1
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Pletenev IA, Bazarevich M, Zagirova DR, Kononkova AD, Cherkasov AV, Efimova OI, Tiukacheva EA, Morozov KV, Ulianov KA, Komkov D, Tvorogova AV, Golimbet VE, Kondratyev NV, Razin SV, Khaitovich P, Ulianov SV, Khrameeva EE. Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome. Nucleic Acids Res 2024:gkae271. [PMID: 38647066 DOI: 10.1093/nar/gkae271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/21/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
Chromatin architecture regulates gene expression and shapes cellular identity, particularly in neuronal cells. Specifically, polycomb group (PcG) proteins enable establishment and maintenance of neuronal cell type by reorganizing chromatin into repressive domains that limit the expression of fate-determining genes and sustain distinct gene expression patterns in neurons. Here, we map the 3D genome architecture in neuronal and non-neuronal cells isolated from the Wernicke's area of four human brains and comprehensively analyze neuron-specific aspects of chromatin organization. We find that genome segregation into active and inactive compartments is greatly reduced in neurons compared to other brain cells. Furthermore, neuronal Hi-C maps reveal strong long-range interactions, forming a specific network of PcG-mediated contacts in neurons that is nearly absent in other brain cells. These interacting loci contain developmental transcription factors with repressed expression in neurons and other mature brain cells. But only in neurons, they are rich in bivalent promoters occupied by H3K4me3 histone modification together with H3K27me3, which points to a possible functional role of PcG contacts in neurons. Importantly, other layers of chromatin organization also exhibit a distinct structure in neurons, characterized by an increase in short-range interactions and a decrease in long-range ones.
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Affiliation(s)
- Ilya A Pletenev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maria Bazarevich
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Diana R Zagirova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Anna D Kononkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Alexander V Cherkasov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Olga I Efimova
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Eugenia A Tiukacheva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow 141700, Russia
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- CNRS UMR9018, Institut Gustave Roussy, Villejuif 94805, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Kirill V Morozov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Kirill A Ulianov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitriy Komkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna V Tvorogova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vera E Golimbet
- Laboratory of Clinical Genetics, Mental Health Research Center, Moscow 115522, Russia
| | - Nikolay V Kondratyev
- Laboratory of Clinical Genetics, Mental Health Research Center, Moscow 115522, Russia
| | - Sergey V Razin
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Philipp Khaitovich
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Sergey V Ulianov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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2
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Shekhovtsov SV, Vorontsova YL, Slepneva IA, Smirnov DN, Khrameeva EE, Shatunov A, Poluboyarova TV, Bulakhova NA, Meshcheryakova EN, Berman DI, Glupov VV. The Impact of Long-Term Hypoxia on the Antioxidant Defense System in the Siberian Frog Rana amurensis. Biochemistry (Mosc) 2024; 89:441-450. [PMID: 38648764 DOI: 10.1134/s0006297924030052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 04/25/2024]
Abstract
The Siberian frog Rana amurensis has a uniquely high tolerance to hypoxia among amphibians, as it is able to withstand several months underwater with almost no oxygen (0.2 mg/liter) vs. several days for other studied species. Since it was hypothesized that hypoxia actives the antioxidant defense system in hypoxia-tolerant animals, one would expect similar response in R. amurensis. Here, we studied the effect of hypoxia in the Siberian frog based on the transcriptomic data, activities of antioxidant enzyme, and content of low-molecular-weight antioxidants. Exposure to hypoxia upregulated expression of three relevant transcripts (catalase in the brain and two aldo-keto reductases in the liver). The activities of peroxidase in the blood and catalase in the liver were significantly increased, while the activity of glutathione S-transferase in the liver was reduced. The content of low-molecular-weight antioxidants (thiols and ascorbate) in the heart and liver was unaffected. In general, only a few components of the antioxidant defense system were affected by hypoxia, while most remained unchanged. Comparison to other hypoxia-tolerant species suggests species-specific adaptations to hypoxia-related ROS stress.
