John Calarco
Associate Professor
Campus
St. George (downtown)
CSB Appointment
Full
Research Areas
Animal Biology, Bioinformatics / Computational Biology, Developmental Biology, Genetics / Genomics, Molecular Biology, Neurobiology, Systems Biology
Education
Ph.D. University of Toronto, 2011
B.Sc. University of Toronto, 2005
Titles and Honors
Medicine by Design Investigator
Canada Research Chair (Tier II) in Neuronal RNA Biology
Primary Undergraduate Department
Cell & Systems Biology
Graduate Programs
Cell & Systems Biology
Research Description
A major goal of our lab is to better understand the role of post-transcriptional gene regulation in the development, differentiation, and function of the nervous system. The nervous system provides an attractive model to study the mechanism and role of cell-type specific gene regulation because it is composed of diverse neuronal cells that require customized regulatory programs to achieve specialized functions. One research area in my group will focus on understanding the mechanisms and function of alternative splicing in the developing and mature nervous system using both mammalian stem cells and C. elegans. Through the process of alternative splicing, multiple messenger RNAs can be generated from single precursor transcripts. The evolution of alternative splicing has greatly contributed to the diversification of metazoan transcriptomes, and in some species can generate up to an order of magnitude greater number of transcript isoforms than the corresponding repertoire of protein-coding genes. We pursue these problems using a combination of biochemistry, cell biology, molecular genetics, and genome-wide analyses. Additionally, several ongoing projects are directing our research towards investigating the role of other layers of co- and post-transcriptional gene regulation in nervous system development and function.
Contact Information
Office Phone: 416-978-5766
Office: RW 513A
Lab: RW 511
Lab Phone: 416-946-7785
Email
Mailing Address
Department of Cell & Systems Biology
University of Toronto
25 Harbord St.
Toronto, ON M5S 3G5
Canada
Recent News
Publications
2024
High-Resolution Imaging and Morphological Phenotyping of through Stable Robotic Sample Rotation and Artificial Intelligence-Based 3-Dimensional Reconstruction.
Pan P, Zhang P, Premachandran S, Peng R, Wang S, Fan Q, Sun Y, Calarco JA, Liu X
2024, Research (Washington, D.C.), 7, 0513, 39479356
Robotic microinjection enables large-scale transgenic studies of Caenorhabditis elegans.
Pan P, Zoberman M, Zhang P, Premachandran S, Bhatnagar S, Pilaka-Akella PP, Sun W, Li C, Martin C, Xu P, Zhang Z, Li R, Hung W, Tang H, MacGillivray K, Yu B, Zuo R, Pe K, Qin Z, Wang S, Li A, Derry WB, Zhen M, Saltzman AL, Calarco JA, Liu X
2024, Nature communications, 15, 8848, 39397017
2023
Correction: A spiral microfluidic device for rapid sorting, trapping, and long-term live imaging of embryos.
Pan P, Qin Z, Sun W, Zhou Y, Wang S, Song P, Wang Y, Ru C, Wang X, Calarco J, Liu X
2023, Microsystems & nanoengineering, 9, 147, 38025885
Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity.
Harris N, Bates SG, Zhuang Z, Bernstein M, Stonemetz JM, Hill TJ, Yu YV, Calarco JA, Sengupta P
2023, Current biology : CB, 33, 1487-1501.e7, 36977417
2022
Approaches for CRISPR/Cas9 Genome Editing in C. elegans.
Martin CJ, Calarco JA
2022, Methods in molecular biology (Clifton, N.J.), 2468, 215-237, 35320567
Two-Color Fluorescent Reporters for Analysis of Alternative Splicing
Calarco JA, Pilaka-Akella PP
2022, Methods Mol Biol, 10.1007/978-1-0716-2521-7_13
Forgetting generates a novel state that is reactivatable
Liu H, Wu T, Canales XG, Wu M, Choi M, Duan F, Calarco JA, Zhang Y
2022, Science Advances, 10.1126/sciadv.abi9071
2021
A Genetic Interaction Screening Approach in C. elegans
Calarco JA
2021, Methods Mol Biol, 10.1007/978-1-0716-1740-3_4
The transcriptional landscape of Shh medulloblastoma
Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim S, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng H, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui C, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD
2021, Nature Communications, 10.1038/s41467-021-21883-0
2020
Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
Koterniak B, Pilaka PP, Gracida X, Schneider L, Pritišanac I, Zhang Y, Calarco JA
2020, Genome Research, 10.1101/gr.267328.120
2019
Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors
Thompson M, Bixby R, Dalton R, Vandenburg A, Calarco JA, Norris AD
2019, eLife, 10.7554/eLife.46726
Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma
Suzuki H, Kumar SA, Shuai S, Diaz-Navarro A, Gutierrez-Fernandez A, De Antonellis P, Cavalli FMG, Juraschka K, Farooq H, Shibahara I, Vladoiu MC, Zhang J, Abeysundara N, Przelicki D, Skowron P, Gauer N, Luu B, Daniels C, Wu X, Forget A, Momin A, Wang J, Dong W, Kim S, Grajkowska WA, Jouvet A, Fèvre-Montange M, Garrè ML, Nageswara Rao AA, Giannini C, Kros JM, French PJ, Jabado N, Ng H, Poon WS, Eberhart CG, Pollack IF, Olson JM, Weiss WA, Kumabe T, López-Aguilar E, Lach B, Massimino M, Van Meir EG, Rubin JB, Vibhakar R, Chambless LB, Kijima N, Klekner A, Bognár L, Chan JA, Faria CC, Ragoussis J, Pfister SM, Goldenberg A, Wechsler-Reya RJ, Bailey SD, Garzia L, Morrissy AS, Marra MA, Huang X, Malkin D, Ayrault O, Ramaswamy V, Puente XS, Calarco JA, Stein L, Taylor MD
2019, Nature, 10.1038/s41586-019-1650-0
2018
Synthetic Genetic Interaction (CRISPR-SGI) Profiling in Caenorhabditis elegans.
