PRE-PRINT PUBLICATIONS

 

2021                        Cevik S, Alabdi L, Pneg X, Beyer T, ZOrluer A, Pir MS, Yenisert F, Shaheen R, Woerz F, HoffamannF, Altunkaynak B, Pir B, Boldt K, Karaman A, Cakiroglu M, Oner SS, Cao Y, Ueffing M, Alkuraya FS, Kaplan OI, WDR31 is a novel ciliopathy protein displaying functional redundancy with GTPase-activating proteins ELMOD and RP2 in recruiting BBSome to cilium; bioRxiv 2021.06.10.445528; doi: https://doi.org/10.1101/2021.06.10.445528

 

PEER-REVIEWED PUBLICATIONS FROM THE LAB

 

2021                        MS Pir, HI Bilgin, A Sayici, F Coskun, FM Torun, P Zhao, Y Kang, S Cevik, Kaplan OI, ConVarT: a search engine for matching human genetic variants with variants from non-human species, Nucleic Acids Res (Accepted) Deposited to bioRxiv 2021.01.07.424951; doi: https://doi.org/10.1101/2021.01.07.424951

 

 2021                       Torun MF, Bilgin, Kaplan OI, MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations, Bioinformatics Advances (Accepted). Deposited to bioRxiv 2021.04.05.426321; doi: https://doi.org/10.1101/2021.04.05.426321

2021                        Cevik, Kaplan OI, The Joubert syndrome protein CEP41 is excluded from the distal segment of cilia in C. elegans, microPublication Biology, https://doi.org/10.17912/micropub.biology.000406

 

2021                        Cevik S, Kaplan OI, Subcellular localization of the voltage-gated K+ channel EGL-36, a member of the KV3 subfamily, in the ciliated sensory neurons in C. elegans, microPublication Biology. 10.17912/micropub.biology.000367 .

 

 

PEER-REVIEWED PUBLICATIONS

2018                        Kimura Y, Tsutsumi K, Konno A, Ikegami K, Hameed S, Kaneko T, Kaplan OI, Teramoto T, Fujiwara M, Ishihara T, Blacque OE,&Setou M, Environmental responsiveness of tubulin glutamylation in sensory cilia is regulated by the p38 MAPK pathway, Scientific Reports.

 

2016                        Kaplan OI, Berber B, Hekim N & Doluca O G-quadruplex prediction in E. coli genome reveals a conserved putative-quadruplex-Hairpin-Duplex switch, Nucleic Acids Res. 2016 Sep 4. pii: gkw769

2013                        Cevik S, Sanders AA, Van Wij E,  Boldt K, , Clarke L, van Reeuwijk J, Hori Y, Horn N, Hetterschijt N, Wdowicz A, Mullins A, Kida K, Kaplan OI, C. van Beersum SE, Man Wu K, Letteboer SFJ, Mans DA, Katada T, Kontani K, Ueffing M, Roepman R, Kremer H & Blacque OE, Active transport and diffusion barriers restrict Joubert Syndrome-associated ARL13B/ARL-13 to an Inv-like ciliary membrane subdomain, Plos Genetics; 9(12): e1003977. doi:10.1371/journal.pgen.1003977

 

2012                        Kaplan OI*, Doroques D*, Cevik S, Bowie RV, Clarke L, Sanders AA, Kida K Sengupta P&Blacque OE, Endocytosis facilitates proteins and membrane transport to C. elegans sensory cilia, Current Biology; * Authors contributed equally , Volume 22, Issue 6, Pages 451–460

2010                        Kaplan OI , Molla-Herman A, Cevik S, Ghossoub R, Kida K, Kimura Y, Jenkins P, Martens JR,  Setou M, Benmerah A & Blacque OE,  AP-1 adaptor facilitates cilium formation and functions with RAB-8 in C. elegans ciliary membrane transport, Journal of Cell Science  ;123(Pt 22):3966-77.

2010                        Kimura Y, Ikegami K, Kurabe N, Tsutsumi K,  Konishi Y, Kaplan OI, Kunitomo H, Iino Y, Blacque OE and Setou M, Bidirectional tubulin modification by glutamylase TTLL-4 and deglutamylase CPH-1 in sensory cilia,  Journal of Biological Chemistry; Jul 23;285(30):22936-41

 

2010                        Cevik S, Hori Y, Kaplan OI,  Kida K,  Toivenon T, Cottell D, Katada T,  Kontani K& Blacque OE, Joubert Syndrome Arl13b functions at ciliary membranes and stabilizes protein transport in C. Elegans,  Journal of Cell Biology, ;188(6):953-69.

2008                        Blacque OE., Cevik S, Kaplan OI, Intraflagellar transport: from molecular characterisation to mechanism, Frontiers in Bioscience, 13:2633-52.

Uncovering Roles of Ciliopathy Associated Genes

Our lab is interested in ciliopathy, over 30 of different human diseases resulting from functional and/or structural defects in cilia. To date, mutations in over 100 different genes have been identified to cause ciliopathy diseases. When any of these 100 genes, which encode proteins localized to cilia, basal body and/or transition zone, is mutated, the structural and/or functional abnormalities in cilia occur, thus leading to a range of symptoms observed in ciliopathy. Joubert syndrome (JS [MIM 213300]) is a ciliopathy disorder with an occurrence of approximately 1/100 000 live births. Our previous work has revealed that Joubert syndrome associated ARL13b is enriched in the proximal cilia, where ARL13b regulates intraflagellar transport (IFT) and ciliary membrane trafficking. We are currently studying disease associated genes in C. elegans.

Systems Medicine for Ciliary Genes

Cilia are an antenna like organelle whose inner basic structure consists of a microtubule-based cytoskeleton namely the ciliary axoneme. Cilia extend from most of cell surfaces, where they act as sensor, perform motility function and regulate embryo development.We employ bioinformatic approaches to identify the unknown ciliary genes that build cilia and transition zone. We use C. elegans. as the primary model organism to confirm the expression and localization of candidate ciliary genes in the ciliated sensory neurons (Figure 1, localization of one candidate gene is shown).

Figure 1: Shown are fluorescence images for transgenic worms expressing GFP labelled ciliary candidate gene . GFP tagged ciliary candidate gene is exclusively expressed in the ciliated sensory neurons , where it was found to localize to the cilium.