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Affiliation(s)
- Sergei V Shekhovtsov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Yana L Vorontsova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630091, Russia
| | - Irina A Slepneva
- Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Dmitry N Smirnov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer Sheva, Israel
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Alexey Shatunov
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Tatiana V Poluboyarova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Nina A Bulakhova
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Ekaterina N Meshcheryakova
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Daniil I Berman
- Institute of Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, 630058, Russia
| | - Viktor V Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630091, Russia
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3
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Kobets VA, Ulianov SV, Galitsyna AA, Doronin SA, Mikhaleva EA, Gelfand MS, Shevelyov YY, Razin SV, Khrameeva EE. HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases. Brief Bioinform 2023; 24:7033301. [PMID: 36759336 PMCID: PMC10025441 DOI: 10.1093/bib/bbad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/04/2023] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
The chromatin interaction assays, particularly Hi-C, enable detailed studies of genome architecture in multiple organisms and model systems, resulting in a deeper understanding of gene expression regulation mechanisms mediated by epigenetics. However, the analysis and interpretation of Hi-C data remain challenging due to technical biases, limiting direct comparisons of datasets obtained in different experiments and laboratories. As a result, removing biases from Hi-C-generated chromatin contact matrices is a critical data analysis step. Our novel approach, HiConfidence, eliminates biases from the Hi-C data by weighing chromatin contacts according to their consistency between replicates so that low-quality replicates do not substantially influence the result. The algorithm is effective for the analysis of global changes in chromatin structures such as compartments and topologically associating domains. We apply the HiConfidence approach to several Hi-C datasets with significant technical biases, that could not be analyzed effectively using existing methods, and obtain meaningful biological conclusions. In particular, HiConfidence aids in the study of how changes in histone acetylation pattern affect chromatin organization in Drosophila melanogaster S2 cells. The method is freely available at GitHub: https://github.com/victorykobets/HiConfidence.
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Affiliation(s)
- Victoria A Kobets
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Aleksandra A Galitsyna
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Semen A Doronin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, 123182, Russia
| | - Elena A Mikhaleva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, 123182, Russia
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Yuri Y Shevelyov
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, 123182, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia
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4
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Rozenwald MB, Galitsyna AA, Sapunov GV, Khrameeva EE, Gelfand MS. A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features. PeerJ Comput Sci 2020; 6:e307. [PMID: 33816958 PMCID: PMC7924456 DOI: 10.7717/peerj-cs.307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/30/2020] [Indexed: 05/03/2023]
Abstract
Technological advances have lead to the creation of large epigenetic datasets, including information about DNA binding proteins and DNA spatial structure. Hi-C experiments have revealed that chromosomes are subdivided into sets of self-interacting domains called Topologically Associating Domains (TADs). TADs are involved in the regulation of gene expression activity, but the mechanisms of their formation are not yet fully understood. Here, we focus on machine learning methods to characterize DNA folding patterns in Drosophila based on chromatin marks across three cell lines. We present linear regression models with four types of regularization, gradient boosting, and recurrent neural networks (RNN) as tools to study chromatin folding characteristics associated with TADs given epigenetic chromatin immunoprecipitation data. The bidirectional long short-term memory RNN architecture produced the best prediction scores and identified biologically relevant features. Distribution of protein Chriz (Chromator) and histone modification H3K4me3 were selected as the most informative features for the prediction of TADs characteristics. This approach may be adapted to any similar biological dataset of chromatin features across various cell lines and species. The code for the implemented pipeline, Hi-ChiP-ML, is publicly available: https://github.com/MichalRozenwald/Hi-ChIP-ML.
