Group of regulatory transcriptomics and epigenomics

Yulia A. Medvedeva
Head of the Group
Ph.D. (Biology)
INB, room 301
Телефон
E-Mail ju.medvedeva@gmail.com

The group is currently working on several projects on epigenetic regulation:

1) Search for the agents targeting epigenetic modifiers to specific genomic locations (with the support from Russian Science Foundation for 2015-2017). Anatoliy Zubritskiy is mostly focused on this project searching for possible genetic determinants of epigenetic modifications using targeted genome editing.

2) Study of the role of lncRNA in transcription and post-transcription regulation. In particular, the group is interested in RNA-RNA and RNA-chromatin interaction. Ivan Antonov research interests include bioinformatics prediction of RNA-RNA interactions, post-transcriptional and epigenetic gene regulation. He is currently studying functions and molecular mechanisms of long non-coding RNAs in mammalian cells.

3) Detection of single CpG methylation markers highly specific for gene expresion. Anna Lioznova is now working on this topic.

Additionally, in late 2017 we started a collaborative project (with the support from RFBS for 2017-2019) on transcription and epigenetic regulation of macrophages during development of Mycobacterium tuberculosis infection. Also, Ivan Antonov works on programmed ribosomal frameshifting.

 

Selected publications:

  1. Mazurov E., Sizykh A., Medvedeva Y. A. HiMoRNA: A Comprehensive Database of Human lncRNAs Involved in Genome-Wide Epigenetic Regulation //Non-coding RNA. – 2022. – Т. 8. – №. 1. – С. 18
  2. Ogunleye A. J., Romanova E., Medvedeva Y. A. Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia //F1000Research. – 2021. – Т. 10
  3. Céline Barlier, Diego Barriales, Alexey Samosyuk, Sascha Jung, Srikanth Ravichandran, Yulia A Medvedeva et al. A Catalogus Immune Muris of the mouse immune responses to diverse pathogens //Cell death & disease. – 2021. – Т. 12. – №. 9. – С. 1-9
  4. Anna Elizarova, Mumin Ozturk, Reto Guler, Yulia A Medvedeva. MIREyA: a computational approach to detect miRNA-directed gene activation //F1000Research. – 2021. – Т. 10
  5. Alexey Sizykh, Khalimat Murtazalieva, Yulia Vyshkvorkina, Alexey Stupnikov, Yulia A Medvedeva. CFM: a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation //F1000Research. – 2021. – Т. 10. – №. 295. – С. 295
  6. Ogunleye A. J., Romanova E., Medvedeva Y. A. Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia //F1000Research. – 2021. – Т. 10
  7. Sumit Mukherjee, Rajesh Detroja, Deepak Balamurali, Elena Matveishina, Yulia A Medvedeva et al. Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells //NAR genomics and bioinformatics. – 2021. – Т. 3. – №. 3. – С. lqab074
  8. Niels Velthuijs, Birgit Meldal, Quinte Geessinck, Pablo Porras, Yulia Medvedeva, Anatoliy Zubritskiy et al. Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes //Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms. – 2021. – Т. 1864. – №. 10. – С. 194749
  9. Antonov I. V. Two Cobalt Chelatase Subunits Can Be Generated from a Single chlD Gene via Programed Frameshifting //Molecular Biology and Evolution. – 2020. – Т. 37. – №. 8. – С. 2268-2278
  10. Antonov I., Medvedeva Y. Direct Interactions with Nascent Transcripts Is Potentially a Common Targeting Mechanism of Long Non-Coding RNAs //Genes. – 2020. – Т. 11. – №. 12. – С. 1483
  11. Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, Altuna Akalin, Ivan V Antonov, et al. Functional annotation of human long noncoding RNAs via molecular phenotyping //Genome research. – 2020. – Т. 30. – №. 7. – С. 1060-1072
  12. Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J Nash, Marco Ghilotti, Christopher JF Cameron, Matthew Valentine, Yulia A Medvedeva et al. RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions //Nature communications. – 2020. – Т. 11. – №. 1. – С. 1-14
  13. Matveishina E., Antonov I., Medvedeva Y. A. Practical guidance in genome-wide RNA: DNA triple helix prediction //International journal of molecular sciences. – 2020. – Т. 21. – №. 3. – С. 830
  14. CpG traffic lights are markers of regulatory regions in human genome, Anna V Lioznova, Abdullah M Khamis, Artem V Artemov, Elizaveta Besedina, Vasily Ramensky, Vladimir B Bajic, Ivan V Kulakovskiy, Yulia A Medvedeva
    BMC genomics 20 (1), 102, 2019
  15. Differential Targeting of c-Maf, Bach-1, and Elmo-1 by microRNA-143 and microRNA-365 Promotes the Intracellular Growth of Mycobacterium tuberculosis in Alternatively IL-4/IL-13 Activated, Ousman Tamgue, Lorna Gcanga, Mumin Ozturk, Lauren Whitehead, Shandre Pillay, Raygaana Jacobs, Sugata Roy, Sebastian Schmeier, Malika Davids6, Yulia A. Medvedeva, Keertan Dheda, Harukazu Suzuki, Frank Brombacher and Reto Guler, Frontiers in Immunology 10, 421
