1
|
Pena R, Lopes P, Gaspar G, Miranda A, Faustino P. Ancestry of the major long-range regulatory site of the α-globin genes in the Portuguese population with the common 3.7 kb α-thalassemia deletion. Mol Biol Rep 2024; 51:612. [PMID: 38704770 PMCID: PMC11070386 DOI: 10.1007/s11033-024-09530-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND The α-Major Regulatory Element (α-MRE), also known as HS-40, is located upstream of the α-globin gene cluster and has a crucial role in the long-range regulation of the α-globin gene expression. This enhancer is polymorphic and several haplotypes were identified in different populations, with haplotype D almost exclusively found in African populations. The purpose of this research was to identify the HS-40 haplotype associated with the 3.7 kb α-thalassemia deletion (-α3.7del) in the Portuguese population, and determine its ancestry and influence on patients' hematological phenotype. METHODS AND RESULTS We selected 111 Portuguese individuals previously analyzed by Gap-PCR to detect the presence of the -α3.7del: 50 without the -α3.7del, 34 heterozygous and 27 homozygous for the -α3.7del. The HS-40 region was amplified by PCR followed by Sanger sequencing. Four HS-40 haplotypes were found (A to D). The distribution of HS-40 haplotypes and genotypes are significantly different between individuals with and without the -α3.7del, being haplotype D and genotype AD the most prevalent in patients with this deletion in homozygosity. Furthermore, multiple correspondence analysis revealed that individuals without the -α3.7del are grouped with other European populations, while samples with the -α3.7del are separated from these and found more closely related to the African population. CONCLUSION This study revealed for the first time an association of the HS-40 haplotype D with the -α3.7del in the Portuguese population, and its likely African ancestry. These results may have clinical importance as in vitro analysis of haplotype D showed a decrease in its enhancer activity on α-globin gene.
Collapse
Affiliation(s)
- Rita Pena
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal
| | - Pedro Lopes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal
| | - Gisela Gaspar
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Armandina Miranda
- Departamento de Promoção da Saúde e Prevenção de Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal
| | - Paula Faustino
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, 1649-016, Portugal.
- Grupo Ecogenética e Saúde Humana, Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal.
- Laboratório Associado TERRA, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
| |
Collapse
|
2
|
Vadolas J, Nualkaew T, Voon HPJ, Vilcassim S, Grigoriadis G. Interplay between α-thalassemia and β-hemoglobinopathies: Translating genotype-phenotype relationships into therapies. Hemasphere 2024; 8:e78. [PMID: 38752170 PMCID: PMC11094674 DOI: 10.1002/hem3.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
α-Thalassemia represents one of the most important genetic modulators of β-hemoglobinopathies. During this last decade, the ongoing interest in characterizing genotype-phenotype relationships has yielded incredible insights into α-globin gene regulation and its impact on β-hemoglobinopathies. In this review, we provide a holistic update on α-globin gene expression stemming from DNA to RNA to protein, as well as epigenetic mechanisms that can impact gene expression and potentially influence phenotypic outcomes. Here, we highlight defined α-globin targeted strategies and rationalize the use of distinct molecular targets based on the restoration of balanced α/β-like globin chain synthesis. Considering the therapies that either increase β-globin synthesis or reactivate γ-globin gene expression, the modulation of α-globin chains as a disease modifier for β-hemoglobinopathies still remains largely uncharted in clinical studies.
Collapse
Affiliation(s)
- Jim Vadolas
- Centre for Cancer ResearchHudson Institute of Medical ResearchClaytonVictoriaAustralia
- Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Tiwaporn Nualkaew
- Centre for Cancer ResearchHudson Institute of Medical ResearchClaytonVictoriaAustralia
- Present address:
Department of Medical Technology, School of Allied Health SciencesWalailak UniversityNakhon Si ThammaratThailand
| | - Hsiao P. J. Voon
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Shahla Vilcassim
- Centre for Cancer ResearchHudson Institute of Medical ResearchClaytonVictoriaAustralia
- School of Clinical Sciences at Monash HealthMonash UniversityClaytonAustralia
| | - George Grigoriadis
- Centre for Cancer ResearchHudson Institute of Medical ResearchClaytonVictoriaAustralia
- School of Clinical Sciences at Monash HealthMonash UniversityClaytonAustralia
| |
Collapse
|
3
|
Razin SV, Ulianov SV, Iarovaia OV. Enhancer Function in the 3D Genome. Genes (Basel) 2023; 14:1277. [PMID: 37372457 DOI: 10.3390/genes14061277] [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: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
In this review, we consider various aspects of enhancer functioning in the context of the 3D genome. Particular attention is paid to the mechanisms of enhancer-promoter communication and the significance of the spatial juxtaposition of enhancers and promoters in 3D nuclear space. A model of an activator chromatin compartment is substantiated, which provides the possibility of transferring activating factors from an enhancer to a promoter without establishing direct contact between these elements. The mechanisms of selective activation of individual promoters or promoter classes by enhancers are also discussed.
Collapse
Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Olga V Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| |
Collapse
|
4
|
Capasso S, Cardiero G, Musollino G, Prezioso R, Testa R, Dembech S, Piluso G, Nigro V, Digilio FA, Lacerra G. Functional analysis of three new alpha-thalassemia deletions involving MCS-R2 reveals the presence of an additional enhancer element in the 5' boundary region. PLoS Genet 2023; 19:e1010727. [PMID: 37216374 DOI: 10.1371/journal.pgen.1010727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
We report three novel deletions involving the Multispecies Conserved Sequences (MCS) R2, also known as the Major Regulative Element (MRE), in patients showing the α-thalassemia phenotype. The three new rearrangements showed peculiar positions of the breakpoints. 1) The (αα)ES is a telomeric 110 kb deletion ending inside the MCS-R3 element. 2) The (αα)FG, 984 bp-long, ends 51 bp upstream to MCS-R2; both are associated with a severe α-thalassemia phenotype. 3) The (αα)CT, 5058 bp-long starts at position +93 of MCS-R2 and is the only one associated to a mild α-thalassemia phenotype. To understand the specific role of different segments of the MCS-R2 element and of its boundary regions we carried out transcriptional and expression analysis. Transcriptional analysis of patients' reticulocytes showed that (αα)ES was unable to produce α2-globin mRNA, while a high level of expression of the α2-globin genes (56%) was detected in (αα)CT deletion, characterized by the presence of the first 93 bp of MCS-R2. Expression analysis of constructs containing breakpoints and boundary regions of the deletions (αα)CT and (αα)FG, showed comparable activity both for MCS-R2 and the boundary region (-682/-8). Considering that the (αα)CT deletion, almost entirely removing MCS-R2, has a less severe phenotype than the (αα)FG α0thalassemia deletion, removing both MCS-R2 almost entirely and an upstream 679 bp, we infer for the first time that an enhancer element must exist in this region that helps to increase the expression of the α-globin genes. The genotype-phenotype relationship of other previously published MCS-R2 deletions strengthened our hypothesis.
