Spring 2006 Volume Nine / Number One

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SPRING 2006 VOLUME NINE / NUMBER ONE

NON-PROFIT U.S. POSTAGE PAID PERMIT 751 SAN DIEGO, CA THE SCRIPPS RESEARCH INSTITUTE

A PUBLICATION OF THE SCRIPPS RESEARCH INSTITUTE

Ofﬁce of Communications—TPC30 ENDEAVOR 10550 North Torrey Pines Road La Jolla, California 92037 www.scripps.edu

PUBLISHER: Keith McKeown

EDITOR: Mika Ono Benedyk

DESIGN: Miriello Graﬁco

PRODUCTION: Miriello Graﬁco Kevin Fung

COVER ILLUSTRATION: Dennis Clouse

PORTRAIT PHOTOGRAPHY: Martin Trailer Bruce Hibbs Jamey Stillings

PRINTING: Precision Litho

© 2006 All material copyrighted by The Scripps Research Institute. “While the last century has been the century of physical sciences, I believe the next century will be the century of biological sciences.”

ANDREW VITERBI, PH.D.

Scripps Research Supporter THE SCRIPPS RESEARCH INSTITUTE Andrew J. Viterbi Looks to the Future ENDEAVOR Inventor, entrepreneur, and Scripps Research trustee Andrew J. Viterbi, Ph.D., has spent half a century capturing and capitalizing on the physical sciences. Best known for the Viterbi Algorithm used in digital communications and other ﬁelds and a co-founder

VOLUME NINE / NUMBER ONE SPRING 2006 of QUALCOMM, Inc., a leading developer and manufacturer of mobile satellite communications and digital wireless telephony, Viterbi nonetheless sees biological sciences as the wave of the future. “While the last century has been the century of physical sciences, I believe the next century will be the century of biological sciences,” says Viterbi. 1723 Viterbi’s interest in the biological sciences ﬁrst led him to Scripps Research as a member of the Scripps Cancer Center Advisory Board. The center is dedicated to FEATURES: ALSO: quickly bringing advanced cancer treatments from the laboratory bench to the patient’s

bedside through breakthrough translational research. Demonstrating his commitment, VITERBI J. ANDREW he and his wife, Erna, made a $2 million gift for state-of-the-art research led by Jorge Nieva, M.D., assistant professor of chemistry at Scripps Research.

02 EXPLORING A NEW GENETIC WORLD: 01 AT THE FOREFRONT “While it’s difﬁcult to bridge the gap between the research laboratory and the clinical environment, translational medicine is critical to effective drug discovery,” CLAES WAHLESTEDT VENTURES BEYOND THE 16 BEHIND THE SCENES says Viterbi. CENTRAL DOGMA A doctoral graduate of the University of Southern California, where the school of engineering was recently named in his honor, Viterbi’s decision to contribute to Scripps Research was inﬂuenced by the freedom afforded to scientists to take their laboratory work in the direction that they think is most promising.

06 LOOKING FOR A JOB DESCRIPTION FOR RNA: “I’m very oriented to independent research institutions such as those in private universities,” he said. “Private institutions have more ﬂexibility and control over their JOHN HOGENESCH BRINGS NEW TOOLS TO THE TASK destiny, particularly in the recruitment of scientists—they’re in a better position to control quality and limit bureaucracy.” As a scientist, businessman, and philanthropist, Viterbi believes in basic research. “Basic research will yield tremendous dividends towards the ﬁght against a variety of diseases. The key is getting extremely intelligent people involved and giving them free

10 THE REMAKING OF RNA reign,” he says. But he is equally devoted to advanced technologies, noting, “More and more, the computer is becoming an indispensable tool in medical research.” MARTHA FEDOR CONNECTS FORM AND FUNCTION A Scripps Research trustee since 2004, Viterbi is a life fellow of the Institute of Electrical and Electronic Engineers and a fellow of the American Academy of Arts and Sciences. Among his many honors, he was inducted into the National Academy of Engineering in 1978 and the National Academy of Sciences in 1996.

ENDEAVOR IS A PUBLICATION OF THE SCRIPPS RESEARCH INSTITUTE

Find out how you can receive ﬁxed annual income for life, now or as part of your retirement planning, This issue of Endeavor magazine features investigators working at the forefront of the ﬁeld of RNA research. Once thought to while also providing a gift to Scripps Research. Please contact Cheryl Dean, at (858) 784-2380 or be a simple stepping stone in the process of translating genetic information from DNA into protein, RNA has turned out to be a [email protected], to learn about joining the many members of the Scripps Legacy Society and far more important player than previously imagined. making the future discoveries of Scripps Research scientists part of your legacy. At the Forefront

