PROFILE PROFILE Profile of Dinshaw J. Patel

Tinsley H. Davis Science Writer

Small-noncoding RNA molecules are the “It was clear to me that the excitement in re- dark matter of . From small search had shifted to the life sciences,” he says. interfering (si) that silence invading Switching fields, Patel performed his first pathogens to microRNAs that fine-tune postdoctoral training with biochemist Robert expression, noncoding RNAs carry out a vast Chambers at New York University School of number of functions within the cell. “It was Medicine, studying transfer RNA molecules. generally believed in the early days of molec- Meanwhile, a former colleague from Caltech, ular biology that RNA was just a passive Angelo Lamola, had moved to AT&T Bell Dinshaw J. Patel. Image courtesy of Memorial intermediate on the pathway from DNA to Laboratories (Bell Labs) in Murray Hill, New Sloan Kettering Cancer Center. protein, but noncoding RNA architecture Jerseyand,in1968,invitedPateltojoinhis and its interactions with partners is much biophysics group as a postdoc. Patel recalls more intricate and interesting,” says struc- that Lamola and the set-up at Bell Labs, with academic jobs, eventually taking a position at tural biologist Dinshaw J. Patel. Elected to only one scientist and one technician per Columbia University Medical School in 1984 the National Academy of Sciences in 2009, laboratory, provided independence and fos- as a Professor in the Biochemistry and Mo- Patel has spent his career deciphering the tered creativity. Soon, Patel had published lecular Biophysics Department. “The envi- shapes of biomolecules and principles under- several single-author papers on isomeriza- ronment changed dramatically,” he recalls. lying molecular complex formation. In his tions in retinal, the chromophore that binds Patel now had responsibility for building a Inaugural Article, Patel, the Abby Rockefeller to rhodopsin in the eye (3). laboratory group, raising grant funds, and Mauzé Chair in Experimental Therapeutics at Two years later, Frank Bovey, head of Bell lecturing students. He began to study the the Memorial Sloan Kettering Cancer Center, Lab’s polymer chemistry division, offered structure of DNA duplexes containing helical explores how the PAZ-binding domain of Patel a permanent position. Patel began using errors, such as mismatches and bulges, and PIWI proteins forms a pocket capable of NMR to study the conformations of biolog- chemical modifications, as well as drug–DNA binding the 3′-ends of piRNAs, noncoding ically active peptides, heme proteins, and complexes that target the double helix. RNA molecules that help maintain the integ- transfer RNAs by monitoring stable ex- In 1992, Patel moved to his current aca- rity of germ-line DNA (1). changeable protons that served as unique demic home at the Memorial Sloan Kettering markers in spectral regions devoid of other Cancer Center, where he says, together with America Beckons “ resonances. NMR was in its infancy in those biochemist James Rothman, he developed the PatelwasborninMumbai,Indiain1942and days, so individuals were focused on de- grew up in the Zoroastrian community. His structural biology program. Patel notes that veloping simple approaches to monitor bio- themoveresultedinsizeablelong-termin- father was a civil engineer, and in an ed- polymer folds, interactions, and structural ucation-rich setting, Patel immersed him- stitutional resources to initiate challenging transitions,” he says, and notes that his “ self in the sciences. “Because India was a projects. SloanKetteringwasonanupward structural and hydrogen exchange studies trajectory under the visionary leadership of developing country, science was what we identified a dinucleotide repeat adopted by Paul Marks,” says Patel, noting that he did learned in textbooks, with minimal practical d(G-C) repeats (4), providing early insights ” n not realize then how special the scientific experience, Patel explains. Drawn to the into the topology of left-handed Z-DNA environment was, with the Rockefeller Uni- United States, at the age of 19 Patel enrolled identified eventually in the Alexander Rich versity and Weill Cornell Medical College just in graduate school at the California Institute group at MIT. By 1983, Patel had earned the of Technology (Caltech). In the laboratory of Bell Laboratories Distinguished Member of across the street. Jack Roberts, Patel got his first experience Technical Staff Award. “In some ways, it Patel explains that collaborations with the working with NMR spectroscopy, a tool to was sort of an awkward thing to be faculty, including mo- visualize molecular structure that would figure working in the life sciences at a telephone lecular and cell biologists Thomas Tuschl, “ prominently in his early career. The creativity companyandbeinghandsomelyrewarded DavidAllis,RobertRoeder,andPaulGreen- “ and intensity of the scientific environment at for it” Patel says, and refers to his 17 years at gard, have been key to his growth. Structural ” ” “ Caltech shaped his future scientific career, Bell Labs as a “transforming period,” gener- biology is powerful, he says, because it Patel says. ating “enthusiasm and hunger for curiosity- precisely defines the positions of atoms in ’ After receiving his Master sdegreein1963 driven discovery.” proteins, nucleic acids, and their complexes.” for research on ring opening rearrangements Importantly, structural insights can allow the in small ring cyclopropane compounds (2), Easing into Academia design of very specific, targeted mutations, Patel moved to New York University to work Eventually, as Bell Labs was breaking up, with photochemist David Schuster. Three Patel explains, “I could see the writing on the This is a Profile of a recently elected member of the National years later, after graduating with a doctorate in wall, especially for someone doing research Academy of Sciences to accompany the member’s Inaugural Article Chemistry, Patel found himself at a crossroads. in the life sciences.” He began to apply for on page 903 in issue 3 of volume 108.