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Affiliation(s)
- Michal B. Rozenwald
- Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | | | - Grigory V. Sapunov
- Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- Intento, Inc., Berkeley, CA, USA
| | | | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
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5
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Samborskaia MD, Galitsyna A, Pletenev I, Trofimova A, Mironov AA, Gelfand MS, Khrameeva EE. Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function. PeerJ 2020; 8:e9566. [PMID: 32864204 PMCID: PMC7425636 DOI: 10.7717/peerj.9566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/27/2020] [Indexed: 12/18/2022] Open
Abstract
Regulation of gene transcription is a complex process controlled by many factors, including the conformation of chromatin in the nucleus. Insights into chromatin conformation on both local and global scales can be provided by the Hi-C (high-throughput chromosomes conformation capture) method. One of the drawbacks of Hi-C analysis and interpretation is the presence of systematic biases, such as different accessibility to enzymes, amplification, and mappability of DNA regions, which all result in different visibility of the regions. Iterative correction (IC) is one of the most popular techniques developed for the elimination of these systematic biases. IC is based on the assumption that all chromatin regions have an equal number of observed contacts in Hi-C. In other words, the IC procedure is equalizing the experimental visibility approximated by the cumulative contact frequency (CCF) for all genomic regions. However, the differences in experimental visibility might be explained by biological factors such as chromatin openness, which is characteristic of distinct chromatin states. Here we show that CCF is positively correlated with active transcription. It is associated with compartment organization, since compartment A demonstrates higher CCF and gene expression levels than compartment B. Notably, this observation holds for a wide range of species, including human, mouse, and Drosophila. Moreover, we track the CCF state for syntenic blocks between human and mouse and conclude that active state assessed by CCF is an intrinsic property of the DNA region, which is independent of local genomic and epigenomic context. Our findings establish a missing link between Hi-C normalization procedures removing CCF from the data and poorly investigated and possibly relevant biological factors contributing to CCF.
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Affiliation(s)
- Margarita D Samborskaia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksandra Galitsyna
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.,Institute of Gene Biology, RAS, Moscow, Russia
| | - Ilya Pletenev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna Trofimova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Mikhail S Gelfand
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Ekaterina E Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
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6
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Bozek K, Khrameeva EE, Reznick J, Omerbašić D, Bennett NC, Lewin GR, Azpurua J, Gorbunova V, Seluanov A, Regnard P, Wanert F, Marchal J, Pifferi F, Aujard F, Liu Z, Shi P, Pääbo S, Schroeder F, Willmitzer L, Giavalisco P, Khaitovich P. Publisher Correction: Lipidome determinants of maximal lifespan in mammals. Sci Rep 2019; 9:6972. [PMID: 31043659 PMCID: PMC6494842 DOI: 10.1038/s41598-019-43122-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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7
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Luzhin AV, Flyamer IM, Khrameeva EE, Ulianov SV, Razin SV, Gavrilov AA. Quantitative differences in TAD border strength underly the TAD hierarchy in Drosophila chromosomes. J Cell Biochem 2018; 120:4494-4503. [PMID: 30260021 DOI: 10.1002/jcb.27737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 09/30/2018] [Indexed: 12/19/2022]
Abstract
Chromosomes in many organisms, including Drosophila and mammals, are folded into topologically associating domains (TADs). Increasing evidence suggests that TAD folding is hierarchical, wherein subdomains combine to form larger superdomains, instead of a sequence of nonoverlapping domains. Here, we studied the hierarchical structure of TADs in Drosophila. We show that the boundaries of TADs of different hierarchical levels are characterized by the presence of different portions of active chromatin, but do not vary in the binding of architectural proteins, such as CCCTC binding factor or cohesin. The apparent hierarchy of TADs in Drosophila chromosomes is not likely to have functional importance but rather reflects various options of long-range chromatin folding directed by the distribution of active and inactive chromatin segments and may represent population average.
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Affiliation(s)
- Artem V Luzhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ekaterina E Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Department of Molecular Biology, Lomonosov Moscow State University, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Department of Molecular Biology, Lomonosov Moscow State University, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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8
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Abstract
Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis. The enrichment of specific functional groups with Denisovan alleles is less pronounced; these groups are responsible for bone and tissue remodeling. This analysis shows that introgression of alleles from Neanderthals and Denisovans to Papuans occurred independently and retention of these alleles may carry specific adaptive advantages.