Calarco JA, Norris AD
2018, Bio-protocol, 8, 29552597
The UBR-1 ubiquitin ligase regulates glutamate metabolism to generate coordinated motor pattern in Caenorhabditis elegans
Copenhaver GP, Chitturi J, Hung W, Rahman AMA, Wu M, Lim MA, Calarco J, Baran R, Huang X, Dennis JW, Zhen M
2018, PLOS Genetics, 10.1371/journal.pgen.1007303
Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons
Gonatopoulos-Pournatzis T, Wu M, Braunschweig U, Roth J, Han H, Best AJ, Raj B, Aregger M, O’Hanlon D, Ellis JD, Calarco JA, Moffat J, Gingras A, Blencowe BJ
2018, Molecular Cell, 10.1016/j.molcel.2018.10.008
Imaging whole nervous systems: insights into behavior from worms to fish
Calarco JA, Samuel ADT
2018, Nature Methods, 10.1038/s41592-018-0276-8
2017
An Elongin-Cullin-SOCS Box Complex Regulates Stress-Induced Serotonergic Neuromodulation.
Gracida X, Dion MF, Harris G, Zhang Y, Calarco JA
2017, Cell reports, 21, 3089-3101, 29241538
CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness.
Norris AD, Gracida X, Calarco JA
2017, eLife, 6, 28718764
Cell type-specific transcriptome profiling in C. elegans using the Translating Ribosome Affinity Purification technique.
Gracida X, Calarco JA
2017, Methods (San Diego, Calif.), 126, 130-137, 28648677
Serotonin-dependent kinetics of feeding bursts underlie a graded response to food availability in C. elegans.
Lee KS, Iwanir S, Kopito RB, Scholz M, Calarco JA, Biron D, Levine E
2017, Nature communications, 8, 14221, 28145493
2016
Neuroendocrine modulation sustains the forward motor state.
Lim MA, Chitturi J, Laskova V, Meng J, Findeis D, Wiekenberg A, Mulcahy B, Luo L, Li Y, Lu Y, Hung W, Qu Y, Ho CY, Holmyard D, Ji N, McWhirter R, Samuel AD, Miller DM, Schnabel R, Calarco JA, Zhen M
2016, eLife, 5, 27855782
Regulation of Tissue-Specific Alternative Splicing: C. elegans as a Model System.
Gracida X, Norris AD, Calarco JA
2016, Advances in experimental medicine and biology, 907, 229-61, 27256389
2015
Efficient Genome Editing in Caenorhabditis elegans with a Toolkit of Dual-Marker Selection Cassettes.
Norris AD, Kim HM, Colaiácovo MP, Calarco JA
2015, Genetics, 201, 449-58, 26232410
Creating Genome Modifications in C. elegans Using the CRISPR/Cas9 System.
Calarco JA, Friedland AE
2015, Methods in molecular biology (Clifton, N.J.), 1327, 59-74, 26423968
2014
EOL-1, the homolog of the mammalian Dom3Z, regulates olfactory learning in C. elegans.
Shen Y, Zhang J, Calarco JA, Zhang Y
2014, The Journal of neuroscience : the official journal of the Society for Neuroscience, 34, 13364-70, 25274815
A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types.
Norris AD, Gao S, Norris ML, Ray D, Ramani AK, Fraser AG, Morris Q, Hughes TR, Zhen M, Calarco JA
2014, Molecular cell, 54, 946-59, 24910101
2013
Heritable genome editing in C. elegans via a CRISPR-Cas9 system.
Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA
2013, Nature methods, 10, 741-3, 23817069
Heritable Custom Genomic Modifications in Caenorhabditis elegans via a CRISPR–Cas9 System
Tzur YB, Friedland AE, Nadarajan S, Church GM, Calarco JA, Colaiácovo MP
2013, Genetics, doi:10.1534/genetics.113.156075