Nucleus and Gene Expression Editorial Overview Elisa Izaurralde and Phillip D Zamore

Available online at www.sciencedirect.com

Nucleus and gene expression Editorial overview Elisa Izaurralde and Phillip D Zamore

Current Opinion in Cell Biology 2009, 21:331–334

Available online 14th May 2009

DOI 10.1016/j.ceb.2009.04.013

Elisa Izaurralde That most information ﬂows from DNA through RNA to protein remains the Department of Biochemistry, Max-Planck- organizing principle of modern molecular biology. Thus we begin this issue Institute for Developmental Biology, with an introduction to DNA replication by Mike O’Donnell and Nina Yao. Spemannstrasse 35, D-72076 Tu¨ bingen, Germany They describe the composition and function of the replisome, the machine e-mail: [email protected] that organizes activities at the replication fork, highlighting the unique challenges solved in the evolution of DNA replication proteins. Not only Elisa Izaurralde leads the does the replisome coordinate DNA copying on the leading and lagging Department of Biochemistry at the strands, it also allows the replication apparatus to skip over DNA lesions and Max Planck Institute for to pass a transcribing RNA polymerase without interrupting either tran- Developmental Biology in Tu¨ bingen, scription or replication. Germany. Her research focuses on the molecular mechanisms that Initiating transcription at the right place, at the right time, and in the right regulate gene expression at the cells is, of course, the primary challenge of gene regulation. Timothy post-transcriptional level, with Sikorski and Stephen Buratowski identify a key paradox in initiating mRNA particular emphasis on mRNA transcription: a conserved set of transcription initiation proteins are used to surveillance, decay, and silencing in recruit a common RNA polymerase, RNA Pol II, to many different transcription initiation sequences (promoters). They describe our current un- animal cells. derstanding of how eukaryotes solve this problem, describing the Phillip D Zamore experimental support for distinct initiation pathways for different promoter types. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, Not all transcription is productive. Synthesis in yeast of seemingly futile United States cryptic unstable transcripts (CUTs), which are copied from intergenic DNA, e-mail: [email protected] underscores the truism that eukaryotic solutions to biological problems are often wasteful. CUTs are typically marked for destruction while still in the Phillip D Zamore is an investigator nucleus, where they are degraded by the nuclear exosome complex [1,2]. of the Howard Hughes Medical The late Dmitry Belostotsky reviews the function and mechanism of the Institute and the Gretchen Stone nuclear and cytoplasmic exosomes, complex assemblies of ribonucleases and Cook Professor of Biomedical other proteins that control RNA stability, participate in 30-end processing of Science in the Department of structured RNAs and in post-transcriptional gene silencing, as well as Biochemistry and Molecular provide quality control for RNA processing, folding, and RNP assembly. Pharmacology at the University of Belostotsky also reviews the growing number of noncoding transcript classes Massachusetts Medical School in whose RNAs are widely distributed across the genome, yet whose abun- Worcester, MA, USA. His laboratory dance suggests that like CUTs, they are degraded nearly as rapidly as they studies how small RNAs guide are made. silencing of gene expression in plants, fungi, and animals and how At the opposite end of the continuum of RNA stability lie highly stable, these RNA silencing pathways can structural RNAs, many of which regulate transcription globally or locally. be used to design novel therapies Among the most intensively studied are xist and its complementary counter- for human disease. part tsix. Jennifer Chow and Edith Heard describe how xist, tsix, and a host of protein factors act sequentially to silence one of the two X chromosomes in mammals. As females have twice as many X chromosomes as males, such X chromosome inactivation serves to equalize the expression of X-linked www.sciencedirect.com Current Opinion in Cell Biology 2009, 21:331–334 332 Nucleus and gene expression