Scientists Discover “Unprecedented” Functional World Community Grid Targets AIDS in Giant Amyloid Plays Beneficial Role In Human Cells Research Effort A group of scientists at The Scripps Research Insti- IBM and Scripps Research have launched a new effort to tute have shown that the amyloid protein structure, help battle AIDS using the massive computational power which has been linked to diseases of the brain including of the World Community Grid, a global community of Alzheimer’s, Parkinson’s, and Huntington’s, carries out Internet users who donate unused time on their personal an important functional role in human physiology. The computers. With computational power already placing discovery raises the possibility that current research it among the top 10 supercomputers in the world, the into curtailing amylolid formation to treat these diseases World Community Grid is the first “virtual supercom- might ultimately do as much harm as good. puter” devoted specifically to AIDS research. Donating “The fact that we have found a structure in humans unused computer time is fast, easy, and secure. For more that is usually only associated with pathology is a critical information on how to participate, go to www.worldcom- 01 new finding,” said Jeffery W. Kelly, Ph.D., whose posi- munitygrid.org. tions at Scripps Research include Lita Annenberg Hazen

Professor of Chemistry, member of The Skaggs Institute Scripps Florida Opens Cutting-Edge Screening FOREFRONT THE AT for Chemical Biology, and vice president of academic af- Technology to Florida Scientists fairs. Kelly led the study with Scripps Research Professor Scripps Florida has launched its “Access to Technologies” William E. Balch, Ph.D. program, which invites scientists from Florida univer- REFERENCE: PLoS Biology, 4(1), 10.1371 (2006). sities and other academic research institutions to use state-of-the-art screening technologies at the institute’s Researchers Find Protein Controls Tumor Growth Jupiter facilities for qualifying projects. Access to Scripps in Certain Breast Cancers Florida’s new High Throughput Screening operation, Scientists from Scripps Research and the Xiamen Uni- similar to that used widely by the pharmaceutical indus- versity School of Life Sciences, Fujian, The People’s try, should speed up the process of discovering new drugs Republic of China, have uncovered a new and potentially to treat a variety of human illnesses. important function for a protein previously thought to For more information, go to the Scripps Florida play a role solely in the innate immune system’s response Access to Technologies website at www.scripps.edu/ to bacterial infection. In the study, researchers showed florida/technologies/hts. that the presence of the protein Nod1 strongly inhibits the growth of estrogen-sensitive human breast cancer cells. Small Molecule Generates Neurons from Adult Richard Ulevitch, Ph.D., chair of the Scripps Re- Stem Cells search Department of Immunology, said, “These unex- A group of scientists from Scripps Research and the Salk pected findings offer the first real evidence that this path- Institute for Biological Studies have uncovered a syn- way may regulate tumor growth and suggest a potentially thetic small molecule that generates functional neurons new mechanism for controlling this type of breast cancer.” from adult neural stem cells. The molecule, named neu- REFERENCE: PNAS, 103(6), 1840-1845 (2006). ropathiazol, selectively and potently induces neuronal differentiation of neural stem or progenitor cells. The results of this study, led by Sheng Ding, Ph.D., a Scripps Research investigator, may ultimately help in the development of future small molecule therapeutics. These could stimulate the regeneration of neurons in patients suffering from neurodegenerative disorders, such as Al- zheimer’s and Parkinson’s disease, or from brain injuries. REFERENCE: Angewandte Chemie, 45(4), 591-593 (2006). “Scientists have been looking for a long time at known disease-causing genes and not finding answers. At least some of the answers may be contained in this new universe of non-coding RNA…”

CLAES WAHLESTEDT, M.D., PH.D.

02 Exploring a New Genetic World

CLAES WAHLESTEDT VENTURES BEYOND THE CENTRAL DOGMA

It is the nature of scientiﬁc inquiry that solving one expression made by Wahlestedt, his collaborators, puzzle often leads to many others. Such is the case and others in the ﬁeld have shaken up a central dog-

CLAES WAHLESTEDT with the Human Genome Project, which deciphered ma of biology that holds that the main function of all three billion nucleotides, the basic building blocks RNA is to translate DNA codes into proteins, which of DNA that comprise the totality of human genes. are needed to sustain life. The massive international research effort, begun in While it has been known for some time that not 1990 and completed in 2003, was one of the great all of a cell’s RNA is involved in protein synthesis, feats of scientific exploration and provided the the importance of so-called “non-coding” RNA has ability, for the first time, to read nature’s complete not been well understood or even thought signifi- genetic blueprint for humans. To scientists like Claes cant. Wahlestedt maintains, however, that “non-cod- Wahlestedt, M.D., Ph.D., professor and director ing” RNA plays a crucial role—one that will become of Central Nervous System Disorders at The increasingly valued as it is better understood—in the Scripps Research Institute’s Florida campus, this processes of expression and repression of hereditary achievement, as astounding as it was, was just the information. starting point. MAPPING THE “TRANSCRIPTOME” “We now have an enormous list of genes, but this is almost equivalent to having a phone book with a For the past several years, Wahlestedt’s research has list of names—it doesn’t tell us how the information concentrated on non-coding RNA. This focus led contained in genes is expressed.” to his participation in an international consortium And therein lies one of the puzzles that Wahlest- involved in an effort akin to the Human Genome edt and his research collaborators have in the past Project—sequencing the human “transcriptome”— few years set out to solve: how does gene expres- defined as all the RNA transcribed from genes sion—the process whereby different cells in our bod- within a given genome. The consortium announced ies use genetic information—actually work? Their results of its work in the September 2, 2005 issue of focus, however, is less on DNA than on its little- the journal Science. recognized cousin, ribonucleic acid, or RNA. Re- “The results of the study give scientists unprec- cent discoveries about the function of RNA in gene edented insights into both the nature of the genome

