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Halimani N, Nesterchuk M, Tsitrina AA, Sabirov M, Andreichenko IN, Dashenkova NO, Petrova E, Kulikov AM, Zatsepin TS, Romanov RA, Mikaelyan AS, Kotelevtsev YV. Knockdown of Hyaluronan synthase 2 suppresses liver fibrosis in mice via induction of transcriptomic changes similar to 4MU treatment. Sci Rep 2024; 14:2797. [PMID: 38307876 PMCID: PMC10837461 DOI: 10.1038/s41598-024-53089-x] [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: 08/25/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
Hepatic fibrosis remains a significant clinical challenge due to ineffective treatments. 4-methylumbelliferone (4MU), a hyaluronic acid (HA) synthesis inhibitor, has proven safe in phase one clinical trials. In this study, we aimed to ameliorate liver fibrosis by inhibiting HA synthesis. We compared two groups of mice with CCl4-induced fibrosis, treated with 4-methylumbelliferone (4MU) and hyaluronan synthase 2 (HAS2) targeting siRNA (siHAS2). The administration of 4MU and siHAS2 significantly reduced collagen and HA deposition, as well as biochemical markers of hepatic damage induced by repeated CCl4 injections. The transcriptomic analysis revealed converging pathways associated with downstream HA signalling. 4MU- and siHAS2-treated fibrotic livers shared 405 upregulated and 628 downregulated genes. These genes were associated with xenobiotic and cholesterol metabolism, mitosis, endoplasmic reticulum stress, RNA processing, and myeloid cell migration. The functional annotation of differentially expressed genes (DEGs) in siHAS2-treated mice revealed attenuation of extracellular matrix-associated pathways. In comparison, in the 4MU-treated group, DEGs were related to lipid and bile metabolism pathways and cell cycle. These findings confirm that HAS2 is an important pharmacological target for suppressing hepatic fibrosis using siRNA.
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Affiliation(s)
- Noreen Halimani
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 143025, Russia.
| | - Mikhail Nesterchuk
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - Alexandra A Tsitrina
- IKI-Ilse Katz Institute for Nanoscale Science & Technology, Nem Gurion University of the Negev, Beersheba, Israel
| | - Marat Sabirov
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, Moscow, 119334, Russia
| | - Irina N Andreichenko
- AO Reproduction Head Centre of Agricultural Animals, Tsentralnaya Street, 3., Podolsk, Moscow Region, 142143, Russia
| | - Nataliya O Dashenkova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, Moscow, 119334, Russia
| | - Elizaveta Petrova
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - Alexey M Kulikov
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, Moscow, 119334, Russia
| | - Timofei S Zatsepin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Roman A Romanov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Arsen S Mikaelyan
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, Moscow, 119334, Russia
| | - Yuri V Kotelevtsev
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation and Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
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Sabirov M, Kyrchanova O, Pokholkova GV, Bonchuk A, Klimenko N, Belova E, Zhimulev IF, Maksimenko O, Georgiev P. Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster. Epigenetics Chromatin 2021; 14:16. [PMID: 33752739 PMCID: PMC7983404 DOI: 10.1186/s13072-021-00391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/21/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Background Pita is required for Drosophila development and binds specifically to a long motif in active promoters and insulators. Pita belongs to the Drosophila family of zinc-finger architectural proteins, which also includes Su(Hw) and the conserved among higher eukaryotes CTCF. The architectural proteins maintain the active state of regulatory elements and the long-distance interactions between them. In particular, Pita is involved in the formation of several boundaries between regulatory domains that controlled the expression of three hox genes in the Bithorax complex (BX-C). The CP190 protein is recruited to chromatin through interaction with the architectural proteins. Results Using in vitro pull-down analysis, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. Then we constructed transgenic lines expressing the Pita protein of the wild-type and mutant variants lacking CP190-interacting regions. We have demonstrated that CP190-interacting region of the Pita can maintain nucleosome-free open chromatin and is critical for Pita-mediated enhancer blocking activity in BX-C. At the same time, interaction with CP190 is not required for the in vivo function of the mutant Pita protein, which binds to the same regions of the genome as the wild-type protein. Unexpectedly, we found that CP190 was still associated with the most of genome regions bound by the mutant Pita protein, which suggested that other architectural proteins were continuing to recruit CP190 to these regions. Conclusions The results directly demonstrate role of CP190 in insulation and support a model in which the regulatory elements are composed of combinations of binding sites that interact with several architectural proteins with similar functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00391-x.
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Affiliation(s)
- Marat Sabirov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Galina V Pokholkova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB RAS), Novosibirsk, Russia
| | - Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB RAS), Novosibirsk, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow, 119334, Russia.
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Khrameeva E, Kurochkin I, Han D, Guijarro P, Kanton S, Santel M, Qian Z, Rong S, Mazin P, Sabirov M, Bulat M, Efimova O, Tkachev A, Guo S, Sherwood CC, Camp JG, Pääbo S, Treutlein B, Khaitovich P. Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains. Genome Res 2020; 30:776-789. [PMID: 32424074 PMCID: PMC7263190 DOI: 10.1101/gr.256958.119] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [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: 09/10/2019] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
Identification of gene expression traits unique to the human brain sheds light on the molecular mechanisms underlying human evolution. Here, we searched for uniquely human gene expression traits by analyzing 422 brain samples from humans, chimpanzees, bonobos, and macaques representing 33 anatomical regions, as well as 88,047 cell nuclei composing three of these regions. Among 33 regions, cerebral cortex areas, hypothalamus, and cerebellar gray and white matter evolved rapidly in humans. At the cellular level, astrocytes and oligodendrocyte progenitors displayed more differences in the human evolutionary lineage than the neurons. Comparison of the bulk tissue and single-nuclei sequencing revealed that conventional RNA sequencing did not detect up to two-thirds of cell-type-specific evolutionary differences.
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Affiliation(s)
| | - Ilia Kurochkin
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Dingding Han
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Patricia Guijarro
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Malgorzata Santel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Zhengzong Qian
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Shen Rong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Pavel Mazin
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Marat Sabirov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Matvei Bulat
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Olga Efimova
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Anna Tkachev
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Song Guo
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology, Basel, 4057, Switzerland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology in Zurich, Basel, 4058, Switzerland
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China.,Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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Kyrchanova O, Wolle D, Sabirov M, Kurbidaeva A, Aoki T, Maksimenko O, Kyrchanova M, Georgiev P, Schedl P. Distinct Elements Confer the Blocking and Bypass Functions of the Bithorax Fab-8 Boundary. Genetics 2019; 213:865-876. [PMID: 31551239 PMCID: PMC6827379 DOI: 10.1534/genetics.119.302694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 07/24/2019] [Accepted: 09/12/2019] [Indexed: 01/05/2023] Open
Abstract
Boundaries in the Drosophila bithorax complex (BX-C) enable the regulatory domains that drive parasegment-specific expression of the three Hox genes to function autonomously. The four regulatory domains (iab-5, iab-6, iab-7, and iab-8) that control the expression of the Abdominal-B (Abd-B) gene are located downstream of the transcription unit, and are delimited by the Mcp, Fab-6, Fab-7, and Fab-8 boundaries. These boundaries function to block cross talk between neighboring regulatory domains. In addition, three of the boundaries (Fab-6, Fab-7, and Fab-8) must also have bypass activity so that regulatory domains distal to the boundaries can contact the Abd-B promoter. In the studies reported here, we have undertaken a functional dissection of the Fab-8 boundary using a boundary-replacement strategy. Our studies indicate that the Fab-8 boundary has two separable subelements. The distal subelement blocks cross talk, but cannot support bypass. The proximal subelement has only minimal blocking activity but is able to mediate bypass. A large multiprotein complex, the LBC (large boundary complex), binds to sequences in the proximal subelement and contributes to its bypass activity. The same LBC complex has been implicated in the bypass activity of the Fab-7 boundary.
