PROFILE PROFILE Profile of James A. Birchler

Farooq Ahmed Freelance Science Writer

Food and fuel: two key elements of human in ethnobotanist Charles Arzeni. Formerly prosperity and survival that have grown a botanist in Africa, Arzeni made up for the scarce as the global population has continued university’s lack of research by sponsoring to grow. According to the World Bank and field trips to far-flung locales like the Ama- the International Monetary Fund, droughts zon rainforest in Colombia. Notes Birchler, and increased demand have led to unaccept- “It’s only because of Arzeni that I went to ably high rates of child and maternal mortality graduate school.” Birchler remained in the across the world (1). Increased fuel costs, the heart of the Midwest and attended Indiana organizations say, have also contributed to University, two and a half hours east of the rising price of staples like corn and soy- where he went to college. bean oil (2). During his first semester in graduate A former Illinois farm boy, James Birchler school, Birchler received a letter informing has developed a technique that may help him to enter the draft for the Vietnam War. tackle these seemingly intractable issues. Because he had received an earlier defer- Now a Curators’ Professor at the University ment, he was nearly assured of being draf- of Missouri and a recently elected member ted. Then, on December 31, 1972—the day of the National Academy of Sciences, Birch- before he was eligible—President Richard ler integrated decades of research on plant Nixon suspended the draft, which was never genetics to create synthetic maize chromo- reinstated. Birchler plants corn in the summer plot at Indiana Univer- somes. These chromosomes, which propa- sity in 1976. Photograph by Edith Birchler. gate naturally in corn, can be outfitted with Inverse Effect and Dosage genes for drought tolerance, biofuel produc- Compensation lence of dosage compensation in maize and tion, or other beneficial properties to pro- Having escaped the Vietnam War, Birchler discovered that it relied on the inverse dos- duce stable lines of bioengineered crops that focused on plant genetics at Indiana, work- may help address some of the global crises ing with Drew Schwartz, whom he credits age effect (4, 5). The effect occurs when there that threaten us. with providing an atmosphere of lively sci- is a negative correlation between gene ex- entific discussion. “That led to research that pression and chromosomal dosage. Scientist Farmers we’re still pursuing, because, in Schwartz’s Birchler was born in Red Bud, IL, southeast Facts About Flies lab, I started changing the dose of chromo- At first, Birchler’sworkwasdismissedasa of St. Louis. His mother and father, both some arms in maize and studying the ex- teachers, ran the family farm. They grew quirk of plant genetics or an experimental pression levels of different genes.” artifact. He joined Ed Grell at Oak Ridge corn, soybeans, and wheat, and raised beef He carried out these experiments by ex- cattle. Birchler credits his upbringing for his National Laboratory in Tennessee as a post- “ ploiting a quirk of maize genetics. Corn has doctoral fellow to recapitulate his findings in early interest in science. Ihadthetypical 10 primary chromosomes called A chromo- fl “ farm-boy chores of plowing fields, cutting fruit ies. Ed was a fountain of facts about somes and a genetically inert supernumerary fl fi hay, and feeding cows. That environment y genetics and the history of the eld. He B chromosome of variable number. Remark- fi gave me an early exposure to zoology and was one of the rst people to show that, if ably, the B chromosome enters only half of botany,” he says. “I could identify all the dif- you varied the gene encoding an enzyme in maize sperm cells. Birchler manipulated the Drosophila ferent species of trees on the farm—with and , you got a proportional amount dosage of chromosomal segments in maize — without their leaves.” He went to high school of gene product so he seemed like a great by using stocks that have regions of the A ” in nearby Sparta, IL, and attended college at choice for me as a postdoctoral mentor. chromosome attached to the B chromosome fi Eastern Illinois University to study education. By reproducing his ndings in another in a genetic trick called B-A translocation. “In high school, I had taken a biology class species, Birchler demonstrated that varying Birchler observed that the magnitude of and had gotten quite interested in the concept chromosome dosage routinely produced the the change in gene expression could be ei- of evolution. At the time, Eastern didn’thave inverse effect and dosage compensation. (6) ther a direct or an inverse correlation with “ fl a biology department, so I majored in botany The y research illustrated the generality of chromosomal dosage (3). Furthermore, in- ” and minored in zoology.” By attending col- the phenomenon, he says. Birchler then creasing a gene’s amount on a chromosome joined Kenneth Paigen’slaboratoryatthe lege, Birchler received a deferment from be- ing drafted to fight in the Vietnam War. did not always increase its level of ex- University of California in Berkeley, where pression. This finding, called dosage com- Deferred Draft pensation, had been thought to occur ex- This is a Profile of a recently elected member of the National At Eastern Illinois, which had no undergrad- clusively in the sex chromosomes of animals. Academy of Sciences to accompany the member’s Inaugural Article uate research program, he found a mentor Birchler went on to demonstrate the preva- on page 14746 in issue 37 of volume 109.

