Publications – Jovanoviclab

Publications:

2020

Aurora B-dependent Ndc80 degradation regulates kinetochore composition in meiosis

Jingxun Chen, Andrew Liao, Emily N. Powers, Hanna Liao, Lori A. Kohlstaedt, Rena Evans, Ryan M. Holly, Jenny Kim Kim, Marko Jovanovic, and Elçin Ünal. Genes & Development. 2020 December 12. doi: 10.1101/gad.333997.119

Proteome Turnover in the Spotlight: Approaches, Applications & Perspectives

Alison Barbara Ross, Julian David Langer, Marko Jovanovic. Molecular & Cellular Proteomics. 2020 November 30. doi:10.1074/mcp.R120.002190

Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome

Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov, Ekaterina Loginicheva, Sofia Porter, Denis A. Mogilenko, Erica Wolin, Patrick Collins, German Demidov , Mykyta Artomov , Konstantin Zaitsev, Sviatoslav Sidorov, Christina Camell, Monika Bambouskova, Laura Arthur, Amanda Swain , Alexandra Panteleeva, Aleksei Dievskii, Evgeny Kurbatsky, Petr Tsurinov, Roman Chernyatchik , Vishwa Deep Dixit, Marko Jovanovic, Sheila A. Stewart , Mark J. Daly, Sergey Dmitriev, Eugene M. Oltz and Maxim N. Artyomov . 2020 November 23. Nature Aging. doi: 10.1038/s43587-020-00002-6

Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast

Amy R Eisenberg, Andrea L Higdon, Ina Hollerer, Alexander P Fields, Irwin Jungreis, Paige D Diamond, Manolis Kellis, Marko Jovanovic, Gloria A Brar. Cell Systems. 2020 August 26. doi:10.1016/j.cels.2020.06.011

Ribosome Dimerization Protects the Small Subunit

Heather A Feaga, Mykhailo Kopylov, Jenny Kim Kim, Marko Jovanovic, Jonathan Dworkin. Journal of Bacteriology. 2020 April 27. doi: 10.1128/JB.00009-20

2019

Targeting Translation of mRNA as a Therapeutic Strategy in Cancer

Ipsita Pal, Maryam Safari, Marko Jovanovic, Susan E. Bates, Changchun Deng. Current Hematologic Malignancy Reports. 2019 June 24. doi: 10.1007/s11899-019-00530-y

Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus–Infected Cells and Liver to Identify Pathways Associated With Disease Development

Joachim Lupberger, Tom Croonenborghs, Armando Andres Roca Suarez, Nicolaas Van Renne, Frank Jühling, Marine A. Oudot, Alessia Virzì, Simonetta Bandiera, Carole Jamey, Gergö Meszaros, Daniel Brumaru, Atish Mukherji, Sarah C. Durand, Laura Heydmann, Eloi R. Verrier, Hussein El Saghire, Nourdine Hamdane, Ralf Bartenschlager, Shaunt Fereshetian, Evelyn Ramberger, Rileen Sinha, Mohsen Nabian, Celine Everaert, Marko Jovanovic, Philipp Mertins, Steven A. Carr, Kazuaki Chayama, Nassim Dali-Youcef, Romeo Ricci, Nabeel M. Bardeesy, Naoto Fujiwara, Olivier Gevaert, Mirjam B. Zeisel, Yujin Hoshida, Nathalie Pochet, and Thomas F. Baumert. Gastroenterology. 2019 August 1. doi: 10.1053/j.gastro.2019.04.003

Approaches for Studying Ribosome Specialization.

Emmott E, Jovanovic M, Slavov N. Trends Biochem Sci. 2019 Feb 18. pii: S0968-0004(19)30017-9.

Small and large ribosomal subunit deficiencies lead to distinct gene expression signatures that reflect cellular growth rate 

Cheng Z, Mugler CF, Keskin A, Hodapp S, Chan LY, Weis K, Mertins P, Regev A, Jovanovic M, Brar GA. Molecular Cell, 2019 Jan 3; 73(1):36-47.

2018

Precise Post-translational Tuning Occurs for Most Protein Complex Components during Meiosis

Eisenberg AR, Andrea Higdon A, Keskin A, Hodapp S, Jovanovic M, Brar GA. Cell Reports, 2018 Dec 26; 25(13): 3603-3617

Ribosome Stoichiometry: From Form to Function.  

Emmott E, Jovanovic M, Slavov N. Trends Biochem Sci. 2018 Nov 22. pii: S0968-0004(18)30219-6.