www.pnas.org/cgi/doi/10.1073/pnas.1512793112 PNAS Early Edition | 1of3 Downloaded by guest on September 29, 2021 senses this,” explains Patel. An enzyme known as Dicer chops the invading RNA into short segments,termedsiRNA.Onestrandofthe siRNA, the guide strand, is used like a fishing lure and fed into a molecular complex that seeks out and degrades complementary viral messenger RNAs, preventing viral protein production. Patel focused his research on Dicer and another nuclease, Argonaute (Ago), which play key roles in RNA interference. In collaboration with molecular biologist Thomas Tuschl, Patel solved the structure of a binary prokaryotic Ago complex, which showed the trajectory of the bound guide strand anchored at both its ends and the accessibility of the appropriate segment for Crystal structures of Thermus thermophilus Argonaute (labeled and color-coded by domains) with recognition of the target RNA (10). He next bound 5′-phosphorylated guide DNA (in red) as a binary complex (A) and with target RNA (in solved structures of the ternary Ago com- blue) as a ternary complex in B. Reprinted with permission from Macmillan Publishers Ltd., ref. 5. plexes bound to RNA targets, revealing insights into how the target strand is ul- timately cleaved (11). Patel later studied allowing an understanding of how selective in his research program. He expanded the eukaryotic versions of Ago and Dicer perturbations affect biological function. his toolkit into X-ray crystallography to in budding yeast with biologist David Patel continued to explore his interest get higher-resolution and timely views of Bartel, finding that, unlike its prokaryotic in higher-order DNA architecture. DNA structures of molecular complexes, and counterparts, Dicer in budding yeast starts typically occurs in double-stranded—or he decided to study RNA, which can fold cleaving in the interior of the invading duplex—form. Patel investigated the NMR- in unique and surprising ways. Patel fo- RNA and works outward (12). based structures of DNA triplexes and cused his structural RNA research on ribo- Viruses counterattack degradation of their quadruplexes, identifying the role of base- switches, ribozymes, and RNA interference. RNAs by evolving protein suppressors that triplet- and tetrad-pairing alignments, as well Riboswitches are noncoding sections of target various steps of the RNA interference as strand directionality and turn motifs, in messenger RNAs that contain a sensing do- pathway. Patel established how the viral defining the structural scaffolds that multi- main that binds small ligands, such as me- suppressor p19 forms a homodimer and uses stranded DNA forms. The work also illumi- tabolites. Binding of a specific ligand changes a caliper-like mechanism to target siRNA nated the diversity of G-quadruplex folds the conformation of the RNA, allowing it to (13). Recounting this phase of his career, adopted by regions of guanine-rich DNA, function as an on-off switch for gene ex- Patel says, “There were several once-in-a- such as those found in oncogenic promoters pression related to the ligand’s concentration. decade moments linked to discoveries of and telomeres (6). Patel’s work on riboswitches defined a range novel folds and interaction principles in our During his first decade at Memorial Sloan of higher-order RNA architectures, ligand studies of RNA interference, where molec- 2+ Kettering, Patel also investigated how certain binding pockets, and the Mg ion-mediated ular details emerged in systems that were environmental carcinogens, called polycyclic intermolecular interactions that contribute to previously undecipherable black boxes.” aromatic hydrocarbons, damage DNA. To- ligand recognition specificity (8). Ribozymes gether with biologist Suse Broyde and are RNA modules that have catalytic activity, Codes to Live by chemist Nicholas Geacintov, Patel elucidated functioning like enzymes. Recently, Patel In 2005, Patel began to explore the field of theroleofchirality—or the carcinogen’s collaborated with chemist Ronald Micura epigenetic regulation, differences in DNA molecular handedness—on the alignment of to study small ribozymes that cleave nucleic expression that are not attributable to the the lesions in the DNA where the carcinogen acids. The work defined how formation of DNA sequence itself. DNA is wound tightly covalently bound. “Such studies that differ- higher-order RNA architecture results in site- around globular proteins called