04 CLAES WAHLESTEDT has led to another significant finding—this one havone finding—this significant another to led has project transcriptome the MYSTERY with work Wahlestedt’s ANOTHER REVEALS TRANSCRIPTOME THE without apurpose.” they function.(See his and Wahlestedt by forth put premise The collaborators is that non-coding RNA somehow reg controlled bynon-codingRNA.” much how discover to surprised were we “Even of the RNA doesn’t fit the one gene/one protein para encoding RNA. se massive this of findings startling the of One for manyyears,”Wahlestedt says. function. The data will serve its as a basis for discovery to organization genome of importance the and ir n ee getr hn h aon o protein- of amount the than greater even and lier ear months few a even imagined have would tists DNA codes—were found by Wahlestedt and his con from translated “messages” transcripts—the RNA quencing project is that more than half of the 40,000 “sense” strand, encodes for proteins. In normal DNA so-called the strands, its of one only and double- stranded is DNA genes. “antisense” with do to ing ple, why would the cell expend so much energy mak non-coding RNA is vast, far more than most scien most than more far vast, is RNA non-coding of amount The non-coding. be to colleagues sortium It seems unlikely that it’s just sitting there in the cell proteins? for code not do that transcripts RNA ing exam “For says. Wahlestedt questions,” interesting many raises it and Project Genome Human the ter how at look to begin can scientists known, are genes Now that the sequences of these atypical non-coding not. are which and expressed are genes which ulates be also may mammals of development the cells, our of components essential the up make proteins while that indicate results “These Wahlestedtsays. digm,” “This is arguably one of the next major steps af Hogenesch article is toreallybeablepracticepreventive, personalized medicine, toassessanindividual’s riskandthentreat “We wanttofindoutwhymostdrugsarereallyonly effective forasmallnumberofpeople.Theholygrail .) that personbeforesymptomsappear, becauseonce ------

our understanding of genetics and how information how and genetics of understanding our change fundamentally may findings these correct, If control of many, perhaps all, cell and body functions. are numerous and they are likely to participate in the research, medicine, and biotechnology biological because antisense genes of significant future has discovery the groundbreaking for This implications W ko ta te N o al ua beings human all of DNA the that individu that know and “Weidentical percent 99.9 is earth on genes andenvironmentalfactors.Why? al should genes these Finding disease. to contribute The goal of much DISEASE genetic research is TO to find genes that ANSWERS FOR SEARCHING is storedinthegenome. are tall, others short, some are heavy,are thin, some are short, some others tall, are people some “Still, says. Wahlestedtother,” each of copies carbon almost are genders and races all of als cystic fibrosis or Huntington’s disease, current meth as such disorders single-gene the basis, genetic ward straightfor relatively a with diseases For disease. the treat and prevent to developed be might drugs that so process, disease the of understanding an low transcripts. The results of this work appear in a sepa gene regulation by affecting the corresponding sense to contributes and common extremely is scription tran antisense that evidence found and scriptome psychiatric disorders—which are affected by many by affected are disorders—which psychiatric “complex” or cancers, diabetes, stroke, disease, diseases—heart common, more single-gene develop have not however,do people, but Most disorders, ods areusuallysufficienttofindthegenesinvolved. rate paper in the September 2, 2005 issue of alset n hs ru aaye te tran the analyzed group his and Wahlestedt RNA, butthetranscripthasreverse sequence. into transcribed be also can strand, “antisense” the strand, DNA other The copied. is strand sense the only and apart, split strands two the transcription, symptoms showupit’s oftentoolate.”

