins bind various classes ofsmall RNAs (for example, miRNAs, small interfering
RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs))
to form RNA-silencing complexes and act as binding
platforms for post-transcriptional mRNA regulatorycomplexes. Surprisingly little is known about the regula­tion of Ago proteins themselves and the complexes theyform. Gunter Meister (University of Regensburg, Regens­burg, Germany) presented work on human Ago2 protein,which is phosphorylated on a conserved tyrosine;
phosphorylation reduces the RNA-binding potential of
Ago2 but leaves all other aspects of Ago2 functions
intact. In contrast, germline-enriched PIWI proteins areknown to contain symmetrically dimethylated arginine.
Mikiko Siomi (Keio University, Tokyo, Japan) has
discovered that arginine methylation enhances Agoprotein complex formation and the efficient loading of
small RNAs in Drosophila. Interestingly, Siomi reported
that tudor-domain proteins are sensitive to argininemodified Ago proteins and may therefore represent key
regulators of piRNA-directed silencing complexes. Thus,
signaling cascades may regulate post-transcriptional
controls during development or in response to changing
environmental conditions.
Although miRNAs are involved in regulatory processes,
paradoxically they have long half-lives, sometimes longer

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than 12 hours. Two talks featured the importance of
rapid turnover for miRNAs in specific biological contexts.
Witold Filipowicz (Friedrich Miescher Institute for
Biomedical Research, Basel, Switzerland) reported thatmany miRNAs in retinal and non-retinal neurons havevery short half-lives and that miRNA turnover isregulated by neuronal activity. He also described identifi­
cation of miRNAs in mouse retina, the abundance of
which is controlled by exposure to light. Sebastien Pfeffer(IBMC, Strasbourg, France) reminded us that the abun­dance of specific cellular miRNAs changes upon infection
with viruses, which can have an impact on viral produc­tion and infectivity. Pfeffer reported the rapid down­
regulation of miR-27, a cellular miRNA that targets
murine cytomegalovirus (MCMV) and exerts an antiviralfunction when overexpressed. Pfeffer has found thatdownregulation of miR-27 occurs at the posttranscriptional level by the induction of rapid decay ofthe mature miRNA.

Open and closed conformations facilitate function
Structure-guided functional studies provide mechanistic
insights into all aspects of RNA biology. Conformationalchanges in the core machineries emerged as a common
theme. Patrick Cramer (Gene Center, University ofMunich, Germany) presented the structure of yeast RNA
polymerase II bound to the transcription initiation factor
TFIIB. He discussed models for the closed and open
promoter complexes in the context of transcription initia­
tion and the transition to elongation. Cramer showedthat the ‘B-linker’ region of TFIIB is essential for DNA
opening, while the ‘B-reader’ region is important fortranscription start-site selection. Ribosome function isalso dependent on open and closed conformations. AlanHinnebusch (National Institute of Child Health andHuman Development, NIH, Bethesda, USA) reported theidentification of multiple motifs (SI1, SI2, SE1 and SE2) inthe amino- and carboxy-terminal tails of the translation
initiation factor eIF1A. He showed that the SE elements
enhance binding of the ternary complex to the 40Sribosome in a conformation conducive to scanning butincompatible with start codon selection (open scanningconformation). SI elements antagonize SE elements todestabilize this open conformation of the ribosome andpromote the transition to a closed, scanning-incom­
patible conformation with tRNAiMet fully engaged in theP-site for AUG selection.
Riboswitches are natural RNA sensors that respond to
intracellular metabolites and ions in order to control
gene expression by controlling translation efficiency,trans­cription termination or RNA stability. Dinshaw
Patel (Memorial Sloan-Kettering Cancer Center, NewYork, USA) presented the structure of the glycine

Page 3 of 3ribo­switch with ligand (closed conformation) andwithout ligand (open conformation). Patel explained thatin contrast to all other known amino-acid riboswitches,
the glycine riboswitch contains only one sensing domain
and in this way discriminates against larger amino acids.
The exon-junction complex (EJC) is a key player inpost-transcriptional gene regulation in metazoans. This
multiprotein complex is loaded onto mRNAs upon
splicing and modulates nuclear mRNA export, nonsensemediated decay (NMD) and translation efficiency ofmRNAs. Elena Conti (Max Planck Institute for
Biochemistry, Munich, Germany) presented the crystal
structure of the mammalian core EJC complex bound tothe NMD effector protein UPF3. She showed how UPF3bridges the UPF and EJC complexes by interacting with
the EJC components Mago, Y14 and eIF4AIII (closedconformation). Conti showed that eIF4AIII and Y14 havehotspots for interactions on their surface that are used torecruit different regulators. The shuttling Mago-Y14
heterodimer binds the EJC disassembly factor PYM inthe cytoplasm. PYM binds to the same pocket in theMago-Y14 heterodimer as UPF3, suggesting a mechanism
whereby mutually exclusive binding sites impart asequential order in the interactions in the NMD pathway.
Niels Gehring (EMBL, Heidelberg, Germany) has
investigated whether the deposition of the EJC influences
the association of the mammalian mRNA export complex
TREX with mRNAs. Although TREX recruitment to the5’ end of the mRNA was independent of splicing, hecould demonstrate that the EJC significantly contributes
to the recruitment of the TREX complex to downstreamsites, which could serve as a failsafe mechanism for TREX
recruitment.
Two key themes emerged from the meeting: first, thecoding potential of genes is extensively regulated posttranscriptionally at numerous stages in an mRNA’s life;
second, the protein complexes that meet mRNA couple
each life stage sequentially with one another, such thattranscription
influences
processing,processing
influences export, export influences stability andtranslation, and so on. Several examples now illustrate
how RNA-protein complexes undergo switching behavior
to determine an mRNA’s fate, depending on the biologicalcontext. This complexity is a clear endorsement for future
meetings like this one, addressing gene expression fromthe point of view of the mRNA’s lifetime.
Published: 25 May 2010

doi:10.1186/gb-2010-11-5-304
Cite this article as: Müller M, et al.: mRNA: a complex(ed) life. Genome Biology
2010, 11:304.