  16. Peripubertal serum dioxin concentrations and subsequent sperm methylome profiles of young Russian adult, J Richard Pilsner, Alex Shershebnev, Yulia A Medvedeva, Alexander Suvorov, Haotian Wu, Andrey Goltsov, Evgeny Loukianov, Tatiana Andreeva, Fedor Gusev, Andrey Manakhov, Luidmila Smigulina, Maria Logacheva, Victoria Shtratnikova, Irina Kuznetsova, Peter Speranskiy-Podobed, Jane S Burns, Paige L Williams, Susan Korrick, Mary M Lee, Evgeny Rogaev, Russ Hauser, Oleg Sergeyev, Reproductive Toxicology 78, 40-49
  17. Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics toolsIV, Antonov, E Mazurov, M Borodovsky, YA Medvedeva, Briefings in bioinformatics 20 (2), 551-564
  18. A novel method for improved accuracy of transcription factor binding site prediction, Abdullah M Khamis, Olaa Motwalli, Romina Oliva, Boris R Jankovic, Yulia A Medvedeva, Haitham Ashoor, Magbubah Essack, Xin Gao, Vladimir B Bajic. Nucleic acids research 46 (12), e72-e72
  19. Triplex target sites of MEG3 RNA-chromatin interactions,I Antonov, YA Medvedeva. F1000Research 7
  20. DNA sequence features that may establish H3K27аc mark, A Zubritskiy, YA Medvedeva. Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2018)
  21. Perinatal exposure to low dose 2, 2′, 4, 4′-tetrabromodiphenyl ether (BDE-47) alters sperm, Alexander Suvorov, Alex Shershebnev, Haotian Wu, Yulia Medvedeva, Oleg Sergeyev, J Richard Pilsner. Reproductive Toxicology 75, 136-143
  22. Antonov I, Marakhonov A, Zamkova M, Medvedeva Y. ASSA: Fast identification of statistically significant interactions between long RNAs. J Bioinform Comput. Biol. 2018 Jan 29
  23. Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy E, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res. 2017 Nov 11. doi: 10.1093/nar/gkx1106.
  24. Artemov AV, Mugue NS, Rastorguev SM, Zhenilo S, Mazur AM, Tsygankova SV, Boulygina ES, Kaplun D, Nedoluzhko AV, Medvedeva YA, Prokhortchouk EB. Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions. Mol Biol Evol. 2017 Sep 1;34(9):2203-2213. doi: 10.1093/molbev/msx156.
  25. de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, de Hoon MJL. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947.
  26. Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature. 2017 Mar 9;543(7644):199-204.
  27. Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J1, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H (2016)  Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. NAR, Nucleic Acids Res.2016 Oct 27. pii: gkw995
  28. Panchin AY., Makeev VJ., Medvedeva YA. (2016) Preservation of methylated CpG dinucleotides in human CpG islands, Biology Direct, 11:11
  29. Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ. (2016) HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res., D1:D116-D125.
  30. Medvedeva YA, Lennartsson A, Ehsani R, Kulakovskiy IV, Vorontsov IE, Panahandeh P, Khimulya G, Kasukawa T; FANTOM  Consortium, Drabløs F. (2015) EpiFactors: a comprehensive database of human epigenetic factors and complexes. Database (Oxford). 2015 Jul 7;2015:bav067. doi: 10.1093/database/bav067.
  31. A.Khamis, A.Hamilton, Y.Medvedeva, T.Alam, I.Alam, M.Essack, B.Umylny, B.Jankovic, N.Naeger, M.Suzuki, M.Harbers, G.Robinson, and V.Bajic (2015) Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. Scientific Reports, Jun 15;5:11136
  32. Alam T, Medvedeva YA, Jia H, Brown JB, Lipovich L, Bajic VB (2014). Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. PLoS One. Oct 2;9(10):e109443.
  33. A.R.R. Forrest, H. Kawaji, M. Rehli, J.K. Baillie, M.J.L. de Hoon, V. Haberle, T. Lassmann, I.V. Kulakovskiy, M. Lizio, M. Itoh, R. Andersson, C.J. Mungall, T.F. Meehan, S. Schmeier, N. Bertin, M. Jørgensen, E. Dimont, E. Arner, C. Schmidl, U. Schaefer, Y. A. Medvedeva, C. Plessy, M. Vitezic, J. Severin, C.A. Semple, Y. Ishizu, M. Francescatto, et al. (2014) A promoter level mammalian expression atlas. Nature. 507(7493):462-70. 2.
  34. Y.A. Medvedeva, A. Khamis, I.V. Kulakovskiy, W. Ba-Alawi, Md.S.I. Bhuyan, H. Kawaji, T. Lassmann, M. Harbers, A.R.R. Forrest and V.B. Bajic (2014). Effects of cytosine methylation on transcription factor binding sites. BMC genomics. 26;15(1):119.
  35. Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ. (2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. Jan;41(Database issue):D195-202.
  36. Antonov I, Baranov PV, Borodovsky M (2013) GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. Nucleic Acids Res. 2013 Jan;41:D152-6
  37. Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M. Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res. 2013 Jul;41(13):6514-30.
    Favorov A, Mularoni L, Cope LM, Medvedeva Y, Mironov AA, Makeev VJ, Wheelan SJ. (2012) Exploring massive, genome scale datasets with the GenometriCorr package. PLoS Comput Biol. May;8(5):e1002529
  38. Medvedeva YA, Fridman MV, Oparina NJ, Malko DB, Ermakova EO, Kulakovskiy IV, Heinzel A, Makeev VJ. (2010) Intergenic, gene terminal, and intragenic CpG islands in the human genome. BMC Genomics. Jan 19;11:48.
  39. Antonov I, Borodovsky M. Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J Bioinform Comput Biol. 2010 Jun; 8(3):535-51.