Collapse
Affiliation(s)
- Serena Capasso
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" (IGB-ABT), National Research Council (CNR), Naples, Italy
| | - Giovanna Cardiero
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" (IGB-ABT), National Research Council (CNR), Naples, Italy
| | - Gennaro Musollino
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" (IGB-ABT), National Research Council (CNR), Naples, Italy
| | - Romeo Prezioso
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" (IGB-ABT), National Research Council (CNR), Naples, Italy
| | - Rosario Testa
- A.O.U. Policlinico Rodolico-San Marco, University of Catania, Catania, Italy
| | - Sabrina Dembech
- Central analysis laboratory, Azienda Ospedaliero-Universitaria, Ospedali Riuniti, Foggia, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania L. Vanvitelli, Naples, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania L. Vanvitelli, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - F Anna Digilio
- Research Institute on Terrestrial Ecosystems (IRET-CNR), National Research Council (CNR), Naples, Italy
| | - Giuseppina Lacerra
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" (IGB-ABT), National Research Council (CNR), Naples, Italy
| |
Collapse
|
5
|
Abstract
Thalassemia syndromes are common monogenic disorders and represent a significant health issue worldwide. In this review, the authors elaborate on fundamental genetic knowledge about thalassemias, including the structure and location of globin genes, the production of hemoglobin during development, the molecular lesions causing α-, β-, and other thalassemia syndromes, the genotype-phenotype correlation, and the genetic modifiers of these conditions. In addition, they briefly discuss the molecular techniques applied for diagnosis and innovative cell and gene therapy strategies to cure these conditions.
Collapse
Affiliation(s)
- Nicolò Tesio
- Department of Clinical and Biological Sciences, San Luigi Gonzaga University Hospital, University of Torino, Regione Gonzole, 10, 10043 Orbassano, Turin, Italy. https://twitter.com/nicolotesio
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Iarovaia OV, Ulianov SV, Ioudinkova ES, Razin SV. Segregation of α- and β-Globin Gene Cluster in Vertebrate Evolution: Chance or Necessity? BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1035-1049. [PMID: 36180994 DOI: 10.1134/s0006297922090140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
The review is devoted to the patterns of evolution of α- and β-globin gene domains. A hypothesis is presented according to which segregation of the ancestral cluster of α/β-globin genes in Amniota occurred due to the performance by α-globins and β-globins of non-canonical functions not related to oxygen transport.
Collapse
Affiliation(s)
- Olga V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Elena S Ioudinkova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
De Simone G, Quattrocchi A, Mancini B, di Masi A, Nervi C, Ascenzi P. Thalassemias: From gene to therapy. Mol Aspects Med 2021; 84:101028. [PMID: 34649720 DOI: 10.1016/j.mam.2021.101028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/19/2021] [Indexed: 12/26/2022]
Abstract
Thalassemias (α, β, γ, δ, δβ, and εγδβ) are the most common genetic disorders worldwide and constitute a heterogeneous group of hereditary diseases characterized by the deficient synthesis of one or more hemoglobin (Hb) chain(s). This leads to the accumulation of unstable non-thalassemic Hb chains, which precipitate and cause intramedullary destruction of erythroid precursors and premature lysis of red blood cells (RBC) in the peripheral blood. Non-thalassemic Hbs display high oxygen affinity and no cooperativity. Thalassemias result from many different genetic and molecular defects leading to either severe or clinically silent hematologic phenotypes. Thalassemias α and β are particularly diffused in the regions spanning from the Mediterranean basin through the Middle East, Indian subcontinent, Burma, Southeast Asia, Melanesia, and the Pacific Islands, whereas δβ-thalassemia is prevalent in some Mediterranean regions including Italy, Greece, and Turkey. Although in the world thalassemia and malaria areas overlap apparently, the RBC protection against malaria parasites is openly debated. Here, we provide an overview of the historical, geographic, genetic, structural, and molecular pathophysiological aspects of thalassemias. Moreover, attention has been paid to molecular and epigenetic pathways regulating globin gene expression and globin switching. Challenges of conventional standard treatments, including RBC transfusions and iron chelation therapy, splenectomy and hematopoietic stem cell transplantation from normal donors are reported. Finally, the progress made by rapidly evolving fields of gene therapy and gene editing strategies, already in pre-clinical and clinical evaluation, and future challenges as novel curative treatments for thalassemia are discussed.
Collapse
Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università Roma Tre, Viale Guglielmo Marconi 446, 00146, Roma, Italy
| | - Alberto Quattrocchi
- Dipartimento di Scienze e Biotecnologie Medico-Chirurgiche, Facoltà di Farmacia e Medicina, "Sapienza" Università di Roma, Corso della Repubblica, 79, 04100, Latina, Italy
| | - Benedetta Mancini
- Dipartimento di Scienze, Università Roma Tre, Viale Guglielmo Marconi 446, 00146, Roma, Italy
| | - Alessandra di Masi
- Dipartimento di Scienze, Università Roma Tre, Viale Guglielmo Marconi 446, 00146, Roma, Italy
| | - Clara Nervi
- Dipartimento di Scienze e Biotecnologie Medico-Chirurgiche, Facoltà di Farmacia e Medicina, "Sapienza" Università di Roma, Corso della Repubblica, 79, 04100, Latina, Italy.
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Guglielmo Marconi 446, 00146, Roma, Italy; Accademia Nazionale dei Lincei, Via della Lungara 10, 00165, Roma, Italy.
| |
Collapse
|
9
|
Keller TCS, Lechauve C, Keller AS, Brooks S, Weiss MJ, Columbus L, Ackerman HC, Cortese-Krott MM, Isakson BE. The role of globins in cardiovascular physiology. Physiol Rev 2021; 102:859-892. [PMID: 34486392 DOI: 10.1152/physrev.00037.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Globin proteins exist in every cell type of the vasculature, from erythrocytes to endothelial cells, vascular smooth muscle cells, and peripheral nerve cells. Many globin subtypes are also expressed in muscle tissues (including cardiac and skeletal muscle), in other organ-specific cell types, and in cells of the central nervous system. The ability of each of these globins to interact with molecular oxygen (O2) and nitric oxide (NO) is preserved across these contexts. Endothelial α-globin is an example of extra-erythrocytic globin expression. Other globins, including myoglobin, cytoglobin, and neuroglobin are observed in other vascular tissues. Myoglobin is observed primarily in skeletal muscle and smooth muscle cells surrounding the aorta or other large arteries. Cytoglobin is found in vascular smooth muscle but can also be expressed in non-vascular cell types, especially in oxidative stress conditions after ischemic insult. Neuroglobin was first observed in neuronal cells, and its expression appears to be restricted mainly to the central and peripheral nervous systems. Brain and central nervous system neurons expressing neuroglobin are positioned close to many arteries within the brain parenchyma and can control smooth muscle contraction and, thus, tissue perfusion and vascular reactivity. Overall, reactions between NO and globin heme-iron contribute to vascular homeostasis by regulating vasodilatory NO signals and scaveging reactive species in cells of the mammalian vascular system. Here, we discuss how globin proteins affect vascular physiology with a focus on NO biology, and offer perspectives for future study of these functions.
