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Iarovaia OV, Ulianov SV, Ioudinkova ES, Razin SV. Segregation of α- and β-Globin Gene Cluster in Vertebrate Evolution: Chance or Necessity? BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1035-1049. [PMID: 36180994 DOI: 10.1134/s0006297922090140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
The review is devoted to the patterns of evolution of α- and β-globin gene domains. A hypothesis is presented according to which segregation of the ancestral cluster of α/β-globin genes in Amniota occurred due to the performance by α-globins and β-globins of non-canonical functions not related to oxygen transport.
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Affiliation(s)
- Olga V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Elena S Ioudinkova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez Granados NY, Kim S, Blein T, Duncan S, Pichot C, Manza-Mianza D, Juery C, Paux E, Moore G, Hirt H, Bergounioux C, Crespi M, Mahfouz MM, Bendahmane A, Liu C, Hall A, Raynaud C, Latrasse D, Benhamed M. Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol 2020; 21:104. [PMID: 32349780 PMCID: PMC7189446 DOI: 10.1186/s13059-020-01998-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/12/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures. RESULTS We examine the hexaploid wheat nuclear architecture by integrating RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Hi-ChIP data. Our results highlight the presence of three levels of large-scale spatial organization: the arrangement into genome territories, the diametrical separation between facultative and constitutive heterochromatin, and the organization of RNA polymerase II around transcription factories. We demonstrate the micro-compartmentalization of transcriptionally active genes determined by physical interactions between genes with specific euchromatic histone modifications. Both intra- and interchromosomal RNA polymerase-associated contacts involve multiple genes displaying similar expression levels. CONCLUSIONS Our results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
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Affiliation(s)
- Lorenzo Concia
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan S Ramirez-Prado
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | | | - Ying Huang
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Magali Perez
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Severine Domenichini
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | | | - Soonkap Kim
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Thomas Blein
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Susan Duncan
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, UK
| | - Clement Pichot
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Caroline Juery
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Etienne Paux
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Heribert Hirt
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, UK
| | - Cécile Raynaud
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France.
- Institut Universitaire de France (IUF), Paris, France.
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Jahan S, Beacon TH, He S, Gonzalez C, Xu W, Delcuve GP, Jia S, Hu P, Davie JR. Chromatin organization of transcribed genes in chicken polychromatic erythrocytes. Gene 2019; 699:80-87. [DOI: 10.1016/j.gene.2019.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
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Iarovaia OV, Kovina AP, Petrova NV, Razin SV, Ioudinkova ES, Vassetzky YS, Ulianov SV. Genetic and Epigenetic Mechanisms of β-Globin Gene Switching. BIOCHEMISTRY (MOSCOW) 2018; 83:381-392. [PMID: 29626925 DOI: 10.1134/s0006297918040090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vertebrates have multiple forms of hemoglobin that differ in the composition of their polypeptide chains. During ontogenesis, the composition of these subunits changes. Genes encoding different α- and β-polypeptide chains are located in two multigene clusters on different chromosomes. Each cluster contains several genes that are expressed at different stages of ontogenesis. The phenomenon of stage-specific transcription of globin genes is referred to as globin gene switching. Mechanisms of expression switching, stage-specific activation, and repression of transcription of α- and β-globin genes are of interest from both theoretical and practical points of view. Alteration of balanced expression of globin genes, which usually occurs due to damage to adult β-globin genes, leads to development of severe diseases - hemoglobinopathies. In most cases, reactivation of the fetal hemoglobin gene in patients with β-thalassemia and sickle cell disease can reduce negative consequences of irreversible alterations of expression of the β-globin genes. This review focuses on the current state of research on genetic and epigenetic mechanisms underlying stage-specific switching of β-globin genes.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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Razin SV, Ulianov SV. Gene functioning and storage within a folded genome. Cell Mol Biol Lett 2017; 22:18. [PMID: 28861108 PMCID: PMC5575855 DOI: 10.1186/s11658-017-0050-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/24/2017] [Indexed: 01/28/2023] Open
Abstract
In mammals, genomic DNA that is roughly 2 m long is folded to fit the size of the cell nucleus that has a diameter of about 10 μm. The folding of genomic DNA is mediated via assembly of DNA-protein complex, chromatin. In addition to the reduction of genomic DNA linear dimensions, the assembly of chromatin allows to discriminate and to mark active (transcribed) and repressed (non-transcribed) genes. Consequently, epigenetic regulation of gene expression occurs at the level of DNA packaging in chromatin. Taking into account the increasing attention of scientific community toward epigenetic systems of gene regulation, it is very important to understand how DNA folding in chromatin is related to gene activity. For many years the hierarchical model of DNA folding was the most popular. It was assumed that nucleosome fiber (10-nm fiber) is folded into 30-nm fiber and further on into chromatin loops attached to a nuclear/chromosome scaffold. Recent studies have demonstrated that there is much less regularity in chromatin folding within the cell nucleus. The very existence of 30-nm chromatin fibers in living cells was questioned. On the other hand, it was found that chromosomes are partitioned into self-interacting spatial domains that restrict the area of enhancers action. Thus, TADs can be considered as structural-functional domains of the chromosomes. Here we discuss the modern view of DNA packaging within the cell nucleus in relation to the regulation of gene expression. Special attention is paid to the possible mechanisms of the chromatin fiber self-assembly into TADs. We discuss the model postulating that partitioning of the chromosome into TADs is determined by the distribution of active and inactive chromatin segments along the chromosome. This article was specially invited by the editors and represents work by leading researchers.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
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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] [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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Ioudinkova ES, Nefedochkina AV, Iarovaia OV, Razin SV. Detection of complementary transcripts for the intergenic region of the chicken α-globin gene domain. Mol Biol 2015. [DOI: 10.1134/s0026893315060229] [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]
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8
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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]
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Quaye IK. Extracellular hemoglobin: the case of a friend turned foe. Front Physiol 2015; 6:96. [PMID: 25941490 PMCID: PMC4403290 DOI: 10.3389/fphys.2015.00096] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/12/2015] [Indexed: 12/14/2022] Open
Abstract
Hemoglobin (Hb) is a highly conserved molecule present in all life forms and functionally tied to the complexity of aerobic organisms on earth in utilizing oxygen from the atmosphere and delivering to cells and tissues. This primary function sustains the energy requirements of cells and maintains cellular homeostasis. Decades of intensive research has presented a paradigm shift that shows how the molecule also functions to facilitate smooth oxygen delivery through the cardiovascular system for cellular bioenergetic homeostasis and signaling for cell function and defense. These roles are particularly highlighted in the binding of Hb to gaseous molecules carbon dioxide (CO2), nitric oxide (NO) and carbon monoxide (CO), while also serving indirectly or directly as sources of these signaling molecules. The functional activities impacted by Hb outside of bioenergetics homeostasis, include fertilization, signaling functions, modulation of inflammatory responses for defense and cell viability. These activities are efficiently executed while Hb is sequestered safely within the confines of the red blood cell (rbc). Outside of rbc confines, Hb disaggregates and becomes a danger molecule to cell survival. In these perpectives, Hb function is broadly dichotomous, either a friend in its natural environment providing and facilitating the means for cell function or foe when dislocated from its habitat under stress or pathological condition disrupting cell function. The review presents insights into how this dichotomy in function manifests.
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Affiliation(s)
- Isaac K Quaye
- Department of Biochemistry, University of Namibia School of Medicine Windhoek, Namibia
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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.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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