1
|
Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Protein arginine methyltransferase 1, a major regulator of biological processes. Biochem Cell Biol 2024; 102:106-126. [PMID: 37922507 DOI: 10.1139/bcb-2023-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.
Collapse
Affiliation(s)
- Sadhana R N Sudhakar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Shahper N Khan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ariel Clark
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | | | - Shrinal Patel
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ted M Lakowski
- College of Pharmacy Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| |
Collapse
|
2
|
Beacon TH, Davie JR. Chicken Erythrocyte: Epigenomic Regulation of Gene Activity. Int J Mol Sci 2023; 24:ijms24098287. [PMID: 37175991 PMCID: PMC10179511 DOI: 10.3390/ijms24098287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The chicken genome is one-third the size of the human genome and has a similarity of sixty percent when it comes to gene content. Harboring similar genome sequences, chickens' gene arrangement is closer to the human genomic organization than it is to rodents. Chickens have been used as model organisms to study evolution, epigenome, and diseases. The chicken nucleated erythrocyte's physiological function is to carry oxygen to the tissues and remove carbon dioxide. The erythrocyte also supports the innate immune response in protecting the chicken from pathogens. Among the highly studied aspects in the field of epigenetics are modifications of DNA, histones, and their variants. In understanding the organization of transcriptionally active chromatin, studies on the chicken nucleated erythrocyte have been important. Through the application of a variety of epigenomic approaches, we and others have determined the chromatin structure of expressed/poised genes involved in the physiological functions of the erythrocyte. As the chicken erythrocyte has a nucleus and is readily isolated from the animal, the chicken erythrocyte epigenome has been studied as a biomarker of an animal's long-term exposure to stress. In this review, epigenomic features that allow erythroid gene expression in a highly repressive chromatin background are presented.
Collapse
Affiliation(s)
- Tasnim H Beacon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| |
Collapse
|
3
|
Razin SV, Ioudinkova ES, Kantidze OL, Iarovaia OV. Co-Regulated Genes and Gene Clusters. Genes (Basel) 2021; 12:907. [PMID: 34208174 PMCID: PMC8230824 DOI: 10.3390/genes12060907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
Collapse
Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena S. Ioudinkova
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Omar L. Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Olga V. Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| |
Collapse
|
4
|
Abstract
The chicken model organism has advanced the areas of developmental biology, virology, immunology, oncology, epigenetic regulation of gene expression, conservation biology, and genomics of domestication. Further, the chicken model organism has aided in our understanding of human disease. Through the recent advances in high-throughput sequencing and bioinformatic tools, researchers have successfully identified sequences in the chicken genome that have human orthologs, improving mammalian genome annotation. In this review, we highlight the importance of chicken as an animal model in basic and pre-clinical research. We will present the importance of chicken in poultry epigenetics and in genomic studies that trace back to their ancestor, the last link between human and chicken in the tree of life. There are still many genes of unknown function in the chicken genome yet to be characterized. By taking advantage of recent sequencing technologies, it is possible to gain further insight into the chicken epigenome.
Collapse
Affiliation(s)
- Tasnim H Beacon
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| |
Collapse
|
5
|
Hoffmann FG, Vandewege MW, Storz JF, Opazo JC. Gene Turnover and Diversification of the α- and β-Globin Gene Families in Sauropsid Vertebrates. Genome Biol Evol 2018; 10:344-358. [PMID: 29340581 PMCID: PMC5786229 DOI: 10.1093/gbe/evy001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2018] [Indexed: 11/24/2022] Open
Abstract
The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globin genes that diversified independently in each lineage. These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.
Collapse
Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | | | - Jay F Storz
- School of Biological Sciences, University of Nebraska
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| |
Collapse
|
6
|
Diepstraten ST, Hart AH. Modelling human haemoglobin switching. Blood Rev 2018; 33:11-23. [PMID: 30616747 DOI: 10.1016/j.blre.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Genetic lesions of the β-globin gene result in haemoglobinopathies such as β-thalassemia and sickle cell disease. To discover and test new molecular medicines for β-haemoglobinopathies, cell-based and animal models are now being widely utilised. However, multiple in vitro and in vivo models are required due to the complex structure and regulatory mechanisms of the human globin gene locus, subtle species-specific differences in blood cell development, and the influence of epigenetic factors. Advances in genome sequencing, gene editing, and precision medicine have enabled the first generation of molecular therapies aimed at reactivating, repairing, or replacing silenced or damaged globin genes. Here we compare and contrast current animal and cell-based models, highlighting their complementary strengths, reflecting on how they have informed the scope and direction of the field, and describing some of the novel molecular and precision medicines currently under development or in clinical trial.