Collapse
Affiliation(s)
- T C Steven Keller
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Christophe Lechauve
- Department of Hematology, St. Jude's Children's Research Hospital, Memphis, TN, United States
| | - Alexander S Keller
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Steven Brooks
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Mitchell J Weiss
- Department of Hematology, St. Jude's Children's Research Hospital, Memphis, TN, United States
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Hans C Ackerman
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Miriam M Cortese-Krott
- Myocardial Infarction Research Laboratory, Department of Cardiology, Pulmunology, and Angiology, Medical Faculty, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany.,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Brant E Isakson
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, United States
| |
Collapse
|
10
|
Razin SV, Ioudinkova ES, Kantidze OL, Iarovaia OV. Co-Regulated Genes and Gene Clusters. Genes (Basel) 2021; 12:907. [PMID: 34208174 PMCID: PMC8230824 DOI: 10.3390/genes12060907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
Collapse
Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena S. Ioudinkova
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Omar L. Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Olga V. Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| |
Collapse
|
11
|
Ulianov SV, Razin SV. The two waves in single-cell 3D genomics. Semin Cell Dev Biol 2021; 121:143-152. [PMID: 34030950 DOI: 10.1016/j.semcdb.2021.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 02/07/2023]
Abstract
For decades, biochemical methods for the analysis of genome structure and function provided cell-population-averaged data that allowed general principles and tendencies to be disclosed. Microscopy-based studies, which immanently involve single-cell analysis, did not provide sufficient spatial resolution to investigate the particularly small details of 3D genome folding. Nevertheless, these studies demonstrated that mutual positions of chromosome territories within cell nuclei and individual genomic loci within chromosomal territories can vary significantly in individual cells. The development of new technologies in biochemistry and the advent of super-resolution microscopy in the last decade have made possible the full-scale study of 3D genome organization in individual cells. Maps of the 3D genome build based on C-data and super-resolution microscopy are highly consistent and, therefore, biologically relevant. The internal structures of individual chromosomes, loci, and topologically associating domains (TADs) are resolved as well as cell-cycle dynamics. 3D modeling allows one to investigate the physical mechanisms underlying genome folding. Finally, joint profiling of genome topology and epigenetic features will allow 3D genomics to handle complex cell-to-cell heterogeneity. In this review, we summarize the present state of studies into 3D genome organization in individual cells, analyze the technical problems of single-cell studies, and outline perspectives of 3D genomics.
Collapse
Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
| |
Collapse
|
12
|
Zittersteijn HA, Harteveld CL, Klaver-Flores S, Lankester AC, Hoeben RC, Staal FJT, Gonçalves MAFV. A Small Key for a Heavy Door: Genetic Therapies for the Treatment of Hemoglobinopathies. Front Genome Ed 2021; 2:617780. [PMID: 34713239 PMCID: PMC8525365 DOI: 10.3389/fgeed.2020.617780] [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: 10/15/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Throughout the past decades, the search for a treatment for severe hemoglobinopathies has gained increased interest within the scientific community. The discovery that ɤ-globin expression from intact HBG alleles complements defective HBB alleles underlying β-thalassemia and sickle cell disease, has provided a promising opening for research directed at relieving ɤ-globin repression mechanisms and, thereby, improve clinical outcomes for patients. Various gene editing strategies aim to reverse the fetal-to-adult hemoglobin switch to up-regulate ɤ-globin expression through disabling either HBG repressor genes or repressor binding sites in the HBG promoter regions. In addition to these HBB mutation-independent strategies involving fetal hemoglobin (HbF) synthesis de-repression, the expanding genome editing toolkit is providing increased accuracy to HBB mutation-specific strategies encompassing adult hemoglobin (HbA) restoration for a personalized treatment of hemoglobinopathies. Moreover, besides genome editing, more conventional gene addition strategies continue under investigation to restore HbA expression. Together, this research makes hemoglobinopathies a fertile ground for testing various innovative genetic therapies with high translational potential. Indeed, the progressive understanding of the molecular clockwork underlying the hemoglobin switch together with the ongoing optimization of genome editing tools heightens the prospect for the development of effective and safe treatments for hemoglobinopathies. In this context, clinical genetics plays an equally crucial role by shedding light on the complexity of the disease and the role of ameliorating genetic modifiers. Here, we cover the most recent insights on the molecular mechanisms underlying hemoglobin biology and hemoglobinopathies while providing an overview of state-of-the-art gene editing platforms. Additionally, current genetic therapies under development, are equally discussed.
Collapse
Affiliation(s)
- Hidde A. Zittersteijn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis L. Harteveld
- Department of Human and Clinical Genetics, The Hemoglobinopathies Laboratory, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arjan C. Lankester
- Department of Pediatrics, Stem Cell Transplantation Program, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | |
Collapse
|
13
|
Luo S, Chen X, Zhong Q, Wang Q, Xu Z, Qin L, Wang J, Yuan D, Yan T, Tang N. Analysis of rare thalassemia caused by HS-40 regulatory site deletion. ACTA ACUST UNITED AC 2021; 25:286-291. [PMID: 32720864 DOI: 10.1080/16078454.2020.1799587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
ABSTRACT Objectives: To investigate the effect of HS-40 regulatory site deletion on α-globin gene expression and its clinical significance. Methods: Venous blood samples of subjects were analyzed using a hematology analyzer and high- performance liquid chromatography; fetal cord blood was analyzed by a capillary electrophoresis analyzer. Gap-polymerase chain reaction (PCR), reverse dot blot (RDB), and multiple-link-dependent probe amplification (MLPA) were used for genotyping of thalassemia. Results: The proband was POLR3 K, HS-40 heterozygous deletion; the proband's wife was -SEA/αα; the fetus was POLR3 K, HS-40 heterozygous deletion combined with -SEA deletion; all of them had microcytic hypochromic anemia. Fetal umbilical cord blood electrophoresis revealed a suspected Hb Bart's band to be 88.4%, and the fetus was, thus, diagnosed as Hb Bart's fetus. The red blood cell parameters of the sporadic case showed that he had microcytic hypochromic anemia. Hemoglobin (Hb) electrophoresis analysis showed Hb H to be 5.3%, leading to a diagnosis of Hb H disease. Gap-PCR and RDB identified the genotype to be -α3.7/αα, βA/βA. MLPA detected heterozygous deletion or -α3.7 deletion on one allele and deletion of the HS-40 regulatory site on the other allele. Conclusion: The deletion of HS-40 regulatory site reduced expression of α-globin. HS-40 heterozygous deletion manifested as mild anemia, which was of microcytic hypochromic type. When compounded with -α3.7/αα, it manifested as Hb H disease; and when compounded with -SEA/αɑ, it manifested as Hb Bart's fetus.