histones. The entiated between directionality-based groove specific cleavage of the nucleic acid’sphos- exposed tails of histones are modified in a and intercalation alignments of the carcino- phodiester backbone and identified which specific manner by enzymes that add or genwerethefirstinthisfield,” says Patel. parts of the twister ribozyme contribute to remove chemical groups. These histone The results helped explain why some lesions the stability of the RNA fold and which modifications form a set of instructions about “ were more accessible to repair machinery facilitate catalysis (9). Such coupling of when and how certain portions of DNA than others and why some introduced mu- structure, recognition, transitions, and cleav- become accessible, a process important in “ tations generated following damage bypass age chemistry have resulted in fundamental cellular development. Here you have an- were resistant to repair (7). Patel notes that mechanistic insights into gene regulation and other code controlled by enzymes that dy- this contribution to carcinogenesis research catalysis, thereby providing unique concepts namically, and site-specifically, write, read, ’ ” resulted in the Distinguished Alumni Award related to RNA s multifaceted functional and erase these marks, explains Patel. ” from New York University in 1997. roles, Patel says. Modification of histone tails contributes NoncodingRNAsalsoplayaroleinpro- to another level of the gene-expression code. RNA: More than Meets the Eye tecting the cell. “Double-stranded DNA or For example, histone H3, with three methyl AtthesametimeashismovetoMemorial RNA is not normally seen in the cytoplasm, groups added at lysine 4 (H3K4me3), is as- Sloan Kettering, Patel made two critical shifts and nature has a defense mechanism that sociated with start sites of transcription. Patel

2of3 | www.pnas.org/cgi/doi/10.1073/pnas.1512793112 Davis Downloaded by guest on September 29, 2021 PROFILE provide fundamental insights, similar to his contributions to the RNA interference field. Expanding Horizons Together with biochemist Rhoderick Brown, Patel also studied the molecular events of lipid acquisition and release by lipid transfer pro- teins. The structural data are consistent with a cleft-like conformational gating mechanism, whereby glycolipid chains sequentially enter and leave the molded-to-fit hydrophobic tunnel in the membrane-associated state during membrane vesicle biogenesis and trafficking (21). Patel continues to explore new areas. He is currently focusing on molecular mechanisms of innate immunity, collaborating with Tuschl, immunologist Winfred Barchet, and chemist Roger Jones to determine confor- mational changes in cGAS, a double-stranded DNA sensor in metazoans that activates adaptor protein STING to start the interferon Crystal structure of mammalian maintenance DNA methyltransferase DNMT1 (containing cascade. The structures showed that, when color-coded CXXC, BAH1, BAH2, and MTase domains) bound to a 19-mer CG-containing exposed to DNA, cGAS generates a pocket DNA in the presence of cofactor AdoHcy. Reproduced from ref. 14. in which ATP and GTP enter to make an unusual cyclic dinucleotide 2′,5′-containing remembers when Rockefeller biologist David work has identified principles underlying cGAMP that activates STING (22). Allis crossed the street to discuss elucidating how methylation in plants is controlled by a Patel remains grateful to all his mentors, the structural basis underlying H3K4me3 specific histone methylation mark through a who have influenced his thinking and recognition by the PHD finger domain of the self-reinforcing loop between a DNA-specific research directions. Indeed, Patel empha- “ largest subunit of the nucleosome-remodeling methyltransferase enzyme and a histone- sizes that science has been a very chal- factor. The resulting structure highlighted not specific lysine methyltransferase (18). The lenging and fulfilling career, with major only the capture of a methylated lysine side two are also identifying and characterizing advances championed by incredibly tal- chain in a molecular cage, but also explained the structure of proteins that mediate the ented and dedicated members of my group, the sequence specificity of the recognition (15). RNA-directed DNA methylation pathway in enhanced by timely collaborations, an open- “I was hooked on establishing the structural plants (19). Patel says that his “contributions ness to emerging opportunities, capitalizing