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Affiliation(s)
- Evgeny E. Akkuratov
- St. Petersburg State University, Institute of Translational Biomedicine, St. Petersburg, Russia
| | - Mikhail S. Gelfand
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute for Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Computer Science, National Research University – Higher School of Economics, Moscow, Russia
- Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina E. Khrameeva
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute for Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
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9
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Triska P, Chekanov N, Stepanov V, Khusnutdinova EK, Kumar GPA, Akhmetova V, Babalyan K, Boulygina E, Kharkov V, Gubina M, Khidiyatova I, Khitrinskaya I, Khrameeva EE, Khusainova R, Konovalova N, Litvinov S, Marusin A, Mazur AM, Puzyrev V, Ivanoshchuk D, Spiridonova M, Teslyuk A, Tsygankova S, Triska M, Trofimova N, Vajda E, Balanovsky O, Baranova A, Skryabin K, Tatarinova TV, Prokhortchouk E. Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe. BMC Genet 2017; 18:110. [PMID: 29297395 PMCID: PMC5751809 DOI: 10.1186/s12863-017-0578-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. RESULTS We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the "Finno-Ugric" origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main "core", being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the "Great Siberian Vortex" directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts. CONCLUSIONS Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations.
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MESH Headings
- Algorithms
- Asia
- DNA
- Datasets as Topic
- Emigration and Immigration/history
- Ethnicity/genetics
- Europe
- Female
- Genetic Variation
- Genetics, Population
- Genotyping Techniques
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Male
- Russia
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Affiliation(s)
- Petr Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nikolay Chekanov
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- "Genoanalytica" CJSC, Moscow, Russia
| | - Vadim Stepanov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Konstantin Babalyan
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | | | - Vladimir Kharkov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | - Irina Khitrinskaya
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Ekaterina E Khrameeva
- "Genoanalytica" CJSC, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, Russia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Sergey Litvinov
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Andrey Marusin
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Alexandr M Mazur
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
| | - Valery Puzyrev
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Dinara Ivanoshchuk
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maria Spiridonova
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Anton Teslyuk
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Svetlana Tsygankova
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Martin Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Natalya Trofimova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Edward Vajda
- Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, USA
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
| | - Ancha Baranova
- Research Centre for Medical Genetics, Moscow, Russia
- School of Systems Biology, George Mason University, Fairfax, VA, USA
- Atlas Biomed Group, Moscow, Russia
| | - Konstantin Skryabin
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- Russian Scientific Centre "Kurchatov Institute", Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Tatarinova
- Vavilov Institute of General Genetics, Moscow, Russia.
- School of Systems Biology, George Mason University, Fairfax, VA, USA.
- Atlas Biomed Group, Moscow, Russia.
- Department of Biology, University of La Verne, La Verne, CA, USA.
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Egor Prokhortchouk
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
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10
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Ulianov SV, Galitsyna AA, Flyamer IM, Golov AK, Khrameeva EE, Imakaev MV, Abdennur NA, Gelfand MS, Gavrilov AA, Razin SV. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. Epigenetics Chromatin 2017; 10:35. [PMID: 28693562 PMCID: PMC5504709 DOI: 10.1186/s13072-017-0142-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 07/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2.7 Mb segment of chicken chromosome 14 harboring the alpha-globin gene cluster in cultured lymphoid cells and cultured erythroid cells before and after induction of terminal erythroid differentiation. RESULTS We found that, similarly to mammalian genome, the chicken genomes is organized in TADs and compartments. Full activation of the alpha-globin gene transcription in differentiated erythroid cells is correlated with upregulation of several adjacent housekeeping genes and the emergence of abundant intergenic transcription. An extended chromosome region encompassing the alpha-globin cluster becomes significantly decompacted in differentiated erythroid cells, and depleted in CTCF binding and CTCF-anchored chromatin loops, while the sub-TAD harboring alpha-globin gene cluster and the upstream major regulatory element (MRE) becomes highly enriched with chromatin interactions as compared to lymphoid and proliferating erythroid cells. The alpha-globin gene domain and the neighboring loci reside within the A-like chromatin compartment in both lymphoid and erythroid cells and become further segregated from the upstream gene desert upon terminal erythroid differentiation. CONCLUSIONS Our findings demonstrate that the effects of tissue-specific transcription activation are not restricted to the host genomic locus but affect the overall chromatin structure and transcriptional output of the encompassing topologically associating domain.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992
| | - Aleksandra A Galitsyna
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051
| | - Ilya M Flyamer
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Arkadiy K Golov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334
| | - Ekaterina E Khrameeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia 143026.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051
| | - Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Nezar A Abdennur
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Mikhail S Gelfand
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia 119992.,Skolkovo Institute of Science and Technology, Skolkovo, Russia 143026.,Institute for Information Transmission Problems (the Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia 127051.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia 125319
| | - Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334
| | - Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia 119334.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia 119992
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11
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Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci Rep 2016; 6:20768. [PMID: 26865217 PMCID: PMC4750364 DOI: 10.1038/srep20768] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/07/2016] [Indexed: 01/11/2023] Open
Abstract
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.