Collapse
Affiliation(s)
- Shiqiang Luo
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Xingyuan Chen
- Department of Laboratory Medicine, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, People's Republic of China
| | - Qingyan Zhong
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Qiuhua Wang
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Zehui Xu
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Liuqun Qin
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Jingren Wang
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Dejian Yuan
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Tizhen Yan
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| | - Ning Tang
- Department of Medical Genetics, Liuzhou Maternal and Child Health Hospital, Liuzhou, People's Republic of China
| |
Collapse
|
14
|
Li H, Zeng J, Zhao Y, Xu X. MZF1 regulates α-globin gene transcription via long-range interactions in erythroid differentiation. Blood Cells Mol Dis 2020; 87:102533. [PMID: 33352376 DOI: 10.1016/j.bcmd.2020.102533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
Precise spatiotemporal gene expression regulation is crucial for human erythropoiesis. However, dramatic changes in the chromatin structure and transcriptome involved in α-globin gene expression during erythropoiesis still not fully understand. To identify candidate regulators for α-globin gene regulation, we carried out an integrated approach by integrating publicly available transcriptomic and epigenomic data. We computed active enhancers by overlapping enriched regions marked with H3K4me1 and H3K27ac and correlated their activity with mRNA expression. Next, we cataloged potential transcription factors via de novo motif analysis. We highlighted the discovery of potential novel transcription factor MZF1 of the α-globin gene in erythroid differentiation. To validate the role of MZF1, we quantified the expression level of MZF1 and α-globin gene in HSPCs, early erythroid progenitors and late erythroid precursors cells. Both the mRNA and protein expression patterns of MZF1 were consistent with the α-globin gene. Also, the qPCR result showed that the expression of the α-globin gene was significantly increased by the MZF1 overexpression. To further investigate the role of MZF1 regulating α-globin gene transcriptional activity during erythroid differentiation, we performed ChIP-qPCR at the α-globin locus. Our results showed that MZF1 recruitment both at 4 upstream HS sites and α-globin gene promoter in erythroid precursor cells. To determine the importance of the MZF1 to enhancer-promoter interaction at the α-globin locus, we compared interaction frequency before and after knockdown of MZF1 by chromosome conformation capture (3C) assay. Upon MZF1 depletion, both the expression of the α-globin gene and all 3C signals were significantly decreased. Taken together, MZF1 plays an important role in regulating α-globin gene expression by binding to long-region enhancers and α-globin gene promoter and facilitates the organization of specific 3D chromatin architecture in erythroid differentiation.
Collapse
Affiliation(s)
- Haoli Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Jingjing Zeng
- The Central Laboratory, The Second People's Hospital of Shenzhen, Shenzhen 518035, People's Republic of China
| | - Yongzhong Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.
| |
Collapse
|
15
|
The 3D Genome as a Target for Anticancer Therapy. Trends Mol Med 2020; 26:141-149. [PMID: 31679987 PMCID: PMC9929230 DOI: 10.1016/j.molmed.2019.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 01/08/2023]
Abstract
The role of 3D genome organization in the precise regulation of gene expression is well established. Accordingly, the mechanistic connections between 3D genome alterations and disease development are becoming increasingly apparent. This opinion article provides a snapshot of our current understanding of the 3D genome alterations associated with cancers. We discuss potential connections of the 3D genome and cancer transcriptional addiction phenomenon as well as molecular mechanisms of action of 3D genome-disrupting drugs. Finally, we highlight issues and perspectives raised by the discovery of the first pharmaceutical strongly affecting 3D genome organization.
Collapse
|
16
|
Li Z, Shang X, Luo S, Zhu F, Wei X, Zhou W, Ye Y, Yan T, Cai R, Xu X. Characterization of two novel Alu element-mediated α-globin gene cluster deletions causing α 0-thalassemia by targeted next-generation sequencing. Mol Genet Genomics 2020; 295:505-514. [PMID: 31897801 DOI: 10.1007/s00438-019-01637-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022]
Abstract
α-thalassemia is an inherited blood disorder commonly caused by deletions or point mutations involving one or both α-globin genes. Recent studies shed new light on the critical role of upstream enhancers multi-species conserved sequences (MCSs) in the ordered regulation of α-globin gene expression. Herein, we reported two unrelated probands with deletions in α-globin genes and MCSs, respectively. The proband from Family A is a compound heterozygote carrying a known α+ mutation (-α3.7) and a novel 60.2 kb deletion causing the absence of both α-globin genes. The proband from Family B, on the other hand, is a compound heterozygote with a known α0 mutation (--SEA) and a novel deletion involving only upstream regulatory elements MCS-R1, R2 and R3, while the α-globin genes remain intact. Notably, both these two patients suffered varied extent of anemia, indicating that the loss of enhancer elements could equally lead to reduced synthesis of α-globin. Upon these observations, we then confirmed the exact breakpoints of these two novel deletions using a targeted next-generation sequencing (NGS) previously established by our group, which may enable further elucidation of the rearrangement mechanisms on these deletions and functional dissection of MCSs. Taken together, our study reports a reliable NGS-based molecular screening approach for accurate identification of copy number variations (CNVs) in the α-globin cluster and the genetic diagnosis of these two probands may help to extend the spectrum of α-thalassemia mutations in Chinese population.
Collapse
Affiliation(s)
- Zhiming Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Genetics Testing Engineering Research Center, Guangzhou, 510515, Guangdong, China
| | - Shiqiang Luo
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, China
| | - Fei Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Genetics Testing Engineering Research Center, Guangzhou, 510515, Guangdong, China
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Genetics Testing Engineering Research Center, Guangzhou, 510515, Guangdong, China
| | - Yuhua Ye
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Guangdong Genetics Testing Engineering Research Center, Guangzhou, 510515, Guangdong, China
| | - Tizhen Yan
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, China
| | - Ren Cai
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China. .,Guangdong Genetics Testing Engineering Research Center, Guangzhou, 510515, Guangdong, China.
| |
Collapse
|
17
|
Piszczek L, Memoli S, Raggioli A, Viosca J, Rientjes J, Hublitz P, Czaban W, Wyrzykowska A, Gross C. Mouse model of the human serotonin transporter-linked polymorphic region. Mamm Genome 2019; 30:319-328. [PMID: 31667540 PMCID: PMC6884432 DOI: 10.1007/s00335-019-09815-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/21/2019] [Indexed: 11/27/2022]
Abstract
Genetic factors play a significant role in risk for mood and anxiety disorders. Polymorphisms in genes that regulate the brain monoamine systems, such as catabolic enzymes and transporters, are attractive candidates for being risk factors for emotional disorders given the weight of evidence implicating monoamines involvement in these conditions. Several common genetic variants have been identified in the human serotonin transporter (5-HTT) gene, including a repetitive sequence located in the promoter region of the locus called the serotonin transporter-linked polymorphic region (5-HTT-LPR). This polymorphism has been associated with a number of mental traits in both humans and primates, including depression, neuroticism, and harm avoidance. Some, but not all, studies found a link between the polymorphism and 5-HTT levels, leaving open the question of whether the polymorphism affects risk for mental traits via changes in 5-HTT expression. To investigate the impact of the polymorphism on gene expression, serotonin homeostasis, and behavioral traits, we set out to develop a mouse model of the human 5-HTT-LPR. Here we describe the creation and characterization of a set of mouse lines with single-copy human transgenes carrying the short and long 5-HTT-LPR variants. Although we were not able to detect differences in expression between the short and long variants, we encountered several technical issues concerning the design of our humanized mice that are likely to have influenced our findings. Our study serves as a cautionary note for future studies aimed at studying human transgene regulation in the context of the living mouse.
Collapse
Affiliation(s)
- Lukasz Piszczek
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy.
