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Mao Y, Peng T, Shao F, Zhao Q, Peng Z. Molecular evolution of the hemoglobin gene family across vertebrates. Genetica 2023:10.1007/s10709-023-00187-9. [PMID: 37069365 DOI: 10.1007/s10709-023-00187-9] [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: 09/02/2022] [Accepted: 04/11/2023] [Indexed: 04/19/2023]
Abstract
Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α2β2) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean dN/dS (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.
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Affiliation(s)
- Yang Mao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
- Clinical Research Center, The Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China
| | - Taotao Peng
- Department of Anesthesiology, Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China.
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2
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Zhao X, Huang Y, Bian C, You X, Zhang X, Chen J, Wang M, Hu C, Xu Y, Xu J, Shi Q. Whole genome sequencing of the fast-swimming Southern bluefin tuna ( Thunnus maccoyii). Front Genet 2022; 13:1020017. [PMID: 36406129 PMCID: PMC9670116 DOI: 10.3389/fgene.2022.1020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/21/2022] [Indexed: 09/08/2024] Open
Abstract
The economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative functional prediction. The final genome assembly is 806.54 Mb, with scaffold and contig N50 values of 3.31 Mb and 67.38 kb, respectively. Genome completeness was evaluated to be 95.8%. The assembled genome contained 23,403 protein-coding genes and 236.1 Mb of repeat sequences (accounting for 29.27% of the entire assembly). Comparative genomics analyses of this fast-swimming tuna revealed that it had more than twice as many hemoglobin genes (18) as other relatively slow-moving fishes (such as seahorse, sunfish, and tongue sole). These hemoglobin genes are mainly localized in two big clusters (termed as "MNˮ and "LAˮ respectively), which is consistent with other reported fishes. However, Thr39 of beta-hemoglobin in the MN cluster, conserved in other fishes, was mutated as cysteine in tunas including the Southern bluefin tuna. Since hemoglobins are reported to transport oxygen efficiently for aerobic respiration, our genomic data suggest that both high copy numbers of hemoglobin genes and an adjusted function of the beta-hemoglobin may support the fast-swimming activity of tunas. In summary, we produced a primary genome assembly and predicted hemoglobin-related roles for the fast-swimming Southern bluefin tuna.
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Affiliation(s)
- Xiaomeng Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Aquatic Breeding Center, BGI Marine, Shenzhen, China
| | - Xinhui Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Aquatic Breeding Center, BGI Marine, Shenzhen, China
| | - Jieming Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Min Wang
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Cancan Hu
- Aquatic Breeding Center, BGI Marine, Shenzhen, China
| | - Yun Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Aquatic Breeding Center, BGI Marine, Shenzhen, China
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Aquatic Breeding Center, BGI Marine, Shenzhen, China
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Aquatic Breeding Center, BGI Marine, Shenzhen, China
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3
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Mussolino C, Strouboulis J. Recent Approaches for Manipulating Globin Gene Expression in Treating Hemoglobinopathies. Front Genome Ed 2021; 3:618111. [PMID: 34713248 PMCID: PMC8525358 DOI: 10.3389/fgeed.2021.618111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Tissue oxygenation throughout life depends on the activity of hemoglobin (Hb) one of the hemeproteins that binds oxygen in the lungs and secures its delivery throughout the body. Hb is composed of four monomers encoded by eight different genes the expression of which is tightly regulated during development, resulting in the formation of distinct hemoglobin tetramers in each developmental stage. Mutations that alter hemoglobin structure or its regulated expression result in a large group of diseases typically referred to as hemoglobinopathies that are amongst the most common genetic defects worldwide. Unprecedented efforts in the last decades have partially unraveled the complex mechanisms that control globin gene expression throughout development. In addition, genome wide association studies have revealed protective genetic traits capable of ameliorating the clinical manifestations of severe hemoglobinopathies. This knowledge has fueled the exploration of innovative therapeutic approaches aimed at modifying the genome or the epigenome of the affected cells to either restore hemoglobin function or to mimic the effect of protective traits. Here we describe the key steps that control the switch in gene expression that concerns the different globin genes during development and highlight the latest efforts in altering globin regulation for therapeutic purposes.
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Affiliation(s)
- Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - John Strouboulis
- Laboratory of Molecular Erythropoiesis, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
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4
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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.
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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.)
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5
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Correction of β-thalassemia by CRISPR/Cas9 editing of the α-globin locus in human hematopoietic stem cells. Blood Adv 2021; 5:1137-1153. [PMID: 33635334 DOI: 10.1182/bloodadvances.2020001996] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
β-thalassemias (β-thal) are a group of blood disorders caused by mutations in the β-globin gene (HBB) cluster. β-globin associates with α-globin to form adult hemoglobin (HbA, α2β2), the main oxygen-carrier in erythrocytes. When β-globin chains are absent or limiting, free α-globins precipitate and damage cell membranes, causing hemolysis and ineffective erythropoiesis. Clinical data show that severity of β-thal correlates with the number of inherited α-globin genes (HBA1 and HBA2), with α-globin gene deletions having a beneficial effect for patients. Here, we describe a novel strategy to treat β-thal based on genome editing of the α-globin locus in human hematopoietic stem/progenitor cells (HSPCs). Using CRISPR/Cas9, we combined 2 therapeutic approaches: (1) α-globin downregulation, by deleting the HBA2 gene to recreate an α-thalassemia trait, and (2) β-globin expression, by targeted integration of a β-globin transgene downstream the HBA2 promoter. First, we optimized the CRISPR/Cas9 strategy and corrected the pathological phenotype in a cellular model of β-thalassemia (human erythroid progenitor cell [HUDEP-2] β0). Then, we edited healthy donor HSPCs and demonstrated that they maintained long-term repopulation capacity and multipotency in xenotransplanted mice. To assess the clinical potential of this approach, we next edited β-thal HSPCs and achieved correction of α/β globin imbalance in HSPC-derived erythroblasts. As a safer option for clinical translation, we performed editing in HSPCs using Cas9 nickase showing precise editing with no InDels. Overall, we described an innovative CRISPR/Cas9 approach to improve α/β globin imbalance in thalassemic HSPCs, paving the way for novel therapeutic strategies for β-thal.