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Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anastassiya Zidkova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Maria D. Logacheva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - N. Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny S. Gerasimov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina E. Khrameeva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga P. Konovalova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Neretina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri V. Nikolsky
- Biomedical Cluster, Skolkovo Foundation, Skolkovo, Russia
- George Mason University, Fairfax, VA, USA
| | - George Starostin
- Russian State University for the Humanities, Moscow, Russia
- Russian Presidential Academy (RANEPA), Moscow, Russia
| | - Vita V. Stepanova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | | | - Martin Tříska
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Petr Tříska
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Tatiana V. Tatarinova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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12
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Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA. History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. J Bioinform Comput Biol 2016; 14:1641002. [PMID: 27021249 DOI: 10.1142/s021972001641002x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three-dimensional (3D) organization of genomes affects critical cellular processes such as transcription, replication, and deoxyribo nucleic acid (DNA) repair. While previous studies have investigated the natural role, the 3D organization plays in limiting a possible set of genomic rearrangements following DNA repair, the influence of specific organizational principles on this process, particularly over longer evolutionary time scales, remains relatively unexplored. In budding yeast S.cerevisiae, chromosomes are organized into a Rabl-like configuration, with clustered centromeres and telomeres tethered to the nuclear periphery. Hi-C data for S.cerevisiae show that a consequence of this Rabl-like organization is that regions equally distant from centromeres are more frequently in contact with each other, between arms of both the same and different chromosomes. Here, we detect rearrangement events in Saccharomyces species using an automatic approach, and observe increased rearrangement frequency between regions with higher contact frequencies. Together, our results underscore how specific principles of 3D chromosomal organization can influence evolutionary events.
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Affiliation(s)
- Ekaterina E Khrameeva
- 1 Institute for Information Transmission, Problems (the Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, Moscow 127051, Russian Federation.,2 Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, build. 3, Moscow 143026, Russian Federation
| | - Geoffrey Fudenberg
- 3 Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Mikhail S Gelfand
- 1 Institute for Information Transmission, Problems (the Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, Moscow 127051, Russian Federation.,4 Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Leninskiye Gory 1-73, Moscow 119991, Russian Federation
| | - Leonid A Mirny
- 3 Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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13
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Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res 2015; 26:70-84. [PMID: 26518482 PMCID: PMC4691752 DOI: 10.1101/gr.196006.115] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/26/2015] [Indexed: 01/06/2023]
Abstract
Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina E Khrameeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia; Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia
| | | | - Ilya M Flyamer
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Pavel Kos
- Physics Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Mikhaleva
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, RAS, 123182 Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, RAS, 123182 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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14
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Khrameeva EE, Ulyanov SV, Gavrilov AA, Shevelyov YY, Gelfand MS, Razin SV. 20 Active chromatin regions are sufficient to define borders of topologically associated domains in D. melanogasterinterphase chromosomes. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1032560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Kaufmann S, Fuchs C, Gonik M, Khrameeva EE, Mironov AA, Frishman D. Inter-chromosomal contact networks provide insights into Mammalian chromatin organization. PLoS One 2015; 10:e0126125. [PMID: 25961318 PMCID: PMC4427453 DOI: 10.1371/journal.pone.0126125] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/30/2015] [Indexed: 11/18/2022] Open
Abstract
The recent advent of conformation capture techniques has provided unprecedented insights into the spatial organization of chromatin. We present a large-scale investigation of the inter-chromosomal segment and gene contact networks in embryonic stem cells of two mammalian organisms: humans and mice. Both interaction networks are characterized by a high degree of clustering of genome regions and the existence of hubs. Both genomes exhibit similar structural characteristics such as increased flexibility of certain Y chromosome regions and co-localization of centromere-proximal regions. Spatial proximity is correlated with the functional similarity of genes in both species. We also found a significant association between spatial proximity and the co-expression of genes in the human genome. The structural properties of chromatin are also species specific, including the presence of two highly interactive regions in mouse chromatin and an increased contact density on short, gene-rich human chromosomes, thereby indicating their central nuclear position. Trans-interacting segments are enriched in active marks in human and had no distinct feature profile in mouse. Thus, in contrast to interactions within individual chromosomes, the inter-chromosomal interactions in human and mouse embryonic stem cells do not appear to be conserved.