CLAES WAHLESTEDT CLAES , M.D., , Science PH.D. ------.

some people get terrible diseases, others don’t. These case, drugs may be found that can target the caus- characteristics must be the result of differences in ative RNA. This is a different approach to drug de- just the .1 percent of DNA that is variable—in com- velopment from what is mostly used today where bination with environmental factors.” most drugs treat symptoms, at best, but don’t cure. Wahlestedt would like to pinpoint the basis for “Scientists have been looking for a long time these DNA differences to learn why one person is at known disease-causing genes and not finding 05 more susceptible to disease than another. “Of course, answers,” Wahlestedt says. “At least some of the the reasons for susceptibility may reside in the world answers may be contained in this new universe of of genes already known, but I believe non-coding non-coding RNA, much of which acts as regula- CLAES WAHLESTEDT CLAES RNA may eventually be found to be involved in the tory guardians of the cell. It’s likely that it is part cause of many of the complex diseases.” of a higher-level control system—if something goes As an expert in pharmacogenomics—the sci- wrong with a cell and disease occurs, it’s possible ence of understanding the correlation between an that these control systems are involved or even the individual patient’s genetic make-up and his or her reason why things go wrong in the first place.” response to drug treatment—Wahlestedt says, “We want to find out why most drugs are really only ef- AT WORK ACROSS THE GLOBE fective for a small number of people. The holy grail A native of Sweden, Wahlestedt received both his is to really be able to practice preventive, personal- medical degree and Ph.D. from Lund University. ized medicine, to assess an individual’s risk and then His collaborative work currently spans three conti- treat that person before symptoms appear, because nents—the United States, where he has been based once symptoms show up it’s often too late. at Scripps Florida since early 2005 and has a grow- Wahlestedt now is applying the insight gained ing lab, the Karolinska Insitute in Sweden where he from studying the transcriptome to understanding has a sizable but shrinking lab at the Center for Ge- more about the genetic variations behind diseases. nomics and Bioinformatics, and Japan, where he has He is closely following the work of another massive long-standing ties at the Riken Institutes in Tokyo mapping project—the International Haplotype Map and Yokohama. Project—HapMap, for short—a partnership of sci- “The work we are doing is very exciting,” says entists and funding agencies from around the world Wahlestedt, who now lives in Palm Beach with his that is helping researchers find genes associated with wife Lisa, a medical doctor, and daughter Ella, 7 and human disease and that will eventually describe the son Thor, 5. “It’s not that often in scientific research common patterns of human genetic variation. that you get to feel you’re venturing into uncharted Through the use of “association studies”—those territory. We feel that with our work, we have a good that look for differences among many individuals— chance to change the scientific outlook dramatically. Wahlestedt is looking at a large number of people That doesn’t happen every day. Right now, we feel with complex diseases and matching them to a large a bit the way Christopher Columbus may have felt. number of unaffected people of the same ethnic There’s sometimes skepticism when an explorer de- background to try to find out whether differences in scribes what he has seen, but if people keep an open their genomes—including non-coding RNA—may mind, they may realize that a world of possibility is be behind their diseases. If this turns out to be the opening up where it did not exist before.”

ANNA SOBKOWSKI

“Our method gives a systematic, high-throughput way to ﬁnd those noncoding RNAs that do have functions. We can now identify the ones we should be focusing on.”

JOHN HOGENESCH, PH.D.

Looking for a Job Description for RNA 07

JOHN HOGENESCH BRINGS NEW TOOLS TO THE TASK JOHN HOGENESCH HOGENESCH JOHN

The most puzzling result of the Human Genome been surprised to find that more than half of the Project, announced in 2001, was that humans had RNA transcripts they observe do not code for pro- no more genes than mice or, worse yet, the little teins (see Wahlestedt story). weed Arabidopsis. It was a source of humility, and Why, then, are these noncoding RNA in the cell? led some scientists to comment that the mechanisms Hogenesch is looking for answers. that generate the complexity of creatures must de- QUESTIONING THE PARADIGM rive from something other than sheer numbers of genes or base pairs. In a study supported by the Novartis Research Foun- Biochemistry professor and neurobiologist John dation and an NIH Kirschstein National Research Hogenesch, Ph.D., and his colleagues at The Scripps Service Award, Hogenesch, postdoc Aaron Willing- Research Institute in Florida and California are ham, Ph.D., Professor Peter G. Schultz, Ph.D., and currently exploring one likely source of that com- their colleagues entered what the journal Science plexity: RNA. has called the “underworld of RNA.” Adapting a For nearly 50 years, molecular biology has taken common method of screening pharmaceuticals, the Francis Crick’s idea that “DNA makes RNA makes team proved that at least some of these noncoding protein” as its paradigm or, as it came to be known, RNA transcripts play crucial roles in cell functions. the “central dogma.” RNA was simply an interven- The study’s results, published in the Septem- ing stage between the gene and the protein that did ber 2, 2005 issue of Science alongside several other the work; genes were discovered and characterized landmark papers on RNA, caused some scientists to by studying their protein products. rethink their assumptions. “We may have seriously By the early 1990s, however, work on the worm misunderstood the nature of genetic programming C. elegans had revealed a flaw in the central dogma. in the higher organisms by assuming that most ge- Small bits of RNA, called microRNA, controlled the netic information is expressed as and transacted by timing of the worm’s development without ever be- proteins,” says John S. Mattick of the University of ing translated into proteins. Moreover, scientists us- Queensland, who wrote an accompanying commen- ing cloning and computational methods to compare tary. Noncoding RNA could, he continued, “consti- the genomes of mice and humankind have recently tute a critical hidden layer of gene regulation.” > 08 JOHN HOGENESCH to biology.” RNAs noncoding these link hard systematically to is part “The concedes. Hogenesch shift,” real a paradigm be all, after could, It RNA. noncoding this dis of causes the for in schemes detection example, says. large-scale for he up, turn functional,” don’t RNAs not Noncoding are RNAs noncoding Could some noncoding RNA simply be, as Ho as be, simply RNA noncoding some Could a normalmouse. many that suggest to evidence much is “There function. Hogenesch himself is not convinced that molecu e, ehp a e hnrd ae motn fr cell for important are hundred, few a perhaps set, overlooks. “So we know the function of a subset of subset a of function the know we “So overlooks. dogma central the that a there’s genome shows the research Hogenesch’s of yet And component of evolution.” work perfectly, it just has to work. That’s the genius likely to be quite is high … The system doesn’t have to leakproof percent 100 process transcription the making for cost the and DNA] from RNA [making transcription not RNA], from proteins [making tion transla in are costs energy to real “the as according Hogenesch, much”, cell the cost really wouldn’t RNA “Nonfunctional possibility: one is this lieves be Hogenesch fluff”? “translational it, puts genesch noncoding genome looks and acts no differently than of megabase entire an missing mouse A periments: ex knock-out in seen be effects their can Nor ease. noncoding RNA transcripts, he suspects only a sub a only suspects he transcripts, RNA noncoding wrong lamppost all these years.” Of the thousands of lar biology has been, as he puts it, “looking under the

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perfectly, itjusthastowork.That’s the TOOL BUILDING FOR BIOLOGY FOR BUILDING TOOL o et hte o nt ocdn RA ral do Ho attracted what cell—was the in havefunction a really RNAs noncoding not or whether test to way efficient an finding of part hard part—the That their book.” for these used has industry explains. pharmaceutical he “The assays,” cell-based with and science Having set up a new robotic cell-based screen cell-based robotic new a up set Having S I a vr cmotbe ih large-scale with comfortable very was I “So many what tissues.(Seehttp://symatlas.gnf.org) e lo rdt te nune f cut, who Schultz, of influence the of credits member a is and also Chair Family Scripps the holds He can usethattooltodoy.” you then x, do to havetool you a once that is beauty The question. biological a answer to building tool it’s But building. tool it’s Sure, to. applied be can techniques those questions other what see to around interested in?’ And once I have them working, I look are the techniques I need to approach a problem I’m ‘What ask, I “First RNA. noncoding study to fined re be could it if wonder to began Hogenesch DNA, protein-coding at look to Florida Scripps at lab ing in expressed are 80 genes and which genes revealing 36,000 tissues, cross-indexes website ing result The Foundation. Research Novartis the of Institute Genomics the Hogenesch at colleagues that with Atlas created Gene the was method ing screen of sort similar a involved that project other An clock.” “body so-called the rhythms, circadian study to method screening cell-based a of developed son the had is Hogenesch professor, who nursing a “gearhead” and self-described chemist a A genesch tothetopicinfirstplace. er t sre dus W to a ae from page a took We drugs. screen to years “The systemdoesn’t have towork

genius ofevolution.”

JOHN HOGENESCH JOHN

, PH.D. ------

Professor John Hogenesch, Ph.D., is deeply involved in the Cell-Based Screening Program at Scripps Florida, which can be used to assign novel functions to genes. (Images from Beckman Coulter IC100 Image Cytometer, analyzed using Cytoshop.)

The Skaggs Institute of Chemical Biology at Scripps Of the eight affected cells, six had their viability Research in California. “Basically, this entire proj- compromised in ways not yet determined. One in- ect has been due to Pete and his vision,” Hogenesch terrupted Hedgehog signaling, a well-studied path- HOGENESCH JOHN says. “Pete is one of few scientists with truly pene- way essential for cell development, maintenance, trating insights into many different scientific areas. and repair. He encourages us to look for the important problems The researchers chose to investigate the remain- in biology and to ask, ‘Can I contribute?’” ing functional noncoding RNA further. This one repressed the transcription factor NFAT (nuclear CELL-BASED SCREENING factor of activated T-cells), which plays a vital role To screen noncoding RNAs in a cell-based array, in the immune response by interacting with T-cells. Hogenesch and his colleagues took advantage of the A remarkably sensitive transcription factor, it is also phenomenon called RNA interference. RNA inter- necessary for the proper development of the heart, ference is a process whereby cells identify and de- blood vessels, muscles, and nerves. The noncoding stroy double-stranded RNA—usually the mark of an RNA that the researchers dubbed NRON (for non- RNA virus, as the cell’s own RNA is single-stranded. coding repressor of NFAT) was found to interact Hogenesch’s team made part of the targeted noncod- with 11 proteins, of which three were members of ing RNA into a double strand, thereby tricking the the “importin” family. Importins regulate transport cell into destroying its own noncoding RNA and si- of molecules into and out of the nucleus. NRON was lencing or “knocking down” the team’s target. found to most closely associate with importin-beta The researchers first chose 512 noncoding RNA 1, suggesting that NRON modulates NFAT by con- sequences, all relatively large (not microRNAs) pres- trolling its location in the cell, perhaps by providing ent in both mice and humans. They then constructed a scaffold for the making of protein complexes that a library of short-hairpin RNAs that would anneal regulate traffic into and out of the nucleus. to—and interfere with—the target RNAs, and tested Hogenesh is reserving judgment for now on the effects of the knockdown on the cell’s signaling whether these results help explain how so few genes pathways and other vital processes. can result in such complex organisms. Only eight of the 512 cells showed a reproduc- “The jury’s still out,” Hogenesch says, “but our ible and measurable effect when a specific noncod- method gives a systematic, high-throughput way to ing RNA sequence was silenced. This “hit rate,” Ho- find those noncoding RNAs that do have functions. genesch notes, is low—an order of magnitude lower We can now identify the ones we should be focusing than the results he sees from cell-based screening of on. Studying them will determine the contribution of protein-coding genes. noncoding RNA to the diversity and complexity of higher organisms.” NANCY MARIE BROWN

“This has been the case all along. Just when you think there are no more remarkable RNA discoveries, another one pops up.”

MARTHA FEDOR, PH.D.

The Remaking of RNA 11

MARTHA FEDOR CONNECTS FORM AND FUNCTION MARTHA FEDOR MARTHA

Welcome to RNA World, a combination of primor- Nobel Prize in Chemistry for the discovery in 1989. dial theme park and research fraternity, where this It was also Fedor’s ﬁrst exposure to the end- rather simple string of nucleotides is now taking star less possibilities posed by this new understanding of billing. After what many now think of as years of RNA—her husband, Professor Jamie Williamson, unwarranted neglect relegated to a handoff role be- also at Scripps Research, was working in Cech’s lab tween genes and proteins, RNA has become the Tom when the prize was announced. Fedor herself was at Hanks of molecules—it writes, acts, produces, and the university doing postdoctoral work after receiv- directs, and it looks darn good doing it. In fact, it ing her doctorate from the University of California, may even have had a hand in founding the theater. Berkley and spending time at Stanford, “looking at A lot of the credit for this newfound spotlight on yeast,” as she describes it. RNA goes to the work of Martha Fedor, an associ- Cech’s discovery led a number of scientists to ate professor at The Scripps Research Institute, and reconsider RNA and the whole primordial soup the- her laboratory colleagues at The Skaggs Institute for ory of life. Suddenly, here was a likely candidate for Chemical Biology. What her research has shown is life’s early beginnings. In a world of pre-biological that RNA, once thought of as kind of a genetic non- evolution, RNA could have provided not only the sequitor, can do more—in fact, a whole lot more. basic genetic material of life but also the enzyme en- gine that created more progeny. Support for the idea PRIMORDIAL SOUP was bolstered by the fact that retroviruses like HIV RNA’s makeover began in the 1980s, when a re- use only RNA as their genetic material, simultane- searcher named Tom Cech at the University of Colo- ously storing that information and replicating it. If rado, Boulder made the astonishing discovery that the RNA theory of early life is correct, then retrovi- RNA enzymes could perform catalytic functions, ruses and RNA are living reminders of how we all quickly gaining them the nickname ribozymes. It got started, a reverse molecular telescope that looks was something no one had ever thought of before— backward into genetic time. so astonishingly new, in fact, that Cech won the Welcome to RNA World. > 12 MARTHA FEDOR rmril N se, u wa se ely ie is likes really she what but stew, RNA primordial func- a be to has there things, these all do things— to and many so do can RNA that most, the me accelerate biological functions. This is what intrigues the layperson a lan the has translates Another biochemistry. in Another degree ﬁngerprinting. DNA with works and chemist forensic a is One business. science the in also are sisters and brothers family.”(Her our in thinker reductionist of the I’m out scenarios. complicated sense making like I universe. the on order imposing like “I says. she biologist,” experimental an of more much I’m ago, eons “While it’s arisen interesting haveto think about how might things doing experiments. prac certain a where Michigan, in born was Fedor BENT PRACTICAL A tional structure.” ex genetic of end-all the were proteins that thought everyone time, world,” long a For RNA things. of kinds to different many rise do gave can RNA that that notion concept the “The “is says, Fedor rpstr o gnmc nomto, ctls to catalyst a information, genomic of repository a that RNA was much more than a transmitter—it was pression. After Tom Cech’s discovery, it became clear guage of high technology into everyday English for English everyday into technology high of guage the of bowl that admires of out arisen have she might what of idea says Fedor siblings. three daughter with oldest an in especially birth, al from sensibility most everybody’s into infused is ticality . ) - - - -

made about a form of the molecule called small non been have discoveries years, few last the In regular basis. a on uncovered being are functions RNA ﬁn de siecle of RNA discovery. Now,the Fedorin says, newliving were they that thought else, everyone four building blocks—that can do a variety of com of variety a do can blocks—that building four molecule—just chemical simple RNA about very intriguing really a that’s it’sthing “The that is structure doesn’tseemtohinderitmuch. the about it—especially about more know to as wanted formless Fedor as aside, was cast RNA was that pasta notion wet the Once of bowl a gene expression. rdae tdn a Bree. eo, ln with along Fedor, Berkeley. at student graduate a was catalyze she could when RNA that made discovery was initial reaction The biochemical a of genetic material because you don’t really want it want really don’t you because material genetic of terms in thing good very a is Which inert. virtually inactive, almost they’re because reactions biological What is most amazing about all this, is Fedorthat at ﬁrst says, glance RNAs seem unlikely to catalyze What’s more,theyassemblethemselves.” can build anything from a car to a factory with them. you but combinations, pair many so only are There pairs. in come that colors different with Tinkertoys like it of think can “You says. she things,” plicated ating a precise structure. But RNA’s simple chemical cre time easier havefar proteins a that sense makes teins have more chemistry to play with than RNA, it coding RNAs and the fact that they play key roles in hs nrgigy ucinl tutr. eas pro Because structure. functional intriguingly this of how - - - -

“The thing that’s really intriguing about RNA is that it’s a very simple chemical molecule—just four building blocks—that can do a variety of complicated things. You can think of it like Tinkertoys with different colors that come in pairs. There are only so many pair combinations, but you can build anything from a car to a factory with them. What’s more, they assemble themselves.”

MARTHA FEDOR, PH.D.

13 to be wildly active; you want it to stay the same from But that still left the exact how of RNA cataly- transference to transference. And yet here was RNA, sis to probe. Like proteins, RNA needs to fold into a catalyzing biological reactions, an ability seemingly precise three-dimensional structure to perform. But FEDOR MARTHA incompatible with its ability to serve as a stable re- while proteins generally have only one stable struc- pository of genetic information. ture, RNA can fold itself into any number of stable structures, with the catch that only one of them is a WHEN EVERYTHING YOU KNOW TURNS OUT TO properly assembled molecular machine; the rest are BE WRONG virtually worthless. If it folds correctly, it works; in- correctly and it gets stuck in a malformed dead end Fedor’s initial research, which began before she ar- and remains woefully inert. rived at Scripps Research in 1997, looked at RNA’s In the lab, Fedor and her colleagues chose the alleged need to bind to metals to perform certain hairpin ribozyme, a good choice because folding functions, gaining them another nickname, metallo- into the correct hairpin structure (which looks, you enzymes. The positive charges of metals supposedly guessed it, just like a hairpin) makes this RNA cut helped RNA balance the highly negative charges itself in two, allowing easy detection of proper as- that accumulate during the most difﬁcult steps in the sembly. They manipulated the folding process by reactions they catalyze. What Fedor did was show inserting inhibitory bits into the ribozyme at differ- just how wrong this theory about RNA was. ent points to see if the folding occurred sequentially, “I found that not all RNAs use metals to cata- from one end to the other as the RNA is made, or if lyze reactions,” she says. “The ribozyme we studied all the parts interacted simultaneously, regardless of didn’t need metals to function because it worked their position in the RNA. perfectly well without them. It surprised a lot of peo- Sequential folding is precisely what they found ple who thought the RNA story was over. This has in simple test tube folding reactions. If they put an in- been the case all along. Just when you think there are hibiting sequence at the end of the RNA, the folding no more remarkable RNA discoveries, another one process produced normal ribozymes, and was more pops up. My boss at the time said it’s a wonderful or less oblivious to the inhibitory part at the end; if feeling when everything you know turns out to be they put it closer to the beginning, the inhibitory bit wrong.” folded back onto the ribozyme part and trapped the Fedor used her work debunking the metalloen- RNA in a functionless form. All of which Fedor ex- zymes theory (R.I.P.) in her job interview at Scripps pected to ﬁnd again when they tried the same thing Research. with living yeast. >

14 MARTHA FEDOR able todevelop somethingthatcouldalterthediseasepathway.” and wecanﬁndawaytocorrectthoseerrors,thenmaybe certain diseases. If weknowhowtheRNA processinggoeswrong, “There areerrorsinRNA processingthatareassociatedwith MARTHA FEDOR, PH.D. FEDOR, MARTHA ( yeast to tube test from folding RNA on research her moved Ph.D., Fedor, Martha When Saccharomyces cerevisiae Saccharomyces shown here), the results were unexpected. unexpected. were results the here), shown

Chemical structure mapping of RNA using a dimethylsulfate modiﬁcation reaction.

Except that they didn’t. No matter where they “One thing we say is that RNA is a potential tool stuck the inhibitory structures in the yeast ribozyme, and potential target,” Fedor says. “There are errors the creature simply folded itself into a corner. So, in RNA processing that are associated with certain FEDOR MARTHA either sequential folding was something that just diseases. If we know how the RNA processing goes didn’t happen in the real world or something else en- wrong, and we can ﬁnd a way to correct those errors, tirely was going on. then we may be able to develop something that could Fedor has a couple of ideas. alter the disease pathway. With rapidly dividing “I don’t think this is a case of nature being cells, like those in cancer, much of the cells’ energy sloppy,” she says, “even though some argue that na- goes into making ribosomes that generate proteins. ture might keep at it until it gets it right. To me, tak- And they do so in a radical way. It’s as if all the parts ing apart misfolded RNAs to recycle their building of a car were laid out on a tarp and suddenly the blocks just seems so wasteful. We can watch RNAs car builds itself. Interfering with RNA self-assembly getting stuck in the wrong structures in the test tube, could lead to shutting the process down, so one of but that’s not what happens inside a cell. Maybe the things we’re interested in is small molecules that nature has ways to orchestrate the folding process block the RNA assembly process.” to make it more efﬁcient that we don’t know any- Fedor and her colleagues are testing two in vivo thing about.” models to see what cells contribute to the RNA folding process so far missing from simple laboratory “A POTENTIAL TOOL AND A POTENTIAL TARGET” reactions. One line of research searches for chaperones that work inside cells. The other investigates This is where the idea of the RNA chaperone comes whether the three types of RNA synthesis machinery in. Fedor theorizes that these chaperones are pro- produce three different patterns of assembly, clari- teins that help RNA during the folding process. For fying whether the machinery that makes RNA also example, when RNA folds itself into an inert struc- helps it fold properly. ture, the chaperones come along and destabilize the “Characterizing how RNA folds and assembles inert structure, essentially giving RNA the chance of offers a very basic insight into the nature of life and a do-over folding. Although some chaperone behav- biology,” Fedor says. “It shows how macromolecules ior has been seen in the lab, no one has been able to achieve the functions that are unique to life and make prove conclusively that they actually help assemble a living organism different than a collection of inert RNA machines in cells. But the whole idea adds an- chemicals. That’s what I say to my students: ‘I’m go- other layer of potentiality to RNA. ing to tell you all about the difference between something that’s alive and a pot of chemical goo.’”

ERIC SAUTER 1 2

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Behind the Scenes 16 1

New Events Bring Over 30 South Florida business executives who support Scripps Florida attended the Together Scientists, late 2005 kick-off lunch for the Scripps Florida Corporate Club at the Raymond F. Kravis Center for Performing Arts in West Palm Beach. Deborah A. Mosca, Ph.D., Donors, and Business senior director, business development, spoke and introduced Polly A. Murphy, Executives V.M.D., Ph.D., Scripps Research’s new senior vice president for business and scien- tiﬁc services. Pictured here are Mike Dyer, regional managing director for Wachovia Wealth Management; Murphy and Mosca; and Tommy Mayes, regional managing

BEHIND THE SCENES director, Wachovia-Calibre Family Ofﬁce, Palm Beach.

2, 3

Approximately 75 guests attended Scripps Research’s ﬁrst annual donor appre- ciation dinner in the fall at the Beckman Center for Chemical Sciences. At the dinner, held for annual donors of $1,000 or more, Scripps Research President Richard A. Lerner, M.D., spoke about the institute’s extraordinary history, cul- ture, and future. Following Lerner’s remarks, Scripps Research department heads described the breakthrough work of their scientists. Pictured here are Ernest Beutler, M.D., chair of molecular and experimental medicine with donors Izetta and Sheldon Magazine. Also pictured is Donald Haake, president of the Donald E. and Delia B. Baxter Foundation, and Steve A. Kay, Ph.D., chair of biochemistry, professor of cell biology, and director of the Institute for Childhood and Neglected Diseases.

Scripps Florida is collaborating with the South Florida Science Museum (SFSM) to create a permanent bioscience exhibit at its planned new museum facility in West Palm Beach. Scripps Florida’s Science Saturday program for high school students, funded by the William R. Kenan, Jr. Charitable Trust, will also expand to include the SFSM facility. Pictured at the SFSM’s recent Diamond Constellation Ball at the Mar-a-Lago Club in Palm Beach are Harry Orf, Ph.D., vice president of scientiﬁc operations for Scripps Florida; Jennifer Busby, Ph.D., associate scientiﬁc director of proteomics; Donald Trump; Teresa Reyes, Ph.D., associate professor of biomedical sciences; and Gala Chair Kathryn Vecellio, wife of Leo A. Vecellio, Jr. The Vecellio Group is a member of the Scripps Florida Corporate Club. “While the last century has been the century of physical sciences, I believe the next century will be the century of biological sciences.”