basis underlying epigenetic regulation research to epigenetic regulation, which recently have on unexpected observations, generous in- following this meeting,” says Patel. been expanded to histone chaperones” (20) stitutional resources, and plenty of luck.” In collaboration with biochemist Michelle Barton and biologist Joan Massague, Patel undertook a series of structure-function stud- 1 Tian Y, Simanshu D, Ma JB, Patel DJ (2011) Structural basis for 12 Weinberg DE, Nakanishi K, Patel DJ, Bartel DP (2011) The inside- piRNA 2′-O-methylated 3′-end recognition by Piwi PAZ (Piwi/ out mechanism of Dicers from budding yeasts. Cell 146(2):262–276. ies that defined the principles underlying Argonaute/Zwille) domains. Proc Natl Acad Sci USA 108(3): 13 Ye K, Malinina L, Patel DJ (2003) Recognition of small interfering multivalent readout of epigenetic marks by 903–910. RNA by a viral suppressor of RNA silencing. Nature 426(6968):874–878. 14 linked reader modules (16). Patel also ex- 2 Patel DJ, Hamilton CL, Roberts JD (1965) Small ring compounds. Song J, Rechkoblit O, Bestor TH, Patel DJ (2011) Structure of DNMT1- XLIV. Interconversion of cyclopropylcarbinyl and allylcarbinyl grignard DNA complex reveals a role for autoinhibition in maintenance DNA Science – plored methylation of DNA during replica- reagents. J Am Chem Soc 87(22):5144–5148. methylation. 331(6020):1036 1040. 15 3 Patel DJ (1969) 220 MHz proton nuclear magnetic resonance Li H, et al. (2006) Molecular basis for site-specific read-out of tion and how the methylation pattern on the Nature spectra of retinals. Nature 221(5183):825–828. histone H3K4me3 by the BPTF PHD finger of NURF. parent strand is transferred to the new, – 4 Patel DJ, Canuel LL, Pohl FM (1979) “Alternating B-DNA” 442(7098):91 95. 16 Tsai W-W, et al. (2010) TRIM24 links a non-canonical histone daughter strand. His team solved the struc- conformation for the oligo(dG-dC) duplex in high-salt solution. Proc signature to breast cancer. Nature 468(7326):927–932. Natl Acad Sci USA 76(6):2508–2511. ture for human enzyme DNMT1 when it is 17 Song J, Teplova M, Ishibe-Murakami S, Patel DJ (2012) Structure- 5 Swarts DC, et al. (2014) The evolutionary journey of Argonaute bound to DNA and showed not only the based mechanistic insights into DNMT1-mediated maintenance DNA proteins. Nat Struct Mol Biol 21(9):745–753. methylation. Science 335(6069):709–712. mechanism by which it adds methyl resi- 6 Wang Y, Patel DJ (1993) Solution structure of the human telomeric 18 Du J, et al. (2012) Dual binding of chromomethylase domains to repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1(4):263–282. dues where needed but also the mechanism H3K9me2-containing nucleosomes directs DNA methylation in 7 Cosman M, et al. (1992) Solution conformation of the major plants. Cell 151(1):167–180. of auto-inhibition (17). As Patel explains, + anti adduct between the carcinogen ( )- -benzo[a]pyrene diol epoxide 19 Law JA, et al. (2013) Polymerase IV occupancy at RNA- this maintenance DNA methyltransferase Proc Natl Acad Sci USA – and DNA. 89(5):1914 1918. directed DNA methylation sites requires SHH1. Nature “ 8 has to put the methyl mark in the right Ren A, Rajashankar KR, Patel DJ (2012) Fluoride ion encapsulation 498(7454):385–389. + Nature place and avoid putting it in the wrong place by Mg2 ions and phosphates in a fluoride riboswitch. 20 Elsässer SJ, et al. (2012) DAXX envelops a histone H3.3-H4 dimer 486(7401):85–89. for H3.3-specific recognition. Nature 491(7425):560–565. ” 2+ through successive cell divisions. 9 Ren A, et al. (2014) In-line alignment and Mg coordination at the 21 Simanshu DK, et al. (2013) Non-vesicular trafficking by a Patel has also been working with Steven cleavage site of the env22 twister ribozyme. Nat Commun 5:5534. ceramide-1-phosphate transfer protein regulates eicosanoids. Nature Jacobsen to study how histone modification 10 Wang Y, et al. (2008) Structure of the guide-strand-containing 500(7463):463–467. argonaute silencing complex. Nature 456(7219):209–213. 22 Gao P, et al. (2013) Cyclic [G(2′,5′)pA(3′,5′)p] is the metazoan and DNA methylation work together to de- 11 Wang Y, et al. (2009) Nucleation, propagation and cleavage of second messenger produced by DNA-activated cyclic GMP- termine epigenetic regulation in plants. The target RNAs in Ago silencing complexes. Nature 461(7265):754–761. AMP synthase. Cell 153(5):1094–1107.

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