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6
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An evolutionarily ancient mechanism for regulation of hemoglobin expression in vertebrate red cells. Blood 2020; 136:269-278. [PMID: 32396940 DOI: 10.1182/blood.2020004826] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/23/2020] [Indexed: 11/20/2022] Open
Abstract
The oxygen transport function of hemoglobin (HB) is thought to have arisen ∼500 million years ago, roughly coinciding with the divergence between jawless (Agnatha) and jawed (Gnathostomata) vertebrates. Intriguingly, extant HBs of jawless and jawed vertebrates were shown to have evolved twice, and independently, from different ancestral globin proteins. This raises the question of whether erythroid-specific expression of HB also evolved twice independently. In all jawed vertebrates studied to date, one of the HB gene clusters is linked to the widely expressed NPRL3 gene. Here we show that the nprl3-linked hb locus of a jawless vertebrate, the river lamprey (Lampetra fluviatilis), shares a range of structural and functional properties with the equivalent jawed vertebrate HB locus. Functional analysis demonstrates that an erythroid-specific enhancer is located in intron 7 of lamprey nprl3, which corresponds to the NPRL3 intron 7 MCS-R1 enhancer of jawed vertebrates. Collectively, our findings signify the presence of an nprl3-linked multiglobin gene locus, which contains a remote enhancer that drives globin expression in erythroid cells, before the divergence of jawless and jawed vertebrates. Different globin genes from this ancestral cluster evolved in the current NPRL3-linked HB genes in jawless and jawed vertebrates. This provides an explanation of the enigma of how, in different species, globin genes linked to the same adjacent gene could undergo convergent evolution.
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7
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Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
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Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
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8
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Philipsen S, Hardison RC. Evolution of hemoglobin loci and their regulatory elements. Blood Cells Mol Dis 2018; 70:2-12. [PMID: 28811072 PMCID: PMC5807248 DOI: 10.1016/j.bcmd.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/13/2017] [Accepted: 08/03/2017] [Indexed: 11/21/2022]
Abstract
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene. Despite substantial divergence in noncoding DNA sequences among mammals, several epigenetic features of the globin gene regulatory regions are preserved across vertebrates. The preserved features include multiple DNase hypersensitive sites, at least one of which is an enhancer, and binding by key lineage-restricted transcription factors such as GATA1 and TAL1, which in turn recruit coactivators such as P300 that catalyze acetylation of histones. The maps of epigenetic features are strongly correlated with activity in gene regulation, and resources for accessing and visualizing such maps are readily available to the community of researchers and students.
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Affiliation(s)
- Sjaak Philipsen
- Department of Cell Biology Ee1071b, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.
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9
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Razin SV, Gavrilov AA. Structural–Functional Domains of the Eukaryotic Genome. BIOCHEMISTRY (MOSCOW) 2018; 83:302-312. [DOI: 10.1134/s0006297918040028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/27/2017] [Indexed: 08/30/2023]
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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] [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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Höglund J, Wang B, Saether SA, Blom MPK, Fiske P, Halvarsson P, Horsburgh GJ, Burke T, Kålås JA, Ekblom R. Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media). Mol Ecol 2017; 26:3458-3471. [PMID: 28345264 DOI: 10.1111/mec.14118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/07/2017] [Indexed: 11/30/2022]
Abstract
We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin α-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.
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Affiliation(s)
- Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Biao Wang
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Mozes Pil Kyu Blom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Peder Fiske
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Peter Halvarsson
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - John Atle Kålås
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Robert Ekblom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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12
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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
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13
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Kovina AP, Petrova NV, Razin SV, Yarovaia OV. Main regulatory element (MRE) of the Danio rerio α/β-globin gene domain exerts enhancer activity toward the promoters of the embryonic-larval and adult globin genes. Mol Biol 2016. [DOI: 10.1134/s002689331606011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Bagadia M, Singh A, Singh Sandhu K. Three Dimensional Organization of Genome Might Have Guided the Dynamics of Gene Order Evolution in Eukaryotes. Genome Biol Evol 2016; 8:946-54. [PMID: 26957031 PMCID: PMC4824123 DOI: 10.1093/gbe/evw050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In eukaryotes, genes are nonrandomly organized into short gene-dense regions or "gene-clusters" interspersed by long gene-poor regions. How these gene-clusters have evolved is not entirely clear. Gene duplication may not account for all the gene-clusters since the genes in most of the clusters do not exhibit significant sequence similarity. In this study, using genome-wide data sets from budding yeast, fruit-fly, and human, we show that: 1) long-range evolutionary repositioning of genes strongly associate with their spatial proximity in the nucleus; 2) presence of evolutionary DNA break-points at involved loci hints at their susceptibility to undergo long-range genomic rearrangements; and 3) correlated epigenetic and transcriptional states of engaged genes highlight the underlying evolutionary constraints. The significance of observation 1, 2, and 3 are particularly stronger for the instances of inferred evolutionary gain, as compared with loss, of linear gene-clustering. These observations suggest that the long-range genomic rearrangements guided through 3D genome organization might have contributed to the evolution of gene order. We further hypothesize that the evolution of linear gene-clusters in eukaryotic genomes might have been mediated through spatial interactions among distant loci in order to optimize co-ordinated regulation of genes. We model this hypothesis through a heuristic model of gene-order evolution.
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Affiliation(s)
- Meenakshi Bagadia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, SAS Nagar 140306, India
| | - Arashdeep Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, SAS Nagar 140306, India
| | - Kuljeet Singh Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, SAS Nagar 140306, India
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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.
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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.
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16
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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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17
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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.
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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
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Feng J, Liu S, Wang X, Wang R, Zhang J, Jiang Y, Li C, Kaltenboeck L, Li J, Liu Z. Channel catfish hemoglobin genes: Identification, phylogenetic and syntenic analysis, and specific induction in response to heat stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2014; 9:11-22. [DOI: 10.1016/j.cbd.2013.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/28/2023]
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Valdes-Quezada C, Arriaga-Canon C, Fonseca-Guzmán Y, Guerrero G, Recillas-Targa F. CTCF demarcates chicken embryonic α-globin gene autonomous silencing and contributes to adult stage-specific gene expression. Epigenetics 2013; 8:827-38. [PMID: 23880533 DOI: 10.4161/epi.25472] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Genomic loci composed of more than one gene are frequently subjected to differential gene expression, with the chicken α-globin domain being a clear example. In the present study we aim to understand the globin switching mechanisms responsible for the epigenetic silencing of the embryonic π gene and the transcriptional activation of the adult α(D) and α(A) genes at the genomic domain level. In early stages, we describe a physical contact between the embryonic π gene and the distal 3' enhancer that is lost later during development. We show that such a level of regulation is achieved through the establishment of a DNA hypermethylation sub-domain that includes the embryonic gene and the adjacent genomic sequences. The multifunctional CCCTCC-binding factor (CTCF), which is located upstream of the α(D) gene promoter, delimits this sub-domain and creates a transition between the inactive sub-domain and the active sub-domain, which includes the adult α(D) gene. In avian-transformed erythroblast HD3 cells that are induced to differentiate, we found active DNA demethylation of the adult α(D) promoter, coincident with the incorporation of 5-hydroxymethylcytosine (5hmC) and concomitant with adult gene transcriptional activation. These results suggest that autonomous silencing of the embryonic π gene is needed to facilitate an optimal topological conformation of the domain. This model proposes that CTCF is contributing to a specific chromatin configuration that is necessary for differential α-globin gene expression during development.
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Affiliation(s)
- Christian Valdes-Quezada
- Instituto de Fisiología Celular; Departamento de Genética Molecular; Universidad Nacional Autónoma de México; México D.F., México
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20
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Ioudinkova ES, Petrova NV, Bunina DA, Vishniakova HS, Sklyar IV, Razin SV, Iarovaia OV. Chromatin structure of the joint α/β-globin gene locus of Danio rerio. DOKL BIOCHEM BIOPHYS 2013; 448:59-61. [PMID: 23478991 DOI: 10.1134/s1607672913010171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Indexed: 11/23/2022]
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21
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Abstract
Insights into the evolution of hemoglobins and their genes are an abundant source of ideas regarding hemoglobin function and regulation of globin gene expression. This article presents the multiple genes and gene families encoding human globins, summarizes major events in the evolution of the hemoglobin gene clusters, and discusses how these studies provide insights into regulation of globin genes. Although the genes in and around the α-like globin gene complex are relatively stable, the β-like globin gene clusters are more dynamic, showing evidence of transposition to a new locus and frequent lineage-specific expansions and deletions. The cis-regulatory modules controlling levels and timing of gene expression are a mix of conserved and lineage-specific DNA, perhaps reflecting evolutionary constraint on core regulatory functions shared broadly in mammals and adaptive fine-tuning in different orders of mammals.
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Affiliation(s)
- Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institute of Genome Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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22
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Razin SV, Ulianov SV, Ioudinkova ES, Gushchanskaya ES, Gavrilov AA, Iarovaia OV. Domains of α- and β-globin genes in the context of the structural-functional organization of the eukaryotic genome. BIOCHEMISTRY (MOSCOW) 2012; 77:1409-1423. [DOI: 10.1134/s0006297912130019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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23
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Ioudinkova ES, Barat A, Pichugin A, Markova E, Sklyar I, Pirozhkova I, Robin C, Lipinski M, Ogryzko V, Vassetzky YS, Razin SV. Distinct distribution of ectopically expressed histone variants H2A.Bbd and MacroH2A in open and closed chromatin domains. PLoS One 2012; 7:e47157. [PMID: 23118866 PMCID: PMC3484066 DOI: 10.1371/journal.pone.0047157] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 09/13/2012] [Indexed: 12/12/2022] Open
Abstract
Background It becomes increasingly evident that nuclesomes are far from being identical to each other. This nucleosome diversity is due partially to the existence of histone variants encoded by separate genes. Among the known histone variants the less characterized are H2A.Bbd and different forms of macroH2A. This is especially true in the case of H2A.Bbd as there are still no commercially available antibodies specific to H2A.Bbd that can be used for chromatin immunoprecipitation (ChIP). Methods We have generated HeLa S3 cell lines stably expressing epitope-tagged versions of macroH2A1.1, H2A.Bbd or canonical H2A and analyzed genomic distribution of the tagged histones using ChIP-on-chip technique. Results The presence of histone H2A variants macroH2A1.1 and H2A.Bbd has been analyzed in the chromatin of several segments of human chromosomes 11, 16 and X that have been chosen for their different gene densities and chromatin status. Chromatin immunoprecipitation (ChIP) followed by hybridization with custom NimbleGene genomic microarrays demonstrated that in open chromatin domains containing tissue-specific along with housekeeping genes, the H2A.Bbd variant was preferentially associated with the body of a subset of transcribed genes. The macroH2A1.1 variant was virtually absent from some genes and underrepresented in others. In contrast, in closed chromatin domains which contain only tissue-specific genes inactive in HeLa S3 cells, both macroH2A1.1 and H2A.Bbd histone variants were present and often colocalized. Conclusions Genomic distribution of macro H2A and H2A.Bbd does not follow any simple rule and is drastically different in open and closed genomic domains.
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Affiliation(s)
- Elena S. Ioudinkova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Ana Barat
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- The Centre for Scientific Computing & Complex Systems Modelling (SCI-SYM), School of Computing, Dublin City University, Dublin, Ireland
| | - Andrey Pichugin
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Elena Markova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Ilya Sklyar
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Iryna Pirozhkova
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Chloe Robin
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Marc Lipinski
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Vasily Ogryzko
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
| | - Yegor S. Vassetzky
- CNRS UMR 8126, Univ. Paris-Sud 11, Institut de cancérologie Gustave Roussy, Villejuif, France
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
- * E-mail:
| | - Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- LIA1066, Laboratoire Franco-Russe de recherches en oncologie, Villejuif, France
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Opazo JC, Butts GT, Nery MF, Storz JF, Hoffmann FG. Whole-genome duplication and the functional diversification of teleost fish hemoglobins. Mol Biol Evol 2012; 30:140-53. [PMID: 22949522 PMCID: PMC3525417 DOI: 10.1093/molbev/mss212] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Subsequent to the two rounds of whole-genome duplication that occurred in the common
ancestor of vertebrates, a third genome duplication occurred in the stem lineage of
teleost fishes. This teleost-specific genome duplication (TGD) is thought to have provided
genetic raw materials for the physiological, morphological, and behavioral diversification
of this highly speciose group. The extreme physiological versatility of teleost fish is
manifest in their diversity of blood–gas transport traits, which reflects the myriad
solutions that have evolved to maintain tissue O2 delivery in the face of
changing metabolic demands and environmental O2 availability during different
ontogenetic stages. During the course of development, regulatory changes in
blood–O2 transport are mediated by the expression of multiple,
functionally distinct hemoglobin (Hb) isoforms that meet the particular
O2-transport challenges encountered by the developing embryo or fetus (in
viviparous or oviparous species) and in free-swimming larvae and adults. The main
objective of the present study was to assess the relative contributions of whole-genome
duplication, large-scale segmental duplication, and small-scale gene duplication in
producing the extraordinary functional diversity of teleost Hbs. To accomplish this, we
integrated phylogenetic reconstructions with analyses of conserved synteny to characterize
the genomic organization and evolutionary history of the globin gene clusters of teleosts.
These results were then integrated with available experimental data on functional
properties and developmental patterns of stage-specific gene expression. Our results
indicate that multiple α- and β-globin genes
were present in the common ancestor of gars (order Lepisoteiformes) and teleosts. The
comparative genomic analysis revealed that teleosts possess a dual set of TGD-derived
globin gene clusters, each of which has undergone lineage-specific changes in gene content
via repeated duplication and deletion events. Phylogenetic reconstructions revealed that
paralogous genes convergently evolved similar functional properties in different teleost
lineages. Consistent with other recent studies of globin gene family evolution in
vertebrates, our results revealed evidence for repeated evolutionary transitions in the
developmental regulation of Hb synthesis.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Ganis JJ, Hsia N, Trompouki E, de Jong JLO, DiBiase A, Lambert JS, Jia Z, Sabo PJ, Weaver M, Sandstrom R, Stamatoyannopoulos JA, Zhou Y, Zon LI. Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. Dev Biol 2012; 366:185-94. [PMID: 22537494 DOI: 10.1016/j.ydbio.2012.03.021] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 02/20/2012] [Accepted: 03/19/2012] [Indexed: 02/02/2023]
Abstract
Globin gene switching is a complex, highly regulated process allowing expression of distinct globin genes at specific developmental stages. Here, for the first time, we have characterized all of the zebrafish globins based on the completed genomic sequence. Two distinct chromosomal loci, termed major (chromosome 3) and minor (chromosome 12), harbor the globin genes containing α/β pairs in a 5'-3' to 3'-5' orientation. Both these loci share synteny with the mammalian α-globin locus. Zebrafish globin expression was assayed during development and demonstrated two globin switches, similar to human development. A conserved regulatory element, the locus control region (LCR), was revealed by analyzing DNase I hypersensitive sites, H3K4 trimethylation marks and GATA1 binding sites. Surprisingly, the position of these sites with relation to the globin genes is evolutionarily conserved, despite a lack of overall sequence conservation. Motifs within the zebrafish LCR include CACCC, GATA, and NFE2 sites, suggesting functional interactions with known transcription factors but not the same LCR architecture. Functional homology to the mammalian α-LCR MCS-R2 region was confirmed by robust and specific reporter expression in erythrocytes of transgenic zebrafish. Our studies provide a comprehensive characterization of the zebrafish globin loci and clarify the regulation of globin switching.
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Affiliation(s)
- Jared J Ganis
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital and Dana Farber Cancer Institute, and Harvard Stem Cell Institute, Harvard Medical School, 1 Blackfan Cir., Karp 7, Boston, MA 02115, USA.
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26
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Mongin E, Dewar K, Blanchette M. Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol 2012; 18:1115-30. [PMID: 21899419 DOI: 10.1089/cmb.2011.0088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In chordates, long-range cis-regulatory regions are involved in the control of transcription initiation (either as repressors or enhancers). Their main characteristics are that (i) they can be located as far as 1 Mb away from the transcription start site of the target gene, (ii) they can regulate more than one gene, and (iii) they are usually orientation-independent. Therefore, proper characterization of functional interactions between long-range cis-regulatory regions and their target genes remains problematic. We present a novel method to predict such interactions based on the analysis of rearrangements between the human and 16 other vertebrate genomes. Our method is based on the assumption that genome rearrangements that would disrupt the functional interaction between a cis-regulatory region and its target gene are likely to be deleterious. Therefore, conservation of synteny through evolution would be an indication of a functional interaction. We use our algorithm to predict the association between a set of 123,905 human candidate regulatory regions to their target gene(s). This genome-wide map of interactions has many potential applications, including the selection of candidate regions prior to in vivo experimental characterization, a better characterization of regulatory regions involved in position effect diseases, and an improved understanding of the mechanisms and importance of long-range regulation.
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Affiliation(s)
- Emmanuel Mongin
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
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27
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Lau YT, Parker SK, Near TJ, Detrich HW. Evolution and function of the globin intergenic regulatory regions of the antarctic dragonfishes (Notothenioidei: Bathydraconidae). Mol Biol Evol 2011; 29:1071-80. [PMID: 22075115 DOI: 10.1093/molbev/msr278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
As the Southern Ocean cooled to -1.8 °C over the past 40 My, the teleostean clade Notothenioidei diversified and, under reduced selection pressure for an oxygen-transporting apparatus, became less reliant on hemoglobin and red blood cells. At the extreme of this trend, the crown group of Antarctic icefishes (Channichthyidae) lost both components of oxygen transport. Under the decreased selection scenario, we hypothesized that the Antarctic dragonfishes (Bathydraconidae, the red-blooded sister clade to the icefishes) evolved lower blood hemoglobin concentrations because their globin gene complexes (α- and β-globin gene pairs linked by a regulatory intergene) transcribe globin mRNAs less effectively than those of basal notothenioids (e.g., the Nototheniidae [notothens]). To test our hypothesis, we 1) sequenced the α/β-intergenes of the adult globin complexes of three notothen and eight dragonfish species and 2) measured globin transcript levels in representative species from each group. The typical nototheniid intergene was ∼3-4 kb in length. The bathydraconid intergenes resolved into three subclasses (long [3.8 kb], intermediate [3.0 kb], and short [1.5-2.3 kb]) that corresponded to the three subclades proposed for the taxon. Although they varied in length due to indels, the three notothen and eight dragonfish intergenes contained a conserved ∼90-nt element that we have previously shown to be required for globin gene transcription. Using the quantitative polymerase chain reaction, we found that globin mRNA levels in red cells from one notothen species and from one species of each dragonfish subclade were equivalent statistically. Thus, our results indicate that the bathydraconids have evolved adult globin loci whose regulatory intergenes tend to be shorter than those of the more basal nototheniids yet are equivalent in transcriptional efficacy. Their low blood hemoglobin concentrations are most likely due to reduction in hematocrit.
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Markova EN, Kantidze OL, Razin SV. Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene. J Cell Biochem 2011; 112:1997-2005. [PMID: 21445863 DOI: 10.1002/jcb.23117] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The transcription factor RUNX1 is a key regulator of haematopoiesis in vertebrates. In humans, the 260-kb long gene coding for this transcription factor is located on chromosome 21. This gene is transcribed from two alternative promoters that are commonly referred to as the distal and the proximal promoters. In model experiments, these two promoters were found to be active in cells of different lineages, although RUNX1 is preferentially expressed in haematopoietic cells. In the present study, we attempted to identify the regulatory elements that could guide tissue-specific expression of the RUNX1 gene. Two such regulatory elements were found within the RUNX1 gene. One of these elements, located within intron 1, is a haematopoietic-specific enhancer. The second regulatory element, located within intron 5.2, contributes to the formation of an active chromatin hub, which integrates the above-mentioned enhancer and the P1 and P2 promoters.
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Affiliation(s)
- Elena N Markova
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, Moscow, Russia
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Abstract
Many evolutionary studies over the past decade have estimated α(sel), the proportion of all nucleotides in the human genome that are subject to purifying selection because of their biological function. Most of these studies have estimated the nucleotide substitution rates from genome sequence alignments across many diverse mammals. Some α(sel) estimates will be affected by the heterogeneity of substitution rates in neutral sequence across the genome. Most will also be inaccurate if change in the functional sequence repertoire occurs rapidly relative to the separation of lineages that are being compared. Evidence gathered from both evolutionary and experimental analyses now indicate that rates of "turnover" of functional, predominantly noncoding, sequence are, indeed, high. They are sufficiently high that an estimated 50% of mouse constrained noncoding sequence is predicted not to be shared with rat, a closely related rodent. The rapidity of turnover results in, at least, a twofold underestimate of α(sel) by analyses that measure constraint across the eutherian phylogeny. Approaches that take account of turnover estimate that the steady-state value of α(sel) lies between 10% and 15%. Experimental studies corroborate the predicted rates of loss and gain of noncoding functional sites. These studies show the limitations inherent in the use of deep sequence conservation for identifying functional sequence. Experimental investigations focusing on lineage-specific, noncoding, and functional sequence are now essential if we are to appreciate the complete functional repertoire of the human genome.
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Affiliation(s)
- Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.
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A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. Genetics 2011; 189:441-54. [PMID: 21840866 DOI: 10.1534/genetics.111.132662] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In mammals, X-chromosome inactivation (XCI) equalizes X-linked gene expression between XY males and XX females and is controlled by a specialized region known as the X-inactivation center (Xic). The Xic harbors two chromatin interaction domains, one centered around the noncoding Xist gene and the other around the antisense Tsix counterpart. Previous work demonstrated the existence of a chromatin transitional zone between the two domains. Here, we investigate the region and discover a conserved element, RS14, that presents a strong binding site for Ctcf protein. RS14 possesses an insulatory function suggestive of a boundary element and is crucial for cell differentiation and growth. Knocking out RS14 results in compromised Xist induction and aberrant XCI in female cells. These data demonstrate that a junction element between Tsix and Xist contributes to the initiation of XCI.
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Yudinkova ES, Bunina DA, Ulyanov SV, Gavrilov AA, Razin SV. Patterns of histone modifications across the chicken alfa-globin genes’ domain. Mol Biol 2011. [DOI: 10.1134/s0026893311030216] [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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Patel VS, Ezaz T, Deakin JE, Graves JAM. Globin gene structure in a reptile supports the transpositional model for amniote α- and β-globin gene evolution. Chromosome Res 2010; 18:897-907. [PMID: 21116705 DOI: 10.1007/s10577-010-9164-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 10/18/2022]
Abstract
The haemoglobin protein, required for oxygen transportation in the body, is encoded by α- and β-globin genes that are arranged in clusters. The transpositional model for the evolution of distinct α-globin and β-globin clusters in amniotes is much simpler than the previously proposed whole genome duplication model. According to this model, all jawed vertebrates share one ancient region containing α- and β-globin genes and several flanking genes in the order MPG-C16orf35-(α-β)-GBY-LUC7L that has been conserved for more than 410 million years, whereas amniotes evolved a distinct β-globin cluster by insertion of a transposed β-globin gene from this ancient region into a cluster of olfactory receptors flanked by CCKBR and RRM1. It could not be determined whether this organisation is conserved in all amniotes because of the paucity of information from non-avian reptiles. To fill in this gap, we examined globin gene organisation in a squamate reptile, the Australian bearded dragon lizard, Pogona vitticeps (Agamidae). We report here that the α-globin cluster (HBK, HBA) is flanked by C16orf35 and GBY and is located on a pair of microchromosomes, whereas the β-globin cluster is flanked by RRM1 on the 3' end and is located on the long arm of chromosome 3. However, the CCKBR gene that flanks the β-globin cluster on the 5' end in other amniotes is located on the short arm of chromosome 5 in P. vitticeps, indicating that a chromosomal break between the β-globin cluster and CCKBR occurred at least in the agamid lineage. Our data from a reptile species provide further evidence to support the transpositional model for the evolution of β-globin gene cluster in amniotes.
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Affiliation(s)
- Vidushi S Patel
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
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Wetten OF, Nederbragt AJ, Wilson RC, Jakobsen KS, Edvardsen RB, Andersen Ø. Genomic organization and gene expression of the multiple globins in Atlantic cod: conservation of globin-flanking genes in chordates infers the origin of the vertebrate globin clusters. BMC Evol Biol 2010; 10:315. [PMID: 20961401 PMCID: PMC2975663 DOI: 10.1186/1471-2148-10-315] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 10/20/2010] [Indexed: 08/30/2023] Open
Abstract
Background The vertebrate globin genes encoding the α- and β-subunits of the tetrameric hemoglobins are clustered at two unlinked loci. The highly conserved linear order of the genes flanking the hemoglobins provides a strong anchor for inferring common ancestry of the globin clusters. In fish, the number of α-β-linked globin genes varies considerably between different sublineages and seems to be related to prevailing physico-chemical conditions. Draft sequences of the Atlantic cod genome enabled us to determine the genomic organization of the globin repertoire in this marine species that copes with fluctuating environments of the temperate and Arctic regions. Results The Atlantic cod genome was shown to contain 14 globin genes, including nine hemoglobin genes organized in two unlinked clusters designated β5-α1-β1-α4 and β3-β4-α2-α3-β2. The diverged cod hemoglobin genes displayed different expression levels in adult fish, and tetrameric hemoglobins with or without a Root effect were predicted. The novel finding of maternally inherited hemoglobin mRNAs is consistent with a potential role played by fish hemoglobins in the non-specific immune response. In silico analysis of the six teleost genomes available showed that the two α-β globin clusters are flanked by paralogs of five duplicated genes, in agreement with the proposed teleost-specific duplication of the ancestral vertebrate globin cluster. Screening the genome of extant urochordate and cephalochordate species for conserved globin-flanking genes revealed linkage of RHBDF1, MPG and ARHGAP17 to globin genes in the tunicate Ciona intestinalis, while these genes together with LCMT are closely positioned in amphioxus (Branchiostoma floridae), but seem to be unlinked to the multiple globin genes identified in this species. Conclusion The plasticity of Atlantic cod to variable environmental conditions probably involves the expression of multiple globins with potentially different properties. The interspecific difference in number of fish hemoglobin genes contrasts with the highly conserved synteny of the flanking genes. The proximity of globin-flanking genes in the tunicate and amphioxus genomes resembles the RHBDF1-MPG-α-globin-ARHGAP17-LCMT linked genes in man and chicken. We hypothesize that the fusion of the three chordate linkage groups 3, 15 and 17 more than 800 MYA led to the ancestral vertebrate globin cluster during a geological period of increased atmospheric oxygen content.
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Affiliation(s)
- Ola F Wetten
- Department of Animal and Aquacultural Sciences, University of Life Sciences, Aas, Norway
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Furlan-Magaril M, Rebollar E, Guerrero G, Fernández A, Moltó E, González-Buendía E, Cantero M, Montoliu L, Recillas-Targa F. An insulator embedded in the chicken α-globin locus regulates chromatin domain configuration and differential gene expression. Nucleic Acids Res 2010; 39:89-103. [PMID: 20813760 PMCID: PMC3017597 DOI: 10.1093/nar/gkq740] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genome organization into transcriptionally active domains denotes one of the first levels of gene expression regulation. Although the chromatin domain concept is generally accepted, only little is known on how domain organization impacts the regulation of differential gene expression. Insulators might hold answers to address this issue as they delimit and organize chromatin domains. We have previously identified a CTCF-dependent insulator with enhancer-blocking activity embedded in the 5′ non-coding region of the chicken α-globin domain. Here, we demonstrate that this element, called the αEHS-1.4 insulator, protects a transgene against chromosomal position effects in stably transfected cell lines and transgenic mice. We found that this insulator can create a regulated chromatin environment that coincides with the onset of adult α-globin gene expression. Furthermore, such activity is in part dependent on the in vivo regulated occupancy of CTCF at the αEHS-1.4 element. Insulator function is also regulated by CTCF poly(ADP-ribosyl)ation. Our results suggest that the αEHS-1.4 insulator contributes in organizing the chromatin structure of the α-globin gene domain and prevents activation of adult α-globin gene expression at the erythroblast stage via CTCF.
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Affiliation(s)
- Mayra Furlan-Magaril
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, México D.F., México
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Gavrilov AA, Zukher IS, Philonenko ES, Razin SV, Iarovaia OV. Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure. Nucleic Acids Res 2010; 38:8051-60. [PMID: 20705651 PMCID: PMC3001081 DOI: 10.1093/nar/gkq712] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed an experimental procedure to analyze the spatial proximity of nuclear matrix-bound DNA fragments. This protocol, referred to as Matrix 3C (M3C), includes a high salt extraction of nuclei, the removal of distal parts of unfolded DNA loops using restriction enzyme treatment, ligation of the nuclear matrix-bound DNA fragments and a subsequent analysis of ligation frequencies. Using the M3C procedure, we have demonstrated that CpG islands of at least three housekeeping genes that surround the chicken α-globin gene domain are assembled into a complex (presumably, a transcription factory) that is stabilized by the nuclear matrix in both erythroid and non-erythroid cells. In erythroid cells, the regulatory elements of the α-globin genes are attracted to this complex to form a new assembly: an active chromatin hub that is linked to the pre-existing transcription factory. The erythroid-specific part of the assembly is removed by high salt extraction. Based on these observations, we propose that mixed transcription factories that mediate the transcription of both housekeeping and tissue-specific genes are composed of a permanent compartment containing integrated into the nuclear matrix promoters of housekeeping genes and a ‘guest’ compartment where promoters and regulatory elements of tissue-specific genes can be temporarily recruited.
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Affiliation(s)
- Alexey A Gavrilov
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
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Philonenko ES, Klochkov DB, Borunova VV, Gavrilov AA, Razin SV, Iarovaia OV. TMEM8 - a non-globin gene entrapped in the globin web. Nucleic Acids Res 2010; 37:7394-406. [PMID: 19820109 PMCID: PMC2794187 DOI: 10.1093/nar/gkp838] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
For more than 30 years it was believed that globin gene domains included only genes encoding globin chains. Here we show that in chickens, the domain of α-globin genes also harbor the non-globin gene TMEM8. It was relocated to the vicinity of the α-globin cluster due to inversion of an ∼170-kb genomic fragment. Although in humans TMEM8 is preferentially expressed in resting T-lymphocytes, in chickens it acquired an erythroid-specific expression profile and is upregulated upon terminal differentiation of erythroblasts. This correlates with the presence of erythroid-specific regulatory elements in the body of chicken TMEM8, which interact with regulatory elements of the α-globin genes. Surprisingly, TMEM8 is not simply recruited to the α-globin gene domain active chromatin hub. An alternative chromatin hub is assembled, which includes some of the regulatory elements essential for the activation of globin gene expression. These regulatory elements should thus shuttle between two different chromatin hubs.
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Affiliation(s)
- Elena S Philonenko
- Institute of Gene Biology of the Russian Academy of Sciences, Vavilov street 34/5, 119334 Moscow, Russia
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Hoffmann FG, Storz JF, Gorr TA, Opazo JC. Lineage-specific patterns of functional diversification in the alpha- and beta-globin gene families of tetrapod vertebrates. Mol Biol Evol 2010; 27:1126-38. [PMID: 20047955 DOI: 10.1093/molbev/msp325] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The alpha- and beta-globin gene families of jawed vertebrates have diversified with respect to both gene function and the developmental timing of gene expression. Phylogenetic reconstructions of globin gene family evolution have provided suggestive evidence that the developmental regulation of hemoglobin synthesis has evolved independently in multiple vertebrate lineages. For example, the embryonic beta-like globin genes of birds and placental mammals are not 1:1 orthologs. Despite the similarity in developmental expression profiles, the genes are independently derived from lineage-specific duplications of a beta-globin pro-ortholog. This suggests the possibility that other vertebrate taxa may also possess distinct repertoires of globin genes that were produced by repeated rounds of lineage-specific gene duplication and divergence. Until recently, investigations into this possibility have been hindered by the dearth of genomic sequence data from nonmammalian vertebrates. Here, we report new insights into globin gene family evolution that were provided by a phylogenetic analysis of vertebrate globins combined with a comparative genomic analysis of three key sauropsid taxa: a squamate reptile (anole lizard, Anolis carolinensis), a passeriform bird (zebra finch, Taeniopygia guttata), and a galliform bird (chicken, Gallus gallus). The main objectives of this study were 1) to characterize evolutionary changes in the size and membership composition of the alpha- and beta-globin gene families of tetrapod vertebrates and 2) to test whether functional diversification of the globin gene clusters occurred independently in different tetrapod lineages. Results of our comparative genomic analysis revealed several intriguing patterns of gene turnover in the globin gene clusters of different taxa. Lineage-specific differences in gene content were especially pronounced in the beta-globin gene family, as phylogenetic reconstructions revealed that amphibians, lepidosaurs (as represented by anole lizard), archosaurs (as represented by zebra finch and chicken), and mammals each possess a distinct independently derived repertoire of beta-like globin genes. In contrast to the ancient functional diversification of the alpha-globin gene cluster in the stem lineage of tetrapods, the physiological division of labor between early- and late-expressed genes in the beta-globin gene cluster appears to have evolved independently in several tetrapod lineages.
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Rincón-Arano H, Guerrero G, Valdes-Quezada C, Recillas-Targa F. Chicken alpha-globin switching depends on autonomous silencing of the embryonic pi globin gene by epigenetics mechanisms. J Cell Biochem 2009; 108:675-87. [PMID: 19693775 DOI: 10.1002/jcb.22304] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Switching in hemoglobin gene expression is an informative paradigm for studying transcriptional regulation. Here we determined the patterns of chicken alpha-globin gene expression during development and erythroid differentiation. Previously published data suggested that the promoter regions of alpha-globin genes contain the complete information for proper developmental regulation. However, our data show a preferential trans-activation of the embryonic alpha-globin gene independent of the developmental or differentiation stage. We also found that DNA methylation and histone deacetylation play key roles in silencing the expression of the embryonic pi gene in definitive erythrocytes. However, drug-mediated reactivation of the embryonic gene during definitive erythropoiesis dramatically impaired the expression of the adult genes, suggesting gene competition or interference for enhancer elements. Our results also support a model in which the lack of open chromatin marks and localized recruitment of chicken MeCP2 contribute to autonomous gene silencing of the embryonic alpha-globin gene in a developmentally specific manner. We propose that epigenetic mechanisms are necessary for in vivo chicken alpha-globin gene switching through differential gene silencing of the embryonic alpha-globin gene in order to allow proper activation of adult alpha-globin genes.
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Affiliation(s)
- Héctor Rincón-Arano
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México 04510, DF, México
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McCracken K, Barger C, Bulgarella M, Johnson K, Kuhner M, Moore A, Peters J, Trucco J, Valqui T, Winker K, Wilson R. Signatures of High‐Altitude Adaptation in the Major Hemoglobin of Five Species of Andean Dabbling Ducks. Am Nat 2009; 174:631-50. [DOI: 10.1086/606020] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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McCRACKEN KG, BARGER CP, BULGARELLA M, JOHNSON KP, SONSTHAGEN SA, TRUCCO J, VALQUI TH, WILSON RE, WINKER K, SORENSON MD. Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl. Mol Ecol 2009; 18:3992-4005. [DOI: 10.1111/j.1365-294x.2009.04352.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Formaldehyde fixation of cells does not greatly reduce the ability to amplify cellular DNA. Anal Biochem 2009; 390:94-6. [DOI: 10.1016/j.ab.2009.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 04/07/2009] [Accepted: 04/13/2009] [Indexed: 11/24/2022]
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Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Handling Counterintuitive Results. J Mol Evol 2009; 68:654-64. [DOI: 10.1007/s00239-009-9238-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 03/30/2009] [Accepted: 04/15/2009] [Indexed: 01/26/2023]
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Iarovaia OV, Borounova VV, Philonenko ES, Kantidze OL, Vassetzky YS, Razin SV. In embryonic chicken erythrocytes actively transcribed alpha globin genes are not associated with the nuclear matrix. J Cell Biochem 2009; 106:170-8. [PMID: 19003974 DOI: 10.1002/jcb.21987] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The spatial organization of a 250 Kb region of chicken chromosome 14, which includes the alpha globin gene cluster, was studied using in situ hybridization of a corresponding BAC probe with nuclear halos. It was found that in non-erythroid cells (DT40) and cultured erythroid cells of definite lineage (HD3) the genomic region under study was partially (DT40 cells) or fully (HD3 cells) associated with the nuclear matrix. In contrast, in embryonic red blood cells (10-day RBC) the same area was located in the crown of DNA loops surrounding the nuclear matrix, although both globin genes and surrounding house-keeping genes were actively transcribed in these cells. This spatial organization was associated with the virtual absence of RNA polymerase II in nuclear matrices prepared from 10-day RBC. In contrast, in HD3 cells a significant portion of RNA polymerase II was present in nuclear matrices. Taken together, these observations suggest that in embryonic erythroid cells transcription does not occur in association with the nuclear matrix.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences 34/5 Vavilov Street, 119344 Moscow, Russia
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44
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Klochkov DB, Gavrilov AA, Vassetzky YS, Razin SV. Early replication timing of the chicken alpha-globin gene domain correlates with its open chromatin state in cells of different lineages. Genomics 2009; 93:481-6. [PMID: 19187796 DOI: 10.1016/j.ygeno.2009.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 12/10/2008] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
Abstract
The vertebrate alpha-globin gene domain is an open chromatin domain overlapping a neighboring house-keeping gene. The tissue-specific cluster of alpha-globin genes and the overlapping housekeeping gene share the same replication origin. We have studied the replication timing of chicken alpha-globin genes in cells of different lineages using the FISH-based approach and found that alpha-globin genes replicate early both in erythroid and in non-erythroid cells, i.e. regardless of their transcriptional activity. Early replication timing of chicken alpha-globin genes in cells of different lineages was in good correlation with the open chromatin configuration of the alpha-globin gene domain in both erythroid and non-erythroid cells. We propose that active transcription of the housekeeping gene overlapping the alpha-globin gene domain enables an access of Origin Recognition Complex (ORC) proteins to the replication origin resulting in early replication of alpha-globin genes even in non-erythroid cells.
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Affiliation(s)
- Denis B Klochkov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia
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45
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McCracken KG, Bulgarella M, Johnson KP, Kuhner MK, Trucco J, Valqui TH, Wilson RE, Peters JL. Gene Flow in the Face of Countervailing Selection: Adaptation to High-Altitude Hypoxia in the A Hemoglobin Subunit of Yellow-Billed Pintails in the Andes. Mol Biol Evol 2009; 26:815-27. [DOI: 10.1093/molbev/msp007] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn MS, Neph S, Sabo PJ, Goldy J, Weaver M, Haydock A, Lee K, Dorschner M, Dermitzakis ET, Antonarakis SE, Stamatoyannopoulos JA. Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol 2008; 9:R168. [PMID: 19055709 PMCID: PMC2646272 DOI: 10.1186/gb-2008-9-12-r168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/24/2008] [Accepted: 12/02/2008] [Indexed: 01/26/2023] Open
Abstract
The fraction of experimentally active conserved non-coding sequences within any given cell type is low, so classical assays are unlikely to expose their potential. Background Conserved non-coding sequences in the human genome are approximately tenfold more abundant than known genes, and have been hypothesized to mark the locations of cis-regulatory elements. However, the global contribution of conserved non-coding sequences to the transcriptional regulation of human genes is currently unknown. Deeply conserved elements shared between humans and teleost fish predominantly flank genes active during morphogenesis and are enriched for positive transcriptional regulatory elements. However, such deeply conserved elements account for <1% of the conserved non-coding sequences in the human genome, which are predominantly mammalian. Results We explored the regulatory potential of a large sample of these 'common' conserved non-coding sequences using a variety of classic assays, including chromatin remodeling, and enhancer/repressor and promoter activity. When tested across diverse human model cell types, we find that the fraction of experimentally active conserved non-coding sequences within any given cell type is low (approximately 5%), and that this proportion increases only modestly when considered collectively across cell types. Conclusions The results suggest that classic assays of cis-regulatory potential are unlikely to expose the functional potential of the substantial majority of mammalian conserved non-coding sequences in the human genome.
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Affiliation(s)
- Catia Attanasio
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel Servet, 1211, Geneva 4, Switzerland.
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Gavrilov AA, Razin SV. Study of spatial organization of chicken α-globin gene domain by 3c technique. BIOCHEMISTRY (MOSCOW) 2008; 73:1192-9. [DOI: 10.1134/s0006297908110047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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St John J, Quinn TW. Recent CR1 non-LTR retrotransposon activity in coscoroba reveals an insertion site preference. BMC Genomics 2008; 9:567. [PMID: 19038033 PMCID: PMC2612034 DOI: 10.1186/1471-2164-9-567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 11/27/2008] [Indexed: 11/17/2022] Open
Abstract
Background Chicken repeat 1 (CR1) is a taxonomically widespread non-LTR retrotransposon. Insertion site bias, or lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site. Results Elucidation of the exact octomer repeat sequence (TTCTGTGA) allowed for the identification of younger insertion events. The number of octomer repeats associated with a CR1 element increases after insertion with CR1s having one octomer being youngest. These young CR1s are flanked by regions of low GC content (38%). Furthermore, a bias for specific bases within the first four positions at the site of insertion was revealed. Conclusion This study focused on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events. Our data suggest that CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, preferentially inserting into regions of lower GC content. Furthermore, there appears to be a base preference (TTCT) for the insertion site. The results of this study increase the current level of understanding regarding the elusive CR1 non-LTR retrotransposon.
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Affiliation(s)
- Judy St John
- Rocky Mountain Center for Conservation Genetics and Systematics, Division of Natural Sciences and Mathematics, University of Denver, Denver, Colorado, USA.
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Borunova VV, Razin SV, Iarovaia OV. Genes surrounding the cluster of tissue-specific alpha-globin genes in chicken genome are expressed in both erythroid and lymphoid cells. DOKL BIOCHEM BIOPHYS 2008; 421:224-6. [PMID: 18853777 DOI: 10.1134/s1607672908040157] [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]
Affiliation(s)
- V V Borunova
- Faculty of Biology, Moscow State University, Moscow, 119991 Russia
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Abstract
Recent data published in BMC Biology from the globin gene clusters in platypus, together with data from other species, show that β-globin genes transposed from one chromosomal location to another. This resolves some controversies about vertebrate globin gene evolution but ignites new ones.
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Affiliation(s)
- Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, University Park, PA 16802, USA.
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