www.pnas.org/cgi/doi/10.1073/pnas.1221539110 PNAS | February 19, 2013 | vol. 110 | no. 8 | 2687–2689 Downloaded by guest on September 27, 2021 he continued studying Drosophila genetics. the molecular biological level, searching for Paigen focused mainly on mouse genetics, the mechanisms. which provided Birchler exposure to an- As an offshoot of the dosage studies, re- other experimental model. searchers Manika Pal-Bhadra and Utpal In 1985, he accepted a position in the Bhadra, in Birchler’s group, discovered department of organismic and evolutionary the phenomenon of transgene silencing in biology at Harvard University. “Iliketojoke Drosophila, which at the time had been that it was the only place I could find a job,” thought to occur only in plants. They ob- he says. “Even though I had a longstanding served that a family of proteins that help interest in evolution,” Birchler continues, “I package DNA, known as Polycomb group had not had any formal training in the sub- proteins, played an integral role in silencing ject, so Harvard was an excellent learning genes in flies and that the mechanism used experience.” small RNA (12, 13). The repressive Poly- The inverse effect. The eyes of Drosophila carrying the comb complex associated with transgene Fruit and Flies white-apricot allele of the white eye color gene with sequences, whereas mutations in the genes With his own laboratory, Birchler was free different functional doses of the Inverse regulator-a (Inr- that process small RNAs reversed the si- a) gene. Clockwise from top: one, two, and three func- to pursue regulatory mechanisms in the ge- lencing effect. Further studies demonstrated nomes of both maize and Drosophila. “Over tional dose(s) of Inr-a. The amount of pigment from the white gene is inversely proportional to the dosage of that the regulation of Drosophila hetero- the next 15 years, in an effort initiated by functional alleles of Inr-a. Photograph by Weiwu Xie. chromatin, the part of a chromosome that my former postdoc Leonard Rabinow, we is normally inactive, involved related molec- were able to reduce the gene dosage effects of them. (8) “They all have some kind of ular mechanisms (14). found with chromosomal segments to single regulatory function and are mainly tran- genes.” Regulatory and signal transduc- Corn Paintings scription factors, chromatin proteins, and tion genes, they found, caused both the While developing genetic trickery in maize, fi components of signal transduction path- ’ inverse and direct effects (7, 8). These nd- ” Birchler s group also examined chromosome ways. In maize, they varied the ploidy of the structure. Research by postdoctoral fellow ings strongly suggested that dosage effects — genome the copy number of the whole set Akio Kato, now of Kyoto Prefectural Uni- were a general property of genetic regulatory — mechanisms. of chromosomes in a species and com- versity, and graduate student Jonathan Lamb During this time, graduate student Mark pared it to varying individual chromosomes led to a method that uses fluorescence to “ Alfenito, in Birchler’s group, also investigated or other genomic pieces. (10) When you distinguish each of the 10 chromosomes of the supernumerary B chromosome in maize, varied pieces, you uncovered modulations maize, which they identified by targeting and identified DNA repeats specifictothe that were quite prevalent. On the other repeated nucleotide sequences on each chro- centromere (9). This discovery inspired work hand, varying the whole genome gave much mosome (15). Birchler explains that this that eventually led to the construction of less of a change.” technique, called chromosome painting, plant artificial chromosomes, which can help Birchler’s Inaugural Article further expli- “produced an explosion of research in our combine beneficial genetic properties onto a cates the gene balance hypothesis (11). To- lab and helped us localize individual genes single chromosome that is independent from gether with Reiner Veitia, a human geneticist in maize and study, among other things, the the rest of the genome. at Institut Jacques Monod and Université distribution and behavior of transposons.” In 1991, the University of Missouri re- Paris Diderot in Paris, he synthesized lines Using this technique, former postdoctoral cruited Birchler to their flagship Columbia of evidence from distinct areas of biology fellow Fangpu Han, now at the Chinese campus. “Missouri has a distinguished history like cancer genetics and evolutionary geno- Academy of Sciences in Beijing, observed of plant geneticists, with Barbara McClintock, mics to suggest that the stoichiometry of that some chromosomes had more than one Ernest Sears, and Lewis Stadler, among macromolecular complexes in a cell is of centromere, the part of the chromosome others, who had worked there in the past.” crucial importance for not only how they involved in movement during cell division, Birchler’s laboratory at the University of although only one was active at a time (16). function but also for their own assembly. fi Missouri has a comprehensive space for plant “We go back to the early days of genetics Chromatin modi cations rather than se- genetics, including a greenhouse within to show that the balance among components quence, it turned out, regulated which of walking distance and maize transformation of these complexes has an impact on gene these centromeres actually functioned. The researchers found that they could direct and corn storage facilities. “We can store expression and even for some features of ’ inactivation using another genetic trick, basically every corn kernel that we ve pro- evolution. For example, the vast majority ” “centromere tug-of-war.” By studying the duced, going back a decade, he reports. of eukaryotic organisms had evolutionary inactivated centromeres, his group also un- Finding Balance cycles in which their whole set of chromo- fi — covered the rst cases of centromere reac- While at Missouri, Birchler began uncovering somes doubled they became tetraploid tivation (17). nature’s careful balance among regulatory from diploid. Then, over time, deletions oc- The fact that centromeres can turn on and genes. “The idea that we’dbeenpercolating curred to bring the genome back to near off, Birchler says, provides insight into how all along was that the stoichiometry of reg- diploid levels. We postulated that, in the chromosomal evolution proceeds. “Cen- ulatory genes modulates the expression of process, macromolecular complexes that con- tromeres evolve very rapidly. We know others,” he says. In Drosophila,heandhis tain transcription factor and signal trans- from the order of genes along chromosomes colleagues found 47 different dosage-sensitive duction components proceeded to diploidy that, as evolution proceeds, chromosomes modifiers of the white eye color gene and much more slowly.” Birchler and Veitia are become scrambled; the placement of the identified the molecular basis for many currently studying this gene balance idea on centromere is different in chromosomes

2688 | www.pnas.org/cgi/doi/10.1073/pnas.1221539110 Ahmed Downloaded by guest on September 27, 2021 PROFILE even of related species.” His group continues painting. The telomeres truncated the chro- 9 Alfenito MR, Birchler JA (1993) Molecular characterization of a maize B chromosome centric sequence. Genetics 135(2): to study the molecular basis for the centro- mosomes until nothing remained except for 589–597. mere reactivation process. the active centromere. At the same time, 10 Guo M, Birchler JA (1994) Trans-acting dosage effects on the they added new genes unaffected by the expression of model gene systems in maize aneuploids. Science Creating Chromosomes 266(5193):1999–2002. Birchler then took the next step in maize truncation. Because these chromosomes con- 11 Birchler JA, Veitia RA (2012) Inaugural Article: Gene balance tained maize-specific centromeres, they hypothesis: Connecting issues of dosage sensitivity across biological genetics: creating engineered minichromo- disciplines. Proc Natl Acad Sci USA 109(37):14746–14753. somes, small chromosomes that possess propagated easily and were not lost, even 12 Pal-Bhadra M, Bhadra U, Birchler JA (1997) Cosuppression additional foreign genes. In an effort led by after generations (19). in Drosophila: Gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent. Cell 90(3): former postdoctoral fellow Weichang Yu, This technique, Birchler notes, has pro- 479–490. his group first introduced the specialized se- found implications for our 21st century food 13 Pal-Bhadra M, Bhadra U, Birchler JA (2002) RNAi related quences at the ends of chromosomes called and energy issues. “Our synthetic chromo- mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol Cell 9(2):315–327. telomeres adjacent to the centromeres of somes offer a platform for stably adding new 14 Pal-Bhadra M, et al. (2004) Heterochromatic silencing and HP1 supernumerary chromosomes (18). They properties to plants. That’s the potential of localization in Drosophila are dependent on the RNAi machinery. verified the placement with chromosome what this can do.” Science 303(5658):669–672. 15 Kato A, Lamb JC, Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 101(37): 1 The World Bank (2012) Developing World Lags on Global Targets 5 Birchler JA, Newton KJ (1981) Modulation of protein levels in 13554–13559. chromosomal dosage series of maize: The biochemical basis of Related to Food and Nutrition, Says IMF-World Bank Report. 16 Han F, Lamb JC, Birchler JA (2006) High frequency of centromere aneuploid syndromes. Genetics 99(2):247–266. Available at http://go.worldbank.org/G9H4D17AT0. Accessed inactivation resulting in stable dicentric chromosomes of maize. Proc 6 Birchler JA, Hiebert JC, Paigen K (1990) Analysis of autosomal December 26, 2012. Natl Acad Sci USA 103(9):3238–3243. 2 dosage compensation involving the alcohol dehydrogenase locus in The World Bank (2012) Food Prices Rise Again on Higher Oil Prices 17 Han F, Gao Z, Birchler JA (2009) Reactivation of an inactive Drosophila melanogaster. Genetics 124(3):679–686. and Adverse Weather. Available at http://go.worldbank.org/ 7 Rabinow L, Nguyen-Huynh AT, Birchler JA (1991) A trans- centromere reveals epigenetic and structural components for 77PBFP3FU0. Accessed December 26, 2012. fi – acting regulatory gene that inversely affects the expression of the centromere speci cation in maize. Plant Cell 21(7):1929 1939. 3 Birchler JA (1979) A study of enzyme activities in a dosage series of 18 white, brown and scarlet loci in Drosophila. Genetics 129(2): Yu W, Lamb JC, Han F, Birchler JA (2006) Telomere-mediated the long arm of chromosome one in maize. Genetics 92(4): 463–480. chromosomal truncation in maize. Proc Natl Acad Sci USA 103(46): – 1211 1229. 8 Birchler JA, Bhadra U, Bhadra MP, Auger DL (2001) Dosage- 17331–17336. 4 Birchler JA (1981) The genetic basis of dosage compensation dependent gene regulation in multicellular eukaryotes: Implications 19 Yu W, Han F, Gao Z, Vega JM, Birchler JA (2007) Construction of alcohol dehydrogenase-1 in maize. Genetics 97(3-4): for dosage compensation, aneuploid syndromes, and quantitative and behavior of engineered minichromosomes in maize. Proc Natl 625–637. traits. Dev Biol 234(2):275–288. Acad Sci USA 104(21):8924–8929.

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