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Gaskill MM, Soluri IV, Branks AE, Boka AP, Stadler MR, Vietor K, Huang HYS, Gibson TJ, Mukherjee A, Mir M, Blythe SA, Harrison MM. Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression. Dev Cell 2023; 58:1610-1624.e8. [PMID: 37478844 PMCID: PMC10528433 DOI: 10.1016/j.devcel.2023.06.010] [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: 11/15/2022] [Revised: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
Abstract
The eukaryotic genome is organized to enable the precise regulation of gene expression. This organization is established as the embryo transitions from a fertilized gamete to a totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early development in Drosophila. GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. This non-uniform distribution is driven by binding to highly abundant GA repeats. At GA repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains essential for the robust regulation of gene expression.
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Affiliation(s)
- Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Isabella V Soluri
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Annemarie E Branks
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan P Boka
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael R Stadler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katherine Vietor
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hao-Yu S Huang
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Apratim Mukherjee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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2
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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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Lu XB, Guo YH, Huang W. Characterization of the cHS4 insulator in mouse embryonic stem cells. FEBS Open Bio 2020; 10:644-656. [PMID: 32087050 PMCID: PMC7137798 DOI: 10.1002/2211-5463.12818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/09/2020] [Accepted: 02/21/2020] [Indexed: 01/16/2023] Open
Abstract
Synthetic biology circuits are often constructed with multiple gene expression units assembled in close proximity, and they can be used to perform complex functions in embryonic stem cells (ESCs). However, mutual interference between transcriptional units has not been well studied in mouse ESCs. To assess the efficiency of insulators at suppressing promoter interference in mouse ESCs, we used an evaluation scheme in which a tunable tetracycline response element promoter is connected to a constant Nanog promoter. The chicken hypersensitive site 4 (cHS4) insulator, widely used both for enhancer blocking and for barrier insulation in vitro and in vivo, was positioned between the two expression units for assessment. By inserting the cassette into various loci of the mouse ESC genome with PiggyBac transposon, we were able to quantitatively examine the protective effect of cHS4 by gradually increasing the transcriptional activity of the tetracycline response element promoter with doxycycline and then measuring the transcriptional activity of the Nanog promoter. Our results indicate that the cHS4 insulator has minimal insulating effects on promoter interference in mouse ESCs. Further studies show that the cHS4 insulation effect may be promoter specific and related to interaction with CCCTC‐binding factor‐mediated loop formation. In addition, we also compared DNA transposition and transgene expression with or without the cHS4 insulator using well‐established ESC reporters. The results indicate that cHS4 has no apparent effects on DNA transposition and transgene expression levels, but exerts modest protective effects on long‐term transgene silencing.
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Affiliation(s)
- Xi-Bin Lu
- Core Research Facilities, Southern University of Science and Technology, Shenzhen, China
| | - Yu-Han Guo
- Forward Pharmaceuticals Limited Co., Shenzhen, China
| | - Wei Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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4
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Jox T, Buxa MK, Bohla D, Ullah I, Mačinković I, Brehm A, Bartkuhn M, Renkawitz R. Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation. Epigenetics Chromatin 2017; 10:32. [PMID: 28680483 PMCID: PMC5496309 DOI: 10.1186/s13072-017-0140-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/27/2017] [Indexed: 12/02/2022] Open
Abstract
Background Chromatin insulators shield promoters and chromatin domains from neighboring enhancers or chromatin regions with opposing activities. Insulator-binding proteins and their cofactors mediate the boundary function. In general, covalent modification of proteins by the small ubiquitin-like modifier (SUMO) is an important mechanism to control the interaction of proteins within complexes. Results Here we addressed the impact of dSUMO in respect of insulator function, chromatin binding of insulator factors and formation of insulator speckles in Drosophila. SUMOylation augments the enhancer blocking function of four different insulator sequences and increases the genome-wide binding of the insulator cofactor CP190. Conclusions These results indicate that enhanced chromatin binding of SUMOylated CP190 causes fusion of insulator speckles, which may allow for more efficient insulation. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0140-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Theresa Jox
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany.,Institute for Molecular Pathology, UKGM, 35392 Giessen, Germany
| | - Melanie K Buxa
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany.,Flohr Consult, Adenauerallee 136, 53113 Bonn, Germany
| