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Kashkin KN, Kotova ES, Alekseenko IV, Bulanenkova SS, Akopov SB, Kopantzev EP, Nikolaev LG, Chernov IP, Didych DA. Efficient Selection of Enhancers and Promoters from MIA PaCa-2 Pancreatic Cancer Cells by ChIP-lentiMPRA. Int J Mol Sci 2022; 23:ijms232315011. [PMID: 36499347 PMCID: PMC9740945 DOI: 10.3390/ijms232315011] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
A library of active genome regulatory elements (putative promoters and enhancers) from MIA PaCa-2 pancreatic adenocarcinoma cells was constructed using a specially designed lentiviral vector and a massive parallel reporter assay (ChIP-lentiMPRA). Chromatin immunoprecipitation of the cell genomic DNA by H3K27ac antibodies was used for primary enrichment of the library for regulatory elements. Totally, 11,264 unique genome regions, many of which are capable of enhancing the expression of the CopGFP reporter gene from the minimal CMV promoter, were identified. The regions tend to be located near promoters. Based on the proximity assay, we found an enrichment of highly expressed genes among those associated with three or more mapped distal regions (2 kb distant from the 5'-ends of genes). It was shown significant enrichment of genes related to carcinogenesis or Mia PaCa-2 cell identity genes in this group. In contrast, genes associated with 1-2 distal regions or only with proximal regions (within 2 kbp of the 5'-ends of genes) are more often related to housekeeping functions. Thus, ChIP-lentiMPRA is a useful strategy for creating libraries of regulatory elements for the study of tumor-specific gene transcription.
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Affiliation(s)
- Kirill Nikitich Kashkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Elena Sergeevna Kotova
- Laboratory of Human Molecular Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Street, 1a, 119435 Moscow, Russia
| | - Irina Vasilievna Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Svetlana Sergeevna Bulanenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Sergey Borisovich Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Eugene Pavlovich Kopantzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Lev Grigorievich Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Igor Pavlovich Chernov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Dmitry Alexandrovich Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-919-777-4620
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Gadaev IY, Ershov VI, Bochkarnikova OV, Sokolova IY, Budanova DA, Kotova ES, Lishuta AS. [LISHUTA EXTRANODAL INVOLVEMENT OF THE HEART IN LYMPHOMAS: A CLINICAL CASE OF LARGE B-CELL LYMPHOMA AND LITERATURE REVIEW]. Klin Med (Mosk) 2016; 94:780-784. [PMID: 30299043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The authors report a case of rare cardiac involvement in lymphoma, one of the manifestations of which was rhythm and conduction disorders with their resolution after chemotherapy. Also presented are clinical manifestations of heart lesions in lymphoma and modern methods of their diagnostics and treatment.
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Kotova ES, Sorokina IV, Akopov SB, Nikolaev LG, Sverdlov ED. Expression of chicken CTCF gene in COS-1 cells and partial purification of CTCF protein. Biochemistry (Mosc) 2014; 78:879-83. [PMID: 24228875 DOI: 10.1134/s0006297913080038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The chicken gene for transcription factor CTCF was expressed in COS-1 mammalian cells. The CTCF protein containing polyhistidine tag was partially purified using metallo-affinity and ion-exchange chromatography. The expressed protein localized in the cell nucleus and was shown to be functionally active in the electrophoretic mobility shift assay and specifically interacted with anti-CTCF antibodies.
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Affiliation(s)
- E S Kotova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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Didych DA, Smirnov NA, Kotova ES, Akopov SB, Nikolaev LG, Sverdlov ED. Functional dissection of an enhancer-like element located within the second intron of the human U2AF1L4 gene. Biochemistry (Mosc) 2011; 76:951-7. [PMID: 22022969 DOI: 10.1134/s0006297911080116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A detailed functional and evolutionary analysis of an enhancer element of the human genome (enhancer 12) located in the second intron of the U2AF1L4 gene, which we identified earlier, is presented. Overlapping fragments of the studied genome region were analyzed for enhancer activity, and the site responsible for the activity of this element was identified using transient transfections of HeLa cells. Comparison of the enhancer 12 sequence with orthologous sequences from seven primate species revealed the existence of evolutionarily conserved sequences within this element. One of the identified conservative regions is likely responsible for the enhancer activity and is able to specifically interact in vitro with proteins of HeLa cell nuclear extract. The ability of orthologous primate sequences to compete with enhancer 12 for binding with HeLa cell nuclear extract proteins and to enhance the activity of the reporter gene in transient transfection of HeLa cells is demonstrated.
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Affiliation(s)
- D A Didych
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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Gus'kova AK, Ponizovskaya AI, Denisova EA, Volkovitskaya VV, L'vovskaya EN, Kotova ES, Gribova IA. Working conditions and health of workers at United Institute of Nuclear Research. Fed Proc Transl Suppl 1966; 25:1063-5. [PMID: 5225269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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