- Research Institute of Molecular Pathology, Vienna, Austria.
| | - Simone Memoli
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Angelo Raggioli
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - José Viosca
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
- Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
| | - Jeanette Rientjes
- Monash Genome Modification Platform (MGMP), Monash University, Clayton, Australia
| | - Philip Hublitz
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Weronika Czaban
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Anna Wyrzykowska
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Cornelius Gross
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy.
| |
Collapse
|
18
|
Razin SV, Ulianov SV, Gavrilov AA. 3D Genomics. Mol Biol 2019; 53:802-812. [DOI: 10.1134/s0026893319060153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 08/30/2023]
|
19
|
Liu L, Kim MH, Hyeon C. Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C. Biophys J 2019; 117:613-625. [PMID: 31337548 DOI: 10.1016/j.bpj.2019.06.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
Adapting a well-established formalism in polymer physics, we develop a minimalist approach to infer three-dimensional folding of chromatin from Hi-C data. The three-dimensional chromosome structures generated from our heterogeneous loop model (HLM) are used to visualize chromosome organizations that can substantiate the measurements from fluorescence in situ hybridization, chromatin interaction analysis by paired-end tag sequencing, and RNA-seq signals. We demonstrate the utility of the HLM with several case studies. Specifically, the HLM-generated chromosome structures, which reproduce the spatial distribution of topologically associated domains from fluorescence in situ hybridization measurement, show the phase segregation between two types of topologically associated domains explicitly. We discuss the origin of cell-type-dependent gene-expression level by modeling the chromatin globules of α-globin and SOX2 gene loci for two different cell lines. We also use the HLM to discuss how the chromatin folding and gene-expression level of Pax6 loci, associated with mouse neural development, are modulated by interactions with two enhancers. Finally, HLM-generated structures of chromosome 19 of mouse embryonic stem cells, based on single-cell Hi-C data collected over each cell-cycle phase, visualize changes in chromosome conformation along the cell-cycle. Given a contact frequency map between chromatic loci supplied from Hi-C, HLM is a computationally efficient and versatile modeling tool to generate chromosome structures that can complement interpreting other experimental data.
Collapse
Affiliation(s)
- Lei Liu
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Min Hyeok Kim
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea.
| |
Collapse
|
20
|
Zhu F, Nair RR, Fisher EMC, Cunningham TJ. Humanising the mouse genome piece by piece. Nat Commun 2019; 10:1845. [PMID: 31015419 PMCID: PMC6478830 DOI: 10.1038/s41467-019-09716-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/23/2019] [Indexed: 12/14/2022] Open
Abstract
To better understand human health and disease, researchers create a wide variety of mouse models that carry human DNA. With recent advances in genome engineering, the targeted replacement of mouse genomic regions with orthologous human sequences has become increasingly viable, ranging from finely tuned humanisation of individual nucleotides and amino acids to the incorporation of many megabases of human DNA. Here, we examine emerging technologies for targeted genomic humanisation, we review the spectrum of existing genomically humanised mouse models and the insights such models have provided, and consider the lessons learned for designing such models in the future. Generation of transgenic mice has become routine in studying gene function and disease mechanisms, but often this is not enough to fully understand human biology. Here, the authors review the current state of the art of targeted genomic humanisation strategies and their advantages over classic approaches.
Collapse
Affiliation(s)
- Fei Zhu
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Remya R Nair
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, OX11 0RD, UK
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, WC1N 3BG, UK.
| | | |
Collapse
|
21
|
Cremer M, Cremer T. Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences. Genes Chromosomes Cancer 2019; 58:427-436. [DOI: 10.1002/gcc.22714] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marion Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
| | - Thomas Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
| |
Collapse
|
22
|
van de Lagemaat LN, Flenley M, Lynch MD, Garrick D, Tomlinson SR, Kranc KR, Vernimmen D. CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands. Epigenetics Chromatin 2018; 11:59. [PMID: 30292235 PMCID: PMC6173865 DOI: 10.1186/s13072-018-0230-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The mechanism by which protein complexes interact to regulate the deposition of post-translational modifications of histones remains poorly understood. This is particularly important at regulatory regions, such as CpG islands (CGIs), which are known to recruit Trithorax (TrxG) and Polycomb group proteins. The CxxC zinc finger protein 1 (CFP1, also known as CGBP) is a subunit of the TrxG SET1 protein complex, a major catalyst of trimethylation of H3K4 (H3K4me3). RESULTS Here, we used ChIP followed by high-throughput sequencing (ChIP-seq) to analyse genomic occupancy of CFP1 in two human haematopoietic cell types. We demonstrate that CFP1 occupies CGIs associated with active transcription start sites (TSSs), and is mutually exclusive with H3K27 trimethylation (H3K27me3), a marker of polycomb repressive complex 2. Strikingly, rather than being restricted to active CGI TSSs, CFP1 also occupies a substantial fraction of active non-CGI TSSs and enhancers of transcribed genes. However, relative to other TrxG subunits, CFP1 was specialised to TSSs. Finally, we found enrichment of CpG-containing DNA motifs in CFP1 peaks at CGI promoters. CONCLUSIONS We found that CFP1 is not solely recruited to CpG islands as it was originally defined, but also other regions including non-CpG island promoters and enhancers.
Collapse
Affiliation(s)
- Louie N. van de Lagemaat
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Maria Flenley
- MRC Molecular Haematology Unit, Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS UK
| | - Magnus D. Lynch
- MRC Molecular Haematology Unit, Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS UK
- Centre for Stem Cells and Regenerative Medicine, 28th Floor Guy’s Tower, Great Maze Pond, London, SE1 9RT UK
- st John’s institute of dermatology, Great Maze Pond, London, SE1 9RT UK
| | - David Garrick
- INSERM, UMRS-1126, Institut Universitaire d’Hématologie, Université Paris Diderot, 75010 Paris, France
| | - Simon R. Tomlinson
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK
| | - Kamil R. Kranc
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Douglas Vernimmen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| |
Collapse
|
23
|
Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, De Ornellas S, Oudelaar AM, Scott C, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ. A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nat Commun 2018; 9:3849. [PMID: 30242161 PMCID: PMC6155075 DOI: 10.1038/s41467-018-06248-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/24/2018] [Indexed: 11/08/2022] Open
Abstract
Self-interacting chromatin domains encompass genes and their cis-regulatory elements; however, the three-dimensional form a domain takes, whether this relies on enhancer-promoter interactions, and the processes necessary to mediate the formation and maintenance of such domains, remain unclear. To examine these questions, here we use a combination of high-resolution chromosome conformation capture, a non-denaturing form of fluorescence in situ hybridisation and super-resolution imaging to study a 70 kb domain encompassing the mouse α-globin regulatory locus. We show that this region forms an erythroid-specific, decompacted, self-interacting domain, delimited by frequently apposed CTCF/cohesin binding sites early in terminal erythroid differentiation, and does not require transcriptional elongation for maintenance of the domain structure. Formation of this domain does not rely on interactions between the α-globin genes and their major enhancers, suggesting a transcription-independent mechanism for establishment of the domain. However, absence of the major enhancers does alter internal domain interactions. Formation of a loop domain therefore appears to be a mechanistic process that occurs irrespective of the specific interactions within.
Collapse
Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Nigel A Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Dominic Waithe
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Izabela Szczerbal
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Mira T Kassouf
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK.
| |
Collapse
|
24
|
Abstract
Thalassemia is a disorder of hemoglobin characterized by reduced or absent production of one of the globin chains in human red blood cells with relative excess of the other. Impaired synthesis of β-globin results in β-thalassemia, whereas defective synthesis of α-globin leads to α-thalassemia. Despite being a monogenic disorder, thalassemia exhibits remarkable clinical heterogeneity that is directly related to the intracellular imbalance between α- and β-like globin chains. Novel insights into the genetic modifiers have contributed to the understanding of the correlation between genotype and phenotype and are being explored as therapeutic pathways to cure this life-limiting disease.
Collapse
Affiliation(s)
- Sachith Mettananda
- Molecular Hematology Unit, Medical Research Council (MRC), Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Department of Paediatrics, Faculty of Medicine, University of Kelaniya, Thalagolla Road, Ragama 11010, Sri Lanka
| | - Douglas R Higgs
- Molecular Hematology Unit, Medical Research Council (MRC), Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; National Institute for Health Research, Oxford Biomedical Research Centre, Blood Theme, Oxford University Hospitals, Headington, Oxford OX3 9DU, UK.
| |
Collapse
|
25
|
Gürsoy G, Xu Y, Kenter AL, Liang J. Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data. Nucleic Acids Res 2017; 45:11547-11558. [PMID: 28981716 PMCID: PMC5714131 DOI: 10.1093/nar/gkx784] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 08/30/2017] [Indexed: 01/23/2023] Open
Abstract
Conformation capture technologies measure frequencies of interactions between chromatin regions. However, understanding gene-regulation require knowledge of detailed spatial structures of heterogeneous chromatin in cells. Here we describe the nC-SAC (n-Constrained-Self Avoiding Chromatin) method that transforms experimental interaction frequencies into 3D ensembles of chromatin chains. nC-SAC first distinguishes specific from non-specific interaction frequencies, then generates 3D chromatin ensembles using identified specific interactions as spatial constraints. Application to α-globin locus shows that these constraints (∼20%) drive the formation of ∼99% all experimentally captured interactions, in which ∼30% additional to the imposed constraints is found to be specific. Many novel specific spatial contacts not captured by experiments are also predicted. A subset, of which independent ChIA-PET data are available, is validated to be RNAPII-, CTCF-, and RAD21-mediated. Their positioning in the architectural context of imposed specific interactions from nC-SAC is highly important. Our results also suggest the presence of a many-body structural unit involving α-globin gene, its enhancers, and POL3RK gene for regulating the expression of α-globin in silent cells.
Collapse
Affiliation(s)
- Gamze Gürsoy
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yun Xu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Amy L Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| |
Collapse
|
26
|
Essebier A, Lamprecht M, Piper M, Bodén M. Bioinformatics approaches to predict target genes from transcription factor binding data. Methods 2017; 131:111-119. [DOI: 10.1016/j.ymeth.2017.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/29/2017] [Accepted: 09/03/2017] [Indexed: 12/28/2022] Open
|
27
|
Huang L, Liu P, Yuan Z, Zhou T, Yu J. The free-energy cost of interaction between DNA loops. Sci Rep 2017; 7:12610. [PMID: 28974770 PMCID: PMC5626758 DOI: 10.1038/s41598-017-12765-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/14/2017] [Indexed: 12/03/2022] Open
Abstract
From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.
Collapse
Affiliation(s)
- Lifang Huang
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Peijiang Liu
- School of Statistics and Mathematics, Guangdong University of Finance & Economics, Guangzhou, 510275, P.R. China
| | - Zhanjiang Yuan
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, 510275, P.R. China.
| | - Jianshe Yu
- Research Centre of Applied Mathematics, Guangzhou University, Guangzhou, 510006, P.R. China.
| |
Collapse
|
28
|
Huang LY, Yan JM, Zhou JY, Li J, Xie XM, Li DZ. A Severe Case of Hemoglobin H Disease due to Compound Heterozygosity for Deletion of the Major α-Globin Regulatory Element (MCS-R2) and α0-Thalassemia. Acta Haematol 2017; 138:61-64. [PMID: 28743121 DOI: 10.1159/000477531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/16/2017] [Indexed: 11/19/2022]
Affiliation(s)
- Lv-Yin Huang
- Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University, Guangzhou, PR China
| | | | | | | | | | | |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
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
|
31
|
Davies JOJ, Oudelaar AM, Higgs DR, Hughes JR. How best to identify chromosomal interactions: a comparison of approaches. Nat Methods 2017; 14:125-134. [PMID: 28139673 DOI: 10.1038/nmeth.4146] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/20/2016] [Indexed: 12/28/2022]
Abstract
Chromosome conformation capture (3C) methods are central to understanding the link between nuclear structure and function, and the physical interactions between distal regulatory elements and promoters. However, no one method is appropriate to address all biological questions, as each variant differs markedly in resolution, reproducibility, throughput and biases. A thorough appreciation of the strengths and weaknesses of each technique is critical when choosing the correct method for a specific application or for gauging how best to interpret different sources of data. In addition, the analysis method must be carefully considered, as this choice can profoundly affect the output. In this Review, we describe and compare the different available 3C-based approaches, with a focus on the analysis of mammalian genomes.
Collapse
Affiliation(s)
- James O J Davies
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - A Marieke Oudelaar
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Douglas R Higgs
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| |
Collapse
|
32
|
Buffry AD, Mendes CC, McGregor AP. The Functionality and Evolution of Eukaryotic Transcriptional Enhancers. ADVANCES IN GENETICS 2016; 96:143-206. [PMID: 27968730 DOI: 10.1016/bs.adgen.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enhancers regulate precise spatial and temporal patterns of gene expression in eukaryotes and, moreover, evolutionary changes in these modular cis-regulatory elements may represent the predominant genetic basis for phenotypic evolution. Here, we review approaches to identify and functionally analyze enhancers and their transcription factor binding sites, including assay for transposable-accessible chromatin-sequencing (ATAC-Seq) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, respectively. We also explore enhancer functionality, including how transcription factor binding sites combine to regulate transcription, as well as research on shadow and super enhancers, and how enhancers can act over great distances and even in trans. Finally, we discuss recent theoretical and empirical data on how transcription factor binding sites and enhancers evolve. This includes how the function of enhancers is maintained despite the turnover of transcription factor binding sites as well as reviewing studies where mutations in enhancers have been shown to underlie morphological change.
Collapse
Affiliation(s)
- A D Buffry
- Oxford Brookes University, Oxford, United Kingdom
| | - C C Mendes
- Oxford Brookes University, Oxford, United Kingdom
| | - A P McGregor
- Oxford Brookes University, Oxford, United Kingdom
| |
Collapse
|
33
|
Martyn GE, Quinlan KGR, Crossley M. The regulation of human globin promoters by CCAAT box elements and the recruitment of NF-Y. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:525-536. [PMID: 27718361 DOI: 10.1016/j.bbagrm.2016.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/01/2023]
Abstract
CCAAT boxes are motifs found within the proximal promoter of many genes, including the human globin genes. The highly conserved nature of CCAAT box motifs within the promoter region of both α-like and β-like globin genes emphasises the functional importance of the CCAAT sequence in globin gene regulation. Mutations within the β-globin CCAAT box result in β-thalassaemia, while mutations within the distal γ-globin CCAAT box cause the Hereditary Persistence of Foetal Haemoglobin, a benign condition which results in continued γ-globin expression during adult life. Understanding the transcriptional regulation of the globin genes is of particular interest, as reactivating the foetal γ-globin gene alleviates the symptoms of β-thalassaemia and sickle cell anaemia. NF-Y is considered to be the primary activating transcription factor which binds to globin CCAAT box motifs. Here we review recruitment of NF-Y to globin CCAAT boxes and the role NF-Y plays in regulating globin gene expression. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
Collapse
Affiliation(s)
- Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia.
| |
Collapse
|
34
|
Vernimmen D, Bickmore WA. The Hierarchy of Transcriptional Activation: From Enhancer to Promoter. Trends Genet 2016; 31:696-708. [PMID: 26599498 DOI: 10.1016/j.tig.2015.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Regulatory elements (enhancers) that are remote from promoters play a critical role in the spatial, temporal, and physiological control of gene expression. Studies on specific loci, together with genome-wide approaches, suggest that there may be many common mechanisms involved in enhancer-promoter communication. Here, we discuss the multiprotein complexes that are recruited to enhancers and the hierarchy of events taking place between regulatory elements and promoters.