genes between the sexes. (In flies, an unrelated structural a housekeeping gene required for snRNP assembly. RNA, roX, acts to upregulate the single X chromosome in snRNAs participate in pre-mRNA splicing as protein– males, allowing its single-copy X-linked genes to catch up RNA complexes whose production requires a remarkable with the corresponding two copies of each gene in number of assembly proteins. Utz Fischer describes our females [3].) The study of X inactivation in mammals current understanding of how SMN protein, as a com- promises to inform our understanding of the more general ponent of the multiprotein SMN complex, acts to facili- problem of mono-allelic gene expression, whose role in tate the assembly of Sm proteins onto the U snRNAs in titrating mRNA production to appropriate levels remains the cytoplasm. The final step in snRNP assembly is the poorly understood. conversion of the 7-monomethyl guanosine cap of the U snRNA into a 2,2,7-trimethyl guanosine cap, permitting Most of the genome is transcribed in eukaryotes — per- its reimportation into the nucleus, where it can participate haps 90% in humans — although just a small percentage in pre-mRNA splicing. The devastating phenotype of encodes proteins. Some of these noncoding transcripts spinal muscular atrophy, thought to reflect the disruption pair to form double-stranded RNA (dsRNA) or are copied of splicing patterns of a subset of mRNAs particularly into dsRNA by RNA-dependent RNA polymerases. Such important for neurons, underscores the importance of dsRNA can be the source of endogenous small interfering snRNP assembly. RNAs (endo-siRNAs) that silence protein-coding genes in trans. In plants, a specialized DNA-dependent RNA Errors in pre-mRNA splicing often produce mRNAs with polymerase, RNA Pol IV, transcribes endo-siRNA-gen- diminished coding potential. When these aberrant tran- erating loci involved in RNA-directed DNA methylation. scripts contain premature stop codons, a specialized qual- Marjorie Matzke and colleagues review our current un- ity control mechanism, the nonsense-mediated decay derstanding of the mechanism, genetics, and biological (NMD) pathway, ensures their destruction before they function of RNA-directed DNA methylation. They can produce aberrant, potentially toxic, protein. Indrani describe our current understanding of how plant RNA Rebbapragada and Jens Lykke-Andersen evaluate the polymerases specialized to transcribe ‘silent’ chromatin evidence supporting prominent explanations for how participate in siRNA production and how such endo- the NMD pathway distinguishes between premature siRNAs, in turn, act on chromatin and DNA. They and appropriate stop codons. One intriguing model is remind us that most RNA-guided silencing mechanisms that premature stop codons reside in regions of the in plants later found parallels in animals, so a thorough mRNA bearing a distinct complement of RNA-binding understanding of the RNA Pol IV mechanism may ulti- proteins deposited during nuclear pre-mRNA splicing, mately lead us to its animal analog. but sensed in the cytoplasm during a ‘pioneer round’ of translation — that is, the initial transit of the mRNA by a In most eukaryotes, the primary transcripts of nearly all ribosome. protein-coding genes are mainly intervening sequence (introns), punctuated by coding segments (exons). The Roy Parker and colleagues continue the theme of RNA pre-mRNA splicing pathway removes introns and joins degradation. They explain that high rates of translational exons from such pre-mRNA transcripts, thus assembling a initiation and mRNA turnover are inversely related: functional mRNA appropriate for export to the cyto- proteins that promote translational initiation discourage plasm. Correctly identifying splice sites is essential to mRNA destruction, whereas proteins that bind the this process. Both splice site identification and the sub- mRNA cap but do not recruit translational initiation sequent breaking and joining of phosphodiester bonds factors, as well as proteins that promote decapping, requires the spliceosomal small nuclear RNAs (snRNAs) repress protein synthesis, and redirect the mRNA to U1, U2, U4, U5, and U6, or their equivalents in the specialized RNA–protein granules called processing or ‘minor’ spliceosome. Beyond simply removing introns, P bodies. Here, mRNAs can be degraded or stored for pre-mRNA splicing expands the genic repertoire of later re-entry into the actively translated pool. mRNAs eukaryotes by allowing a single gene to encode alterna- stalled in the process of translation also accumulate in tive forms of a single protein or alternative mRNA regu- stress granules. The movements of mRNAs among poly- latory sequences or both. Such alternative splicing is somes, P bodies, and stress granules are poorly under- thought to occur in most human genes. Britta Hartman stood. Moreover, as Parker and colleagues note, we do not and Juan Valca´rcel summarize our current understanding yet understand why mRNAs that have exited the poly- of how successful alternative splicing expands the num- some pool should accumulate in granules, since cells ber of functions encoded by our genes and how failures of unable to form such structures can nonetheless decap alternative splicing contribute to human disease. mRNA and repress translation.

Both constitutive and alternative pre-mRNA splicing Of course, the localization of mRNAs to discrete intra- require ﬁve distinct snRNPs. Spinal muscular atrophy, cellular sites is not restricted to mRNAs targeted for a neuronal disease, is caused by insufﬁcient SMN protein, destruction or storage. Henry Krause and colleagues

Current Opinion in Cell Biology 2009, 21:331–334 www.sciencedirect.com Editorial overview Izaurralde and Zamore 333