Global Proteome Remodeling during ER Stress Involves Hac1-Driven Expression of Long Undecoded Transcript Isoforms.

Van Dalfsen KM, Hodapp S, Keskin A, Otto GM, Berdan CA, Higdon A, Cheunkarndee T, Nomura DK, Jovanovic M, Brar GA. Dev Cell. 2018 Jul 16;46(2):219-235.e8. doi: 10.1016/j.devcel.2018.06.016.

Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus

Quinodoz SA, Ollikainen N, Tabak B, Palla Ali, Schmidt JM, Detmar E, Lai M, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Cell. 2018 Jun 4. pii:S0092-8674(18)30636-6.

Alternative 3' UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments.

Tushev G, Glock C, Heumüller M, Biever A, Jovanovic M, Schuman EM. Neuron. 2018 May 2;98(3):495-511.

Electrophilic properties of itaconate and derivatives regulate the IκBζ-ATF3 inflammatory axis.

Bambouskova M, Gorvel L, Lampropoulou V, Sergushichev A, Loginicheva E, Johnson K, Korenfeld D, Mathyer ME, Kim H, Huang LH, Duncan D, Bregman H, Keskin A, Santeford A, Apte RS, Sehgal R, Johnson B, Amarasinghe GK, Soares MP, Satoh T, Akira S, Hai T, de Guzman Strong C, Auclair K, Roddy TP, Biller SA, Jovanovic M, Klechevsky E, Stewart KM, Randolph GJ, Artyomov MN. Nature. 2018 Apr;556(7702):501-504.

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis.

Khajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, Jovanovic M, Ellis SR, Fulco CP, Engreitz JM, Schütz S, Lian J, Gripp KW, Weinberg OK, Pinkus GS, Gehrke L, Regev A, Lander ES, Gazda HT, Lee WY, Panse VG, Carr SA, Sankaran VG. Cell. 2018 Mar 22;173(1):90-103.e19.

Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis.

Cheng Z, Otto GM, Powers EN, Keskin A, Mertins P, Carr SA, Jovanovic M^#, Brar GA^# . Cell. 2018 Feb 22;172(5):910-923.e16. doi: 10.1016/j.cell.2018.01.035. (^#corresponding authors)

2015

Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic M*, Rooney M*, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez E, Fields A, Schwartz S, Raychowdhury R, Mumbach M, Eisenhaure T, Rabani M, Gennert D, Delorey T, Lu D, Weissman J, Carr SA, Hacohen N, Regev A. Science. 2015 Mar 6;347(6226):1259038. (*contributed equally)

A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation

Fields AP*, Rodriguez EH*, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, and Weissman JS. Molecular Cell, 2015 Dec 3;60(5):816-27. (*contributed equally)

A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks

Parnas O*, Jovanovic M*, Eisenhaure T*, Herbst R, Dixit A, Ye CJ, Przybylski D, Platt R, Tirosh I, Sanjana N, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A. Cell. 2015 Jul 30;162(3):675-86. (*contributed equally)

Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.

Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Götze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner M. Genome Research. 2015 Jul 31.

2014

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Hacohen N, Schier AF, Blackshear PJ, Friedman N, Amit I, Regev A. Cell, 2014 Dec 18;159(7):1698-710. pdf (read here)

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling.

Platt RJ*, Chen S*, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F. Cell. 2014 Oct 9;159(2):440-55. (*contributed equally)

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA.  

Schwartz S*, Bernstein DA*, Mumbach MR*, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. Cell. 2014 Sep 25;159(1):148-62. (*contributed equally)

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5' Sites.

Schwartz S*, Mumbach MR*, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. Cell Reports. 2014 Jul 10;8(1): 284-96. (*contributed equally)

2013

High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.

Schwartz S*, Agarwala SD*, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A. Cell. 2013 Dec 5;155(6):1409-21. (*contributed equally)

2012

RIP‑chip‑SRM - a New Combinatorial Large‑Scale Approach Identifies a Set of Translationally Regulated bantam/miR‑58 Targets in C. elegans

Jovanovic M, Reiter L*, Clark A*, Weiss M, Picotti P, Rehrauer H, Frei A, Neukomm L, Kaufman E, Wollscheid B, Simard M, Miska M, Aebersold R, Gerber A, Hengartner MO. Genome Research. 2012 Jul;22(7):1360-71. (*contributed equally)