Collapse
Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| |
Collapse
|
35
|
Liu T, Zhang J, Zhou T. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression. PLoS Comput Biol 2016; 12:e1004917. [PMID: 27153118 PMCID: PMC4859557 DOI: 10.1371/journal.pcbi.1004917] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023] Open
Abstract
According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
Collapse
Affiliation(s)
- Tuoqi Liu
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| |
Collapse
|
36
|
Yang R, Kerschner JL, Gosalia N, Neems D, Gorsic LK, Safi A, Crawford GE, Kosak ST, Leir SH, Harris A. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res 2016; 44:3082-94. [PMID: 26673704 PMCID: PMC4838340 DOI: 10.1093/nar/gkv1358] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/21/2015] [Accepted: 11/24/2015] [Indexed: 12/18/2022] Open
Abstract
Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms.CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of the CFTR locus. We found the boundaries of the CFTRTAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure.
Collapse
Affiliation(s)
- Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jenny L Kerschner
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nehal Gosalia
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Daniel Neems
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lidija K Gorsic
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alexias Safi
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Gregory E Crawford
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Brackley CA, Brown JM, Waithe D, Babbs C, Davies J, Hughes JR, Buckle VJ, Marenduzzo D. Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models. Genome Biol 2016; 17:59. [PMID: 27036497 PMCID: PMC4815170 DOI: 10.1186/s13059-016-0909-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops. To test the model, we perform FISH experiments and compare with Capture-C data. Starting merely from the locations of protein binding sites, our model accurately predicts the experimentally observed chromatin interactions, revealing a population of 3D conformations.
Collapse
Affiliation(s)
- Chris A. Brackley
- />SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ UK
| | - Jill M. Brown
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Dominic Waithe
- />Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Christian Babbs
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - James Davies
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Jim R. Hughes
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Veronica J. Buckle
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Davide Marenduzzo
- />SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ UK
| |
Collapse
|
39
|
Mettananda S, Gibbons RJ, Higgs DR. Understanding α-globin gene regulation and implications for the treatment of β-thalassemia. Ann N Y Acad Sci 2015; 1368:16-24. [PMID: 26695885 DOI: 10.1111/nyas.12988] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Over the past three decades, a vast amount of new information has been uncovered describing how the globin genes are regulated. This knowledge has provided significant insights into the general understanding of the regulation of human genes. It is now known that molecular defects within and around the α- and β-globin genes, as well as in the distant regulatory elements, can cause thalassemia. Unbalanced production of globin chains owing to defective synthesis of one, and the continued unopposed synthesis of another, is the central causative factor in the cellular pathology and pathophysiology of thalassemia. A large body of clinical, genetic, and experimental evidence suggests that altering globin chain imbalance by reducing the production of α-globin synthesis ameliorates the disease severity in patients with β-thalassemia. With the development of new genetic-based therapeutic tools that have a potential to decrease the expression of a selected gene in a tissue-specific manner, the possibility of decreasing expression of the α-globin gene to improve the clinical severity of β-thalassemia could become a reality.
Collapse
Affiliation(s)
- Sachith Mettananda
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Department of Pediatrics, Faculty of Medicine, University of Kelaniya, Sri Lanka
| | - Richard J Gibbons
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Oxford National Institute for Health Research Biomedical Research Centre, Blood Theme, Oxford University Hospital, Oxford, United Kingdom
| |
Collapse
|
40
|
α-Globin as a molecular target in the treatment of β-thalassemia. Blood 2015; 125:3694-701. [PMID: 25869286 DOI: 10.1182/blood-2015-03-633594] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 03/31/2015] [Indexed: 12/31/2022] Open
Abstract
The thalassemias, together with sickle cell anemia and its variants, are the world's most common form of inherited anemia, and in economically undeveloped countries, they still account for tens of thousands of premature deaths every year. In developed countries, treatment of thalassemia is also still far from ideal, requiring lifelong transfusion or allogeneic bone marrow transplantation. Clinical and molecular genetic studies over the course of the last 50 years have demonstrated how coinheritance of modifier genes, which alter the balance of α-like and β-like globin gene expression, may transform severe, transfusion-dependent thalassemia into relatively mild forms of anemia. Most attention has been paid to pathways that increase γ-globin expression, and hence the production of fetal hemoglobin. Here we review the evidence that reduction of α-globin expression may provide an equally plausible approach to ameliorating clinically severe forms of β-thalassemia, and in particular, the very common subgroup of patients with hemoglobin E β-thalassemia that makes up approximately half of all patients born each year with severe β-thalassemia.
Collapse
|
41
|
Sorolla A, Tallack MR, Oey H, Harten SK, Daxinger LC, Magor GW, Combes AN, Ilsley M, Whitelaw E, Perkins AC. Identification of novel hypomorphic and null mutations in Klf1 derived from a genetic screen for modifiers of α-globin transgene variegation. Genomics 2015; 105:116-22. [DOI: 10.1016/j.ygeno.2014.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/18/2014] [Accepted: 09/20/2014] [Indexed: 10/24/2022]
|
42
|
Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
43
|
Iarovaia OV, Ioudinkova ES, Petrova NV, Dolgushin KV, Kovina AV, Nefedochkina AV, Vassetzky YS, Razin SV. Evolution of α- and β-globin genes and their regulatory systems in light of the hypothesis of domain organization of the genome. BIOCHEMISTRY (MOSCOW) 2014; 79:1141-50. [PMID: 25539999 DOI: 10.1134/s0006297914110017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The α- and β-globin gene domains are a traditional model for study of the domain organization of the eucaryotic genome because these genes encode hemoglobin, a physiologically important protein. The α-globin and β-globin gene domains are organized in completely different ways, while the expression of globin genes is tightly coordinated, which makes it extremely interesting to study the origin of these genes and the evolution of their regulatory systems. In this review, the organization of the α- and β-globin gene domains and their genomic environment in different taxonomic groups are comparatively analyzed. A new hypothesis of possible evolutionary pathways for segregated α- and β-globin gene domains of warm-blooded animals is proposed.
Collapse
Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Over the last three decades, studies of the α- and β-globin genes clusters have led to elucidation of the general principles of mammalian gene regulation, such as RNA stability, termination of transcription, and, more importantly, the identification of remote regulatory elements. More recently, detailed studies of α-globin regulation, using both mouse and human loci, allowed the dissection of the sequential order in which transcription factors are recruited to the locus during lineage specification. These studies demonstrated the importance of the remote regulatory elements in the recruitment of RNA polymerase II (PolII) together with their role in the generation of intrachromosomal loops within the locus and the removal of polycomb complexes during differentiation. The multiple roles attributed to remote regulatory elements that have emerged from these studies will be discussed.