Collapse
Affiliation(s)
- Sarah T Diepstraten
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Adam H Hart
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
| |
Collapse
|
7
|
Kovina AP, Petrova NV, Gushchanskaya ES, Dolgushin KV, Gerasimov ES, Galitsyna AA, Penin AA, Flyamer IM, Ioudinkova ES, Gavrilov AA, Vassetzky YS, Ulianov SV, Iarovaia OV, Razin SV. Evolution of the Genome 3D Organization: Comparison of Fused and Segregated Globin Gene Clusters. Mol Biol Evol 2017; 34:1492-1504. [DOI: 10.1093/molbev/msx100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
8
|
Razin SV, Gavrilov AA, Kos P, Ulianov SV. Self-organization of a chromatin fibril into topologically-associated domains. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
3D genomics imposes evolution of the domain model of eukaryotic genome organization. Chromosoma 2016; 126:59-69. [DOI: 10.1007/s00412-016-0604-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/11/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
|
10
|
Nefedochkina AV, Petrova NV, Ioudinkova ES, Kovina AP, Iarovaia OV, Razin SV. Characterization of the enhancer element of the Danio rerio minor globin gene locus. Histochem Cell Biol 2016; 145:463-73. [PMID: 26847176 DOI: 10.1007/s00418-016-1413-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2016] [Indexed: 12/23/2022]
Abstract
In Danio rerio, the alpha- and beta-globin genes are present in two clusters: a major cluster located on chromosome 3 and a minor cluster located on chromosome 12. In contrast to the segregated alpha- and beta-globin gene domains of warm-blooded animals, in Danio rerio, each cluster contains both alpha- and beta-globin genes. Expression of globin genes present in the major cluster is controlled by an erythroid-specific enhancer similar to the major regulatory element of mammalian and avian alpha-globin gene domains. The enhancer controlling expression of the globin genes present in the minor locus has not been identified yet. Based on the distribution of epigenetic marks, we have selected two genomic regions that might harbor an enhancer of the minor locus. Using transient transfection of constructs with a reporter gene, we have demonstrated that a ~500-bp DNA fragment located ~1.7 Kb upstream of the αe4 gene possesses an erythroid-specific enhancer active with respect to promoters present in both the major and the minor globin gene loci of Danio rerio. The identified enhancer element harbors clustered binding sites for GATA-1, NF-E2, and EKLF similar to the enhancer of the major globin locus on chromosome 3. Both enhancers appear to have emerged as a result of independent evolution of a duplicated regulatory element present in an ancestral single alpha-/beta-globin locus that existed before teleost-specific genome duplication.
Collapse
Affiliation(s)
- Anastasia V Nefedochkina
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334.,Molecular Biology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Natalia V Petrova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334
| | - Elena S Ioudinkova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334
| | - Anastasia P Kovina
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334.,Molecular Biology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Olga V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow, Russia, 119334. .,Molecular Biology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia, 119992.
| |
Collapse
|
11
|
Dolgushin KV, Iudinkova ES, Petrova NV, Razin SV, Iarovaia OV. Joint locus of a/b-globin genes in Danio rerio is segregated into structural subdomains active at different stages of development. Mol Biol 2015. [DOI: 10.1134/s0026893315030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
14
|
Iarovaia OV, Ioudinkova ES, Petrova NV, Dolgushin KV, Kovina AV, Nefedochkina AV, Vassetzky YS, Razin SV. Evolution of α- and β-globin genes and their regulatory systems in light of the hypothesis of domain organization of the genome. BIOCHEMISTRY (MOSCOW) 2014; 79:1141-50. [PMID: 25539999 DOI: 10.1134/s0006297914110017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The α- and β-globin gene domains are a traditional model for study of the domain organization of the eucaryotic genome because these genes encode hemoglobin, a physiologically important protein. The α-globin and β-globin gene domains are organized in completely different ways, while the expression of globin genes is tightly coordinated, which makes it extremely interesting to study the origin of these genes and the evolution of their regulatory systems. In this review, the organization of the α- and β-globin gene domains and their genomic environment in different taxonomic groups are comparatively analyzed. A new hypothesis of possible evolutionary pathways for segregated α- and β-globin gene domains of warm-blooded animals is proposed.
Collapse
Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Gushchanskaya ES, Artemov AV, Ulyanov SV, Logacheva MD, Penin AA, Kotova ES, Akopov SB, Nikolaev LG, Iarovaia OV, Sverdlov ED, Gavrilov AA, Razin SV. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes. Epigenetics 2014; 9:951-63. [PMID: 24736527 DOI: 10.4161/epi.28794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments.
Collapse
Affiliation(s)
- Ekaterina S Gushchanskaya
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Molecular Biology; Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Artem V Artemov
- Faculty of Bioengineering and Bioinformatics; Lomonosov Moscow State University; Moscow, Russia; Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow, Russia
| | - Sergey V Ulyanov
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Maria D Logacheva
- Laboratory of Evolutionary Genomics; Lomonosov Moscow State University; Moscow, Russia
| | - Aleksey A Penin
- Laboratory of Evolutionary Genomics; Lomonosov Moscow State University; Moscow, Russia
| | - Elena S Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Sergey B Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Lev G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Olga V Iarovaia
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Eugene D Sverdlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Molecular Biology; Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| |
Collapse
|