describe the global nature of mRNA localization, high- splicing, can regulate when and where the regulators lighting how high-throughput methods are revealing that regulate. Repression by miRNAs is widely controlled by mRNA localization may be the norm, not the exception. this additional level of regulation. Mouse mRNAs, for For some localized RNAs the function of localization is example, tend to have longer 30-UTRs, as a consequence well established, but for many, we do not yet understand of alternative polyadenylation site selection, as develop- how restricting the mRNA to a specific subcellular region ment progresses, consistent with the idea that control of or structure contributes to the function of the mRNA or mRNA stability and translation by 30-UTR-binding its protein product. proteins and miRNAs increases as cells become more developmentally restricted [4,5]. Christopher Brosnan and Olivier Voinnet return us to the study of noncoding RNAs, describing the various classes How miRNAs repress translation remains contentious. and functions of ncRNAs in both prokaryotes and eukar- Marina Chekulaeva and Witold Filipowicz review the yotes. They remind us that in eukaryotes, ‘long’ ncRNAs evidence for the prominent, competing models: control of typically regulate transcription, whereas many (but not initiation, control of elongation, and destruction of nas- all) ‘small’ ncRNAs act post-transcriptionally. These cent polypeptides. They also distill the evidence for small silencing RNAs include Piwi-interacting RNAs activation by miRNA-guided protein complexes under (piRNAs), endo-siRNAs, and microRNAs (miRNAs). special cellular circumstances. miRNAs also recruit New classes of small silencing RNAs and new biological mRNAs to P bodies, and Chekulaeva and Filipowicz functions for known small silencing RNAs continue to discuss the relationship between the accelerated decay emerge. Mikiko Siomi and colleagues focus on the role of often observed when a miRNA binds an mRNA target small silencing RNAs in germ-line cells, where piRNAs and the recruitment of mRNAs to P bodies. Finally, the and endo-siRNAs protect the genome from transposons authors present the growing number of examples in which and repetitive sequences. They describe our current un- miRNA function is itself regulated, by controlling derstanding of how these small RNAs are made, how they miRNA processing, or by regulating access of the miRNA repress transposon expression, paying particular attention to its binding site on the target mRNA. to mice and flies, where piRNAs have been most exten- sively studied. This issue of Current Opinion in Cell Biology concludes with two more detailed explorations of the role miRNAs play Unlike piRNAs and siRNAs, miRNAs direct mRNAs to P in development and disease. Eric Olsen and colleagues bodies, triggering mRNA decay, and/or translational describe the role miRNAs play in the development of repression. Before turning to the biochemical and bio- muscle. Of particular interest is the recent discovery that logical functions of miRNAs, we first provide a synopsis miRNAs play a direct role in several heart pathologies. by Maria Rodina and Wolfgang Wintermeyer of our These discoveries suggest that transient inhibition of current understanding of the mechanism of eukaryotic specific miRNAs may provide therapy for human disease. translation itself. Ribosome-catalyzed, mRNA-directed In particular, antisense inhibition of miR-21, whose con- protein synthesis has been studied for far longer and in centration increases in failing hearts, protected heart much greater detail than translational regulation. The damage in rodents from experimentally induced pressure movements of proteins and RNAs are far better under- overload. George Calin and colleagues review the con- stood for translation than for any of the other pathways nections between cancer and miRNA dysregulation. reviewed in this issue, and it is easy to envy the rich miRNAs have been found to act as oncogenes and tumor symbolic language used to describe ribosome dynamics. suppressors, and miRNA profiling appears to improve identification of the origins of undifferentiated cancer In describing the sequence of events in translational types. miRNAs recognize their target mRNAs through initiation, elongation, and termination, Rodina and Win- surprisingly few nucleotides — perhaps just six or seven, termeyer introduce us to the steps that can serve as targets and Calin and colleagues review the evidence that single- of protein-guided or RNA-guided regulation. Rachel nucleotide polymorphisms in miRNA-binding sites influ- Groppo and Joel Richter then describe how distinct trans- ence cancer risk. The authors conclude by evaluating the lational regulators act to alter the rates of each of these prospects for miRNA reintroduction and inhibition as steps, repressing the production of protein from an mRNA. cancer therapies. Translational control can be global or restricted to a single mRNA or to a set of mRNAs that act in a common pathway. Thus, this issue begins in the nucleus, moves to the Most well studied translational regulators slow the rate of cytoplasm, and ends in the clinic. The journey reflects translational initiation, often by competing with translation our belief that cures for human disease begin with the initiation factors for binding the mRNA cap. Often, regu- deepest possible understanding of how genes are latory proteins that repress translation bind to the 30- regulated, how and why they become dysregulated, untranslated region (UTR), so that the use of alternative and how we can exploit biology to bring them back to 30-UTRs, by alternative polyadenylation or pre-mRNA their original, appropriately regulated state. www.sciencedirect.com Current Opinion in Cell Biology 2009, 21:331–334 334 Nucleus and gene expression

References 3. Deng X, Meller VH: Non-coding RNA in ﬂy dosage compensation. Trends Biochem Sci 2006, 31:526-532. 1. Neil H, Malabat C, d’Aubenton-Carafa Y, Xu Z, Steinmetz LM, 4. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB: Jacquier A: Widespread bidirectional promoters are the major Proliferating cells express mRNAs with shortened 30 source of cryptic transcripts in yeast. Nature 2009, 457:1038- untranslated regions and fewer microRNA target sites. 1042. Science 2008, 320:1643-1647. 2. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, 5. Ji Z, Lee JY, Pan Z, Jiang B, Tian B: Progressive lengthening of 30 Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM: untranslated regions of mRNAs by alternative polyadenylation Bidirectional promoters generate pervasive transcription in during mouse embryonic development. Proc Natl Acad Sci U S yeast. Nature 2009, 457:1033-1038. A 2009, 106:7028-7033.

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