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Affiliation(s)
- Stefanie Kaufmann
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Christiane Fuchs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technical University Munich, Institute for Mathematical Sciences, Garching, Germany
| | - Mariya Gonik
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Munich, Germany
| | - Ekaterina E. Khrameeva
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Andrey A. Mironov
- Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrij Frishman
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
- Institute for Bioinformatics and Systems Biology, HMGU German Research Center for Environmental Health, Neuherberg, Germany
- Department of Bioinformatics, St Petersburg State Polytechnical University, St Petersburg, Russia
- * E-mail:
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16
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Khrameeva EE, Gelfand MS. Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. BMC Bioinformatics 2012; 13 Suppl 6:S4. [PMID: 22537043 PMCID: PMC3358657 DOI: 10.1186/1471-2105-13-s6-s4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
High-throughput sequencing of whole genomes and transcriptomes allows one to generate large amounts of sequence data very rapidly and at a low cost. The goal of most mRNA sequencing studies is to perform the comparison of the expression level between different samples. However, given a broad variety of modern sequencing protocols, platforms and versions thereof, it is not clear to what extent the obtained results are consistent across platforms and laboratories. The comparison of 117 human mRNA and genome high-throughput sequencing experiments performed on the Illumina and SOLiD platforms at 26 institutions all over the world demonstrated high dependency of the gene coverage profiles on the producing laboratory. Gene coverage profiles showed laboratory-specific non-uniformity that survived the 3'-bias correction and mappability normalization, suggesting that there are other yet unknown mRNA-associated biases.
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Affiliation(s)
- Ekaterina E Khrameeva
- Institute for Information Transmission Problems, Russian Academy of Sciences, 19 Bolshoy Karetny per., Moscow, 127994, Russia.
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17
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Pervouchine DD, Khrameeva EE, Pichugina MY, Nikolaienko OV, Gelfand MS, Rubtsov PM, Mironov AA. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA 2012; 18:1-15. [PMID: 22128342 PMCID: PMC3261731 DOI: 10.1261/rna.029249.111] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pre-mRNA structure impacts many cellular processes, including splicing in genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each gene, we now report RNA structures that could be involved in the regulation of splicing in mammals. Statistically, we demonstrate strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. As an example, we validated the RNA structure in the human SF1 gene using minigenes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.
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Affiliation(s)
- Dmitri D Pervouchine
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119992, GSP-2 Russia.
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18
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Khrameeva EE, Drutsa VL, Vrzheshch EP, Dmitrienko DV, Vrzheshch PV. Mutants of monomeric red fluorescent protein mRFP1 at residue 66: structure modeling by molecular dynamics and search for correlations with spectral properties. Biochemistry (Mosc) 2008; 73:1085-95. [PMID: 18991554 DOI: 10.1134/s0006297908100040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To study the interrelation between the spectral and structural properties of fluorescent proteins, structures of mutants of monomeric red fluorescent protein mRFP1 with all possible point mutations of Glu66 (except replacement by Pro) were simulated by molecular dynamics. A global search for correlations between geometrical structure parameters and some spectral characteristics (absorption maximum wavelength, integral extinction coefficient at the absorption maximum, excitation maximum wavelength, emission maximum wavelength, and quantum yield) was performed for the chromophore and its 6 A environment in mRFP1, Q66A, Q66L, Q66S, Q66C, Q66H, and Q66N. The correlation coefficients (0.81-0.87) were maximal for torsion angles in phenolic and imidazolidine rings as well as for torsion angles in the regions of connection between these rings and chromophore attachment to beta-barrel. The data can be used to predict the spectral properties of fluorescent proteins based on their structures and to reveal promising positions for directed mutagenesis.
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Affiliation(s)
- E E Khrameeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
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