Collapse
Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- * E-mail:
| |
Collapse
|
45
|
Schwarzer W, Spitz F. The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains. Curr Opin Genet Dev 2014; 27:74-82. [PMID: 24907448 DOI: 10.1016/j.gde.2014.03.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 02/06/2023]
Abstract
Specificity and precision of expression are essential for the genes that regulate developmental processes. The specialized cis-acting modules, such as enhancers, that define gene expression patterns can be distributed across large regions, raising questions about the nature of the mechanisms that underline their action. Recent data has exposed the structural 3D context in which these long-range enhancers are operating. Here, we present how these studies shed new light on principles driving long-distance regulatory relationships. We discuss the molecular mechanisms that enable and accompany the action of long-range acting elements and the integration of multiple distributed regulatory inputs into the coherent and specific regulatory programs that are key to embryonic development.
Collapse
Affiliation(s)
- Wibke Schwarzer
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| |
Collapse
|
46
|
Funnell APW, Vernimmen D, Lim WF, Mak KS, Wienert B, Martyn GE, Artuz CM, Burdach J, Quinlan KGR, Higgs DR, Whitelaw E, Pearson RCM, Crossley M. Differential regulation of the α-globin locus by Krüppel-like Factor 3 in erythroid and non-erythroid cells. BMC Mol Biol 2014; 15:8. [PMID: 24885809 PMCID: PMC4033687 DOI: 10.1186/1471-2199-15-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/06/2014] [Indexed: 12/17/2022] Open
Abstract
Background Krüppel-like Factor 3 (KLF3) is a broadly expressed zinc-finger transcriptional repressor with diverse biological roles. During erythropoiesis, KLF3 acts as a feedback repressor of a set of genes that are activated by Krüppel-like Factor 1 (KLF1). Noting that KLF1 binds α-globin gene regulatory sequences during erythroid maturation, we sought to determine whether KLF3 also interacts with the α-globin locus to regulate transcription. Results We found that expression of a human transgenic α-globin reporter gene is markedly up-regulated in fetal and adult erythroid cells of Klf3−/− mice. Inspection of the mouse and human α-globin promoters revealed a number of canonical KLF-binding sites, and indeed, KLF3 was shown to bind to these regions both in vitro and in vivo. Despite these observations, we did not detect an increase in endogenous murine α-globin expression in Klf3−/− erythroid tissue. However, examination of murine embryonic fibroblasts lacking KLF3 revealed significant de-repression of α-globin gene expression. This suggests that KLF3 may contribute to the silencing of the α-globin locus in non-erythroid tissue. Moreover, ChIP-Seq analysis of murine fibroblasts demonstrated that across the locus, KLF3 does not occupy the promoter regions of the α-globin genes in these cells, but rather, binds to upstream, DNase hypersensitive regulatory regions. Conclusions These findings reveal that the occupancy profile of KLF3 at the α-globin locus differs in erythroid and non-erythroid cells. In erythroid cells, KLF3 primarily binds to the promoters of the adult α-globin genes, but appears dispensable for normal transcriptional regulation. In non-erythroid cells, KLF3 distinctly binds to the HS-12 and HS-26 elements and plays a non-redundant, albeit modest, role in the silencing of α-globin expression.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| |
Collapse
|
47
|
Gushchanskaya ES, Artemov AV, Ulyanov SV, Logacheva MD, Penin AA, Kotova ES, Akopov SB, Nikolaev LG, Iarovaia OV, Sverdlov ED, Gavrilov AA, Razin SV. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes. Epigenetics 2014; 9:951-63. [PMID: 24736527 DOI: 10.4161/epi.28794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments.
Collapse
Affiliation(s)
- Ekaterina S Gushchanskaya
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Molecular Biology; Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Artem V Artemov
- Faculty of Bioengineering and Bioinformatics; Lomonosov Moscow State University; Moscow, Russia; Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow, Russia
| | - Sergey V Ulyanov
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Maria D Logacheva
- Laboratory of Evolutionary Genomics; Lomonosov Moscow State University; Moscow, Russia
| | - Aleksey A Penin
- Laboratory of Evolutionary Genomics; Lomonosov Moscow State University; Moscow, Russia
| | - Elena S Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Sergey B Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Lev G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Olga V Iarovaia
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Eugene D Sverdlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Molecular Biology; Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| |
Collapse
|
48
|
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 2014; 46:205-12. [PMID: 24413732 DOI: 10.1038/ng.2871] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/12/2013] [Indexed: 12/19/2022]
Abstract
Gene expression during development and differentiation is regulated in a cell- and stage-specific manner by complex networks of intergenic and intragenic cis-regulatory elements whose numbers and representation in the genome far exceed those of structural genes. Using chromosome conformation capture, it is now possible to analyze in detail the interaction between enhancers, silencers, boundary elements and promoters at individual loci, but these techniques are not readily scalable. Here we present a high-throughput approach (Capture-C) to analyze cis interactions, interrogating hundreds of specific interactions at high resolution in a single experiment. We show how this approach will facilitate detailed, genome-wide analysis to elucidate the general principles by which cis-acting sequences control gene expression. In addition, we show how Capture-C will expedite identification of the target genes and functional effects of SNPs that are associated with complex diseases, which most frequently lie in intergenic cis-acting regulatory elements.
Collapse
|
49
|
Marques AC, Hughes J, Graham B, Kowalczyk MS, Higgs DR, Ponting CP. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol 2013; 14:R131. [PMID: 24289259 PMCID: PMC4054604 DOI: 10.1186/gb-2013-14-11-r131] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers. RESULTS We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. These two classes of 5' capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. Nevertheless, elncRNAs are more tissue-restricted, less highly expressed and less well conserved during evolution. Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis. CONCLUSIONS We have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci.
Collapse
|
50
|
Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal lari R, Lupien M, Markowitz S, Scacheri PC. Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res 2013; 24:1-13. [PMID: 24196873 PMCID: PMC3875850 DOI: 10.1101/gr.164079.113] [Citation(s) in RCA: 264] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA variants (SNPs) that predispose to common traits often localize within noncoding regulatory elements such as enhancers. Moreover, loci identified by genome-wide association studies (GWAS) often contain multiple SNPs in linkage disequilibrium (LD), any of which may be causal. Thus, determining the effect of these multiple variant SNPs on target transcript levels has been a major challenge. Here, we provide evidence that for six common autoimmune disorders (rheumatoid arthritis, Crohn's disease, celiac disease, multiple sclerosis, lupus, and ulcerative colitis), the GWAS association arises from multiple polymorphisms in LD that map to clusters of enhancer elements active in the same cell type. This finding suggests a “multiple enhancer variant” hypothesis for common traits, where several variants in LD impact multiple enhancers and cooperatively affect gene expression. Using a novel method to delineate enhancer–gene interactions, we show that multiple enhancer variants within a given locus typically target the same gene. Using available data from HapMap and B lymphoblasts as a model system, we provide evidence at numerous loci that multiple enhancer variants cooperatively contribute to altered expression of their gene targets. The effects on target transcript levels tend to be modest and can be either gain- or loss-of-function. Additionally, the genes associated with multiple enhancer variants encode proteins that are often functionally related and enriched in common pathways. Overall, the multiple enhancer variant hypothesis offers a new paradigm by which noncoding variants can confer susceptibility to common traits.
Collapse
Affiliation(s)
- Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44122, USA
| | | | | | | | | | | | | | | | | |
Collapse
|