Rare Diseases: Models & Mechanisms Network

Profile

Varshney, Gaurav

Basic Information

First Name
Last Name
Organization
Department
Website http://varshneylab.omrf.org

Contact Information

Email gaurav-varshney@omrf.org
Phone 4052712185

About My Research

Zebrafish Research Focus

I am interested in leveraging the cutting-edge genomic technologies to solve the challenging problems in genetics/genomics on a large-scale. I spearheaded a large-scale mutagenesis project to generate thousands of mutants using random insertional mutagenesis. I generated more than 5000 mutants (~20,000 alleles), and transferred to the zebrafish stock center for the distribution to the community, the allele information was disseminated through a dedicated database and integrated into the ZFIN database. When targeted mutagenesis methods using CRISPR/Cas9 became available, it really radically changed my approach because now it was possible to perform targeted mutagenesis, and knockouts could be created at will. I developed a high-throughput workflow for targeted mutagenesis and targeted more than 500 genes thus far. This workflow is being used by several labs around the world, and has changed the way knockouts can be generated in zebrafish. Additionally, combining two mutagenesis approaches, we performed a large-scale genetic screen to identify genes involved in sensory hair cell regeneration and other tissues. We identified many novel regeneration specific genes and functionally validated in zebrafish. Currently, I am using zebrafish and high-throughput mutagenesis to model human diseases on a large scale.

Gene ID Symbol Name Tier
100034503 grhl2b grainyhead-like transcription factor 2b TIER1
325494 pars2 prolyl-tRNA synthetase 2, mitochondrial TIER3
561673 nars2 asparaginyl-tRNA synthetase 2, mitochondrial TIER3
108179007 LOC108179007 tryptophanyl-tRNA synthetase 1 TIER1
436639 tjp2b tight junction protein 2b (zona occludens 2) TIER1
100170827 vars2 valyl-tRNA synthetase 2, mitochondrial TIER1
445178 aarsd1 alanyl-tRNA synthetase domain containing 1 TIER3
492513 clic5a chloride intracellular channel 5a TIER1
751732 ears2 glutamyl-tRNA synthetase 2, mitochondrial TIER3
404725 gjb8 gap junction protein beta 8 TIER1
564819 loxhd1a lipoxygenase homology PLAT domains 1a TIER1
503521 pcdh15b protocadherin-related 15b TIER2
368628 tmprss3b transmembrane serine protease 3b TIER1
103911405 otog otogelin TIER1
571036 dalrd3 DALR anticodon binding domain containing 3 TIER3
566645 espnlb espin like b TIER1
560592 myo15aa myosin XVAa TIER1
562037 eprs1 glutamyl-prolyl-tRNA synthetase 1 TIER1
569778 lars1b leucyl-tRNA synthetase 1b TIER3
559616 cabp2b calcium binding protein 2b TIER1
368476 pcdh15a protocadherin-related 15a TIER1
571240 tmc2a transmembrane channel-like 2a TIER1
100001648 vma12 vacuolar ATPase assembly factor VMA12 TIER1
100003670 msrb1b methionine sulfoxide reductase B1b TIER1
563122 marveld2b MARVEL domain containing 2b TIER1
447904 ildr1b immunoglobulin-like domain containing receptor 1b TIER1
393410 gpsm2 G protein signaling modulator 2 TIER1
555187 cars2 cysteinyl-tRNA synthetase 2, mitochondrial TIER1
393822 slc22a4 solute carrier family 22 member 4 TIER1
564412 ush1c Usher syndrome 1C TIER1
337230 gars1 glycyl-tRNA synthetase 1 TIER1
792787 aars2 alanyl-tRNA synthetase 2, mitochondrial (putative) TIER1
100037331 coq2 coenzyme Q2 4-hydroxybenzoate polyprenyltransferase TIER1
415105 adgrv1 adhesion G protein-coupled receptor V1 TIER1
280647 kars1 lysyl-tRNA synthetase 1 TIER3
352916 msrb1a methionine sulfoxide reductase B1a TIER1
567237 tmc1 transmembrane channel-like 1 TIER1
449661 tars1 threonyl-tRNA synthetase 1 TIER1
572226 cabp2a calcium binding protein 2a TIER1
337070 rars1 arginyl-tRNA synthetase 1 TIER1
566876 wfs1a Wolfram syndrome 1a (wolframin) TIER1
557908 mettl13 methyltransferase 13, eEF1A lysine and N-terminal methyltransferase TIER1
503940 spen spen family transcriptional repressor TIER1
550380 gjb3 gap junction protein beta 3 TIER1
334393 iars1 isoleucyl-tRNA synthetase 1 TIER3
447847 hars histidyl-tRNA synthetase TIER1
795494 si:ch211-256m1.8 si:ch211-256m1.8 TIER3
449665 gpsm2l G protein signaling modulator 2, like TIER1
360209 pvalb9 parvalbumin 9 TIER1
406666 gab1 GRB2-associated binding protein 1 TIER1
100333596 hgfb hepatocyte growth factor b TIER1
553404 lrrc47 leucine rich repeat containing 47 TIER3
556580 wfs1b Wolfram syndrome 1b (wolframin) TIER1
793910 msraa methionine sulfoxide reductase Aa TIER1
570113 myo15ab myosin XVAb TIER1
327329 qrsl1 glutaminyl-tRNA amidotransferase subunit QRSL1 TIER3
405833 clic5b chloride intracellular channel 5b TIER1
503745 wars2 tryptophanyl tRNA synthetase 2, mitochondrial TIER3
114427 vars1 valyl-tRNA synthetase 1 TIER1
555569 otogl otogelin-like TIER1
368284 cars1 cysteinyl-tRNA synthetase 1 TIER1
566999 lhfpl5b LHFPL tetraspan subfamily member 5b TIER1
100331283 otofb otoferlin b TIER1
494168 six1a SIX homeobox 1a TIER1
393589 rars2 arginyl-tRNA synthetase 2, mitochondrial TIER3
558720 marveld2a MARVEL domain containing 2a TIER1
393745 wars1 tryptophanyl-tRNA synthetase 1 TIER3
558325 lhfpl5a LHFPL tetraspan subfamily member 5a TIER1
563962 slc26a3.1 solute carrier family 26 member 3 TIER1
394188 qars1 glutaminyl-tRNA synthetase 1 TIER1
100330276 tars3 threonyl-tRNA synthetase 3 TIER3
100536073 tbc1d24 TBC1 domain family, member 24 TIER1
556702 yars2 tyrosyl-tRNA synthetase 2, mitochondrial TIER3
565446 tjp2a tight junction protein 2a (zona occludens 2) TIER1
360208 pvalb8 parvalbumin 8 TIER1
555744 grhl2a grainyhead-like transcription factor 2a TIER1
541317 gatb glutamyl-tRNA(Gln) amidotransferase, subunit B TIER3
368235 yars1 tyrosyl-tRNA synthetase 1 TIER1
493608 farsb phenylalanyl-tRNA synthetase subunit beta TIER3
100536888 espnla espin like a TIER1
566565 mars2 methionyl-tRNA synthetase 2, mitochondrial TIER1
100126021 lars2 leucyl-tRNA synthetase 2, mitochondrial TIER1
393364 ildr1a immunoglobulin-like domain containing receptor 1a TIER1
445405 sars1 seryl-tRNA synthetase 1 TIER1
567061 espn espin TIER1
493781 hgfa hepatocyte growth factor a TIER1
394154 sars2 seryl-tRNA synthetase 2, mitochondrial TIER3
324940 aars1 alanyl-tRNA synthetase 1 TIER1
567304 tmc2b transmembrane channel-like 2b TIER1
557046 slc26a2 solute carrier family 26 member 2 TIER1
793097 fars2 phenylalanyl-tRNA synthetase 2, mitochondrial TIER1
571144 dars2 aspartyl-tRNA synthetase 2, mitochondrial TIER1
692329 farsa phenylalanyl-tRNA synthetase subunit alpha TIER3
100001219 iars2 isoleucyl-tRNA synthetase 2, mitochondrial TIER1
405857 msrb2 methionine sulfoxide reductase B2 TIER1
100000148 tmprss3a transmembrane serine protease 3a TIER1
558036 lmx1a LIM homeobox transcription factor 1, alpha TIER1
338183 mars1 methionyl-tRNA synthetase 1 TIER1
568332 nars1 asparaginyl-tRNA synthetase 1 TIER1
324025 dars1 aspartyl-tRNA synthetase 1 TIER1
557476 otofa otoferlin a TIER1
100150283 loxhd1b lipoxygenase homology PLAT domains 1b TIER1
Term Name Aspect Overlap Size
GO:0006418 tRNA aminoacylation for protein translation BP 21 40
GO:0004812 aminoacyl-tRNA ligase activity MF 21 40
GO:0043039 tRNA aminoacylation BP 21 44
GO:0016875 ligase activity, forming carbon-oxygen bonds MF 21 40

Publications

PubMed ID Title
27640875 DNA-guided genome editing using structure-guided endonucleases.
27425195 Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling sev...
27809318 A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis...
26049161 GeIST: a pipeline for mapping integrated DNA elements.
31236475 Altered Swimming Behaviors in Zebrafish Larvae Lacking Cannabinoid Receptor 2.
26906613 Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy?
30886848 Expanding the CRISPR Toolbox in Zebrafish for Studying Development and Disease.
28040780 Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Inj...
28369060 The Zic family homologue Odd-paired regulates Alk expression in Drosophila.
26818075 Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in...
26639914 Understanding and Editing the Zebrafish Genome.
26438539 CRISPRz: a database of zebrafish validated sgRNAs.
26253739 CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity.
29872546 Guided genetic screen to identify genes essential in the regeneration of hair cells and other tis...
28936359 Extracellular HSP60 triggers tissue regeneration and wound healing by regulating inflammation and...
26635538 A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy S...
26161877 Mutagenesis Screen Identifies agtpbp1 and eps15L1 as Essential for T lymphocyte Development in Ze...