Khmelinskii Lab
Research Publications Group Members Biography2024
Gameiro E, Juárez-Núñez KA, Fung JJ, Shankar S, Luke B and Khmelinskii A (2024) Genome-wide conditional degron libraries for functional genomics. bioRxiv , doi: https://doi.org/10.1101/2024.05.29.596381 Link
2023
Kong KYE, Reinbold C, Knop M and Khmelinskii A (2023) Building yeast libraries to dissect terminal degrons with fluorescent timers. Methods Enzymol , 686:297–319 Link
Kong KYE*, Shankar S*, Rühle F and Khmelinskii A (2023) Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun , 14:8363 (*indicates joint contribution) Link
Reinbold C, Kong KYE, Kats I, Khmelinskii A and Knop M (2023) Multiplexed protein stability (MPS) profiling of terminal degrons using fluorescent timer libraries in Saccharomyces cerevisiae. Methods Enzymol , 686:321–344 Link
Sanchez N, de Leon N, Valle R, Fung JJ, Khmelinskii A and Roncero C (2023) Multiple quality control mechanisms monitor yeast chitin synthase folding in the endoplasmic reticulum. Mol Biol Cell , 34:mbc.E23-05-0186 Link
Schindler N*, Tonn M*, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A and Luke B (2023) Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun , 14:1227 (* indicates joint contribution) Link
2022
Caydasi AK, Khmelinskii A, Darieva Z, Kurtulmus B, Knop M and Pereira G (2022) SWR1 chromatin remodeling complex prevents mitotic slippage during spindle position checkpoint arrest. Mol Biol Cell , 34:ar11 Link
Fung JJ*, Blöcher-Juárez K* and Khmelinskii A (2022) High-throughput analysis of protein turnover with tandem fluorescent protein timers - the unfolded protein response: methods and protocols. Methods Mol Biol , 2378:85-100 (*indicates joint contribution) Link
2021
Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T and Knop M (2021) Up-regulation of ubiquitin–proteasome activity upon loss of NatA-dependent N-terminal acetylation. Life Sci Alliance , 5:e202000730 Link
Kong KYE, Coelho JPL, Feige MJ and Khmelinskii A (2021) Quality control of mislocalized and orphan proteins. Exp Cell Res , 403:112617 Link
Kong KYE*, Fischer B*, Meurer M*, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M# and Khmelinskii A# (2021) Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase Mol Cell , 81:2460-2476.e11 (*indicates joint contribution, #indicates joint correspondence) Link
2020
Ivanova E and Khmelinskii A (2020) (Photo)convert to pooled visual screening. Mol Syst Biol, 16:e9640 Link
Kuzmin E*, VanderSluis B*, Nguyen Ba AN, Wang W, Koch EN, Usaj M, Khmelinskii A, Usaj MM, van Leeuwen J, Kraus O, Tresenrider A, Pryszlak M, Hu MC, Varriano B, Costanzo M, Knop M, Moses A, Myers CL, Andrews BJ and Boone C (2020) Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science, 368:eaaz5667 (*indicates joint contribution) Link
Renz C, Albanèse V, Tröster V, Albert TK, Santt O, Jacobs SC, Khmelinskii A, Léon S and Ulrich HD (2020) Ubc13-Mms2 cooperates with a family of RING E3s in membrane protein sorting. J Cell Sci, 133:jcs244566 Link
2019
Caydasi AK, Khmelinskii A, Darieva Z, Kurtulmus B, Knop M and Pereira G (2019) SWR1 chromatin remodeling complex prevents mitotic slippage during spindle position checkpoint arrest. bioRxiv, 34:ar11 Link
Dederer V, Khmelinskii A, Huhn AG, Okreglak V, Knop M and Lemberg MK (2019) Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins. eLife, 8:e45506 Link
Renz C, Tröster V, Albert TK, Santt O, Jacobs SC, Khmelinskii A and Ulrich HD (2019) The ubiquitin-conjugating enzyme Ubc13-Mms2 cooperates with a family of FYVE-type-RING ubiquitin protein ligases in K63-polyubiquitylation at internal membranes. bioRxiv, 133:jcs244566 Link
2018
Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A and Knop M (2018) Mapping degradation signals and pathways in a eukaryotic N-terminome. Mol Cell, 70:488–501.e5 Link
Kowalski L, Bragoszewski P, Khmelinskii A, Glow E, Knop M and Chacinska A (2018) Determinants of the cytosolic turnover of mitochondrial intermembrane space proteins. BMC Biol, 16:66 Link