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Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Daniel Wolle
- Department of Molecular Biology, Princeton University, New Jersey 08544
| | - Marat Sabirov
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Amina Kurbidaeva
- Department of Molecular Biology, Princeton University, New Jersey 08544
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, New Jersey 08544
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, New Jersey 08544
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
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Kyrchanova O, Kurbidaeva A, Sabirov M, Postika N, Wolle D, Aoki T, Maksimenko O, Mogila V, Schedl P, Georgiev P. The bithorax complex iab-7 Polycomb response element has a novel role in the functioning of the Fab-7 chromatin boundary. PLoS Genet 2018; 14:e1007442. [PMID: 30110328 PMCID: PMC6110506 DOI: 10.1371/journal.pgen.1007442] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/27/2018] [Accepted: 07/30/2018] [Indexed: 12/22/2022] Open
Abstract
Expression of the three bithorax complex homeotic genes is orchestrated by nine parasegment-specific regulatory domains. Autonomy of each domain is conferred by boundary elements (insulators). Here, we have used an in situ replacement strategy to reanalyze the sequences required for the functioning of one of the best-characterized fly boundaries, Fab-7. It was initially identified by a deletion, Fab-71, that transformed parasegment (PS) 11 into a duplicate copy of PS12. Fab-71 deleted four nuclease hypersensitive sites, HS*, HS1, HS2, and HS3, located between the iab-6 and iab-7 regulatory domains. Transgenic and P-element excision experiments mapped the boundary to HS*+HS1+HS2, while HS3 was shown to be the iab-7 Polycomb response element (PRE). Recent replacement experiments showed that HS1 is both necessary and sufficient for boundary activity when HS3 is also present in the replacement construct. Surprisingly, while HS1+HS3 combination has full boundary activity, we discovered that HS1 alone has only minimal function. Moreover, when combined with HS3, only the distal half of HS1, dHS1, is needed. A ~1,000 kD multiprotein complex containing the GAF protein, called the LBC, binds to the dHS1 sequence and we show that mutations in dHS1, that disrupt LBC binding in nuclear extracts, eliminate boundary activity and GAF binding in vivo. HS3 has binding sites for GAF and Pho proteins that are required for PRE silencing. In contrast, HS3 boundary activity only requires the GAF binding sites. LBC binding with HS3 in nuclear extracts, and GAF association in vivo, depend upon the HS3 GAF sites, but not the Pho sites. Consistent with a role for the LBC in HS3 boundary activity, the boundary function of the dHS1+HS3mPho combination is lost when the flies are heterozygous for a mutation in the GAF gene. Taken together, these results reveal a novel function for the iab-7 PREs in chromosome architecture. Polycomb group proteins (PcG) are important epigenetic regulators of developmental genes in all higher eukaryotes. In Drosophila, these proteins are bound to specific regulatory DNA elements called Polycomb group Response Elements (PREs). Drosophila PREs are made up of binding sites for a complex array of DNA binding proteins, including GAF and Pho. In the regulatory region of the bithorax complex (BX-C), the boundary/insulator elements organize the autonomous regulatory domains, and their active or repressed states are regulated by PREs. Here, we studied functional properties of sequences that constitute the Fab-7 boundary and the adjacent iab-7 PRE. It was previously thought that the sole function of the iab-7 PRE is to recruit PcG proteins in parasegments anterior to PS12 and silence the iab-7 domain. However, we found that the iab-7 PRE also functions as a component of the Fab-7 boundary. The boundary activity of the iab-7 PRE sequence depends upon a large complex called the LBC. We show that it is possible to reconstitute a fully functional boundary by combining the LBC binding sequences in HS1 with the iab-7 PRE. Moreover, its boundary function is independent of its PcG silencing activity.
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Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Amina Kurbidaeva
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Marat Sabirov
- Group of Molecular Organization of Genome, Institute of Gene Biology, Russian Acsademy of Sciences, Moscow, Russia
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Wolle
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Oksana Maksimenko
- Group of Molecular Organization of Genome, Institute of Gene Biology, Russian Acsademy of Sciences, Moscow, Russia
| | - Vladic Mogila
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
- * E-mail: (PS); (PG)
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (PS); (PG)
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