Georgi


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Georgi Marinov

Post-Doctoral Researcher

marinovg(at)iu.edu

(812) 856-0115

Background

Ph.D. 2014 Biology, California Institute of Technology
B.S. 2008 Biology, Massachusetts Institute of Technology

Research

My research interests are focused on the evolution of gene regulatory mechanisms and the use of functional genomics tools to understand it. In the last few years, the combination of technological advances in sequencing technology and the major advances in the experimental and analytical functional genomic toolkit, in particular originating from the ENCODE and modENCODE consortia, have made possible the genome-wide functional genomic characterization of the regulatory biology of any species.

On a general level, eukaryotes in the ciliate clade are of great interest from that perspective, due to the separation of somatic and germline genomes that is typical to the group, the dramatic reorganization of the genome that is associated with the transition between the two, and the unusual somatic genome organization that has evolved in some lineages within the group.

Within ciliates, the Paramecium aurelia species complex and other Paramecium species represent a unique system among all eukaryotes for understanding the mechanisms and driving forces of the evolution of gene regulation. The P. aurelia complex consists of at least fifteen morphologically identical but in fact deeply diverging (hundreds of millions of years ago) species, with genomes characterized by a large number of genes, the result of two rounds of whole genome duplication (WGD) preceding their divergence (the WGD events are not shared with other Paramecium species). All Paramecium somatic genomes have very short intergenic regions and introns, suggesting potentially simplified regulatory grammar compared to multicellular organisms, and all Paramecium species are characterized by very high estimated effective population sizes. All previous studies comparing the gene regulatory landscapes between different species have been limited to metazoans (flies and mammals), leaving open numerous questions about how and whether the patterns observed generalize to organisms with very different genomic and population genetic characteristics.

My project involves the mapping of transcription factor binding sites and regulatory states in the genomes of the different Paramecium species, using functional genomic techniques, and their comparison, which will allow these questions to be addressed.

Publications

1. ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9(4):e1001046.

2. Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold BJ, Willard HF, Myers RM. 2012. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res 22(5):860--869.

3. Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. 2012. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 13(8):418.

4. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57--74

5. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Roder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigo R, Gingeras TR. 2012. Landscape of transcription in human cells. Nature 489(7414):101--108.

6. Landt SG*, Marinov GK*, Kundaje A*, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, Desalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. 2012. ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia. Genome Res 22(9):1813--1831.

7. Raskatov JA, Nickols NG, Hargrove AE, Marinov GK, Wold B, Dervan PB. 2012. Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide. Proc Natl Acad Sci U S A 109(4):16041--16045.

8. Yang F, Nichols NG, Li BC, Marinov GK, Said JW, Dervan PB. 2013. Antitumor activity of a pyrrole-imidazole polyamide Proc Natl Acad Sci U S A 110(5):1863--1868.

9. Le Thomas A*, Rogers AK*, Webster A*, Marinov GK*, Liao SE, Perkins EM, Hur JK, Aravin AA, Fejes-Toth K. 2013. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev 27:390--399.

10. Wang YE, Marinov GK, Wold BJ, Chan DC. 2013. Genome-wide analysis reveals coating of the mitochondrial genome by TFAM. PLoS ONE 8(8):e74513.

11. Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison R, Myers RM, Wold B. 2013. Integrating and mining the chromatin landscape of cell-type specificity using Self-Organizing Maps. Genome Res 23:2136--2148.

12. Marinov GK*, Williams BA*, McCue K, Schroth GP, Gertz J, Myers RM, Wold BJ. 2014. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res 24:496--510.

13. Marinov GK, Kundaje A, Park PJ, Wold BJ. 2014. Large-scale quality analysis of published ChIP-seq data. G3 4(2):209--223.

14. Marinov GK*, Wang YE*, Chan DC, Wold BJ. 2014. Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors. PLoS ONE 9(1):e84713.

15. Kellis M*, Wold BJ*, Snyder MP*, Bernstein BE*, Kundaje A$\ddag$, Marinov GK$\ddag$, Ward LD$\ddag$, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski L, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. 2014. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A 111(17):6131--6138.

16. Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, Newberry K, DeSalvo G, Ou S, Myers RM, Vielmetter J, Wold BJ. 2014. Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies. Sci Rep 4:5152.

17. Le Thomas A*, Stuwe E*, Li S, Du J, Marinov GK, Rozhkov N, Chen YC, Luo Y, Sachidanandam R, Toth KF, Patel D, Aravin AA. 2014. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev 28:1667--1680.

18. Le Thomas A, Marinov GK, Aravin AA. 2014. A Transgenerational Process Defines piRNA Biogenesis in Drosophila virilis. Cell Rep 8:1617--1623.

19. The Mouse ENCODE Consortium. 2014. A comparative encyclopedia of DNA elements in the mouse genome. Nature 515(7527):355--364.

20. Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. 2014. Principles of regulatory information conservation between mouse and human. Nature 515(7527):371--375.

21. Abelin ACT, Marinov GK, Williams BA, McCue K, Wold BJ. 2014. A ratiometric-based measure of gene co-expression. BMC Bioinformatics 15:331.

22. Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams BA, Schroth GP, Elowitz MB, Wold BJ. 2015. Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming. Cell Stem Cell 16(1):88--101.

23. Marinov GK*, Wang J,*, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Fejes Toth K, Brennecke J. 2015. Pitfalls of mapping high throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. 32:765--771.

24. Smalley MD, Marinov GK, Bertani LE, DeSalvo G. 2015. Genome Sequence of Magnetospirillum magnetotacticum Strain MS-1. Genome Announc 3(2):e00233--15.

25. Mehta A, Zhao JL, Sinha N, Marinov GK, Mann M, Kowalczyk MS, Galimidi RP, Du X, Erikci E, Regev A, Chowdhury K, Baltimore D. 2015. The MicroRNA-132 and MicroRNA-212 Cluster Regulates Hematopoietic Stem Cell Maintenance and Survival with Age by Buffering FOXO3 Expression. Immunity 42(6):1021--1032

26. Manakov SA, Pezic D, Marinov GK, Pastor WA, Sachidanandam R, Aravin AA. 2015. MIWI2 and MILI Have Differential Effects on piRNA Biogenesis and DNA Methylation. Cell Rep 12(8):1234--1243.

27. Mehta A, Mann M, Zhao JL, Marinov GK, Majumdar D, Garcia-Flores Y, Du X, Erikci E, Chowdhury K, Baltimore D. 2015. The microRNA-212/132 cluster regulates B cell development by targeting Sox4. J Exp Med 212:1679--1692.

28. Lynch M, Marinov GK. 2015. The bioenergetic costs of a gene. Proc Natl Acad Sci U S A 112:15690--15695.

29. Marinov GK, Lynch M. 2015. Diversity and Divergence of Dinofagellate Histone Proteins. G3 [Epub ahead of print]