Meurer M, Duan Y, Sass E, Kats I, Herbst K, Buchmuller BC, Dederer V, Huber F, Kirrmaier D, Štefl M, Van Laer K, Dick TP, Lemberg MK, Khmelinskii A#, Levy ED# and Knop M# (2018) Genome-wide C-SWAT library for high-throughput yeast genome tagging. Nat Methods, 15:598–600 (#indicates joint correspondence) Link
2017
Bunina D, Štefl M, Huber F, Khmelinskii A, Meurer M, Barry JD, Kats I, Kirrmaier D, Huber W and Knop M (2017) Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities. Nucleic Acids Res, 45:11144–11158 Link
Caydasi AK, Khmelinskii A, Duenas-Sanchez R, Kurtulmus B, Knop M and Pereira G (2017) Temporal and compartment-specific signals coordinate mitotic exit with spindle position. Nat Commun, 8:14129 Link
2016
Huber F, Bunina D, Gupta I, Khmelinskii A, Meurer M, Theer P, Steinmetz LM and Knop M (2016) Protein abundance control by non-coding antisense transcription. Cell Rep, 15:2625–2636 Link
Khmelinskii A, Meurer M, Ho C-T, Besenbeck B, Fuller J, Lemberg MK, Bukau B, Mogk A and Knop M (2016) Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers. Mol Biol Cell, 27:360–370 Link
Yofe I#, Weill U, Meurer M, Chuartzman S#, Zalckvar E, Goldman O, Ben-Dor S, Schütze C, Wiedemann N, Knop M, Khmelinskii A# and Schuldiner M# (2016) One library to make them all: Streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat Methods, 13:371–378 (#indicates joint correspondence) Link
2014
Khmelinskii A*, Blaszczak E*, Pantazopoulou M, Fischer B, Omnus DJ, Le Dez G, Brossard A, Gunnarsson A, Barry JD, Meurer M, Kirrmaier D, Boone C, Huber W, Rabut G, Ljungdahl PO and Knop M (2014) Protein quality control at the inner nuclear membrane. Nature, 516:410–413 (*indicates joint contribution) Link
Khmelinskii A and Knop M (2014) Analysis of protein dynamics with tandem fluorescent protein timers. Methods Mol Biol, 1174:195-210 Link
Kinkhabwala A, Khmelinskii A and Knop M (2014) Analytical model for macromolecular partitioning during yeast cell division. BMC Biophys, 7:10 Link
Meitinger F, Khmelinskii A, Morlot S, Kurtulmus B, Palani S, Andres-Pons A, Hub B, Knop M, Charvin G and Pereira G (2014) A memory system of negative polarity cues prevents replicative aging. Cell, 159:1056–1069 Link
2013
Donà E, Barry JD, Valentin G, Quirin C, Khmelinskii A, Kunze A, Durdu S, Newton LR, Fernandez-Minan A, Huber W, Knop M and Gilmour D (2013) Directional tissue migration through a self-generated chemokine gradient. Nature, 503:285–289 Link
2012
Khmelinskii A*, Keller PJ*, Bartosik A, Meurer M, Barry JD, Mardin BR, Kaufmann A, Trautmann S, Wachsmuth M, Pereira G, Huber W, Schiebel E and Knop M (2012) Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Nat Biotechnol, 30:708–714 (*indicates joint contribution) Link
2011
Khmelinskii A*, Meurer M*, Duishoev N, Delhomme N and Knop M (2011) Seamless gene tagging by endonuclease-driven homologous recombination. PLoS One, 6:e23794 (*indicates joint contribution) Link
Khmelinskii A, Meurer M, Knop M and Schiebel E (2011) Artificial tethering to nuclear pores promotes partitioning of extrachromosomal DNA during yeast asymmetric cell division. Curr Biol, 21:R17–R18 Link
2010
Khmelinskii A, Keller PJ, Lorenz H, Schiebel E and Knop M (2010) Segregation of yeast nuclear pores. Nature, 466:E1 Link
Roostalu J#, Schiebel E and Khmelinskii A# (2010) Cell cycle control of spindle elongation. Cell Cycle, 9:1084–1090 (#indicates joint correspondence) Link
2009
Khmelinskii A, Roostalu J, Roque H, Antony C and Schiebel E (2009) Phosphorylation-dependent protein interactions at the spindle midzone mediate cell cycle regulation of spindle elongation. Dev Cell, 17:244–256 Link
Khmelinskii A and Schiebel E (2009) Chromosome segregation: Monopolin goes spindle. Curr Biol, 19:R482–R484 Link
2008
Khmelinskii A and Schiebel E (2008) Assembling the spindle midzone in the right place at the right time. Cell Cycle, 7:283–286 Link
2007
Khmelinskii A*, Lawrence C*, Roostalu J and Schiebel E (2007) Cdc14-regulated midzone assembly controls anaphase B. J Cell Biol, 177:981–993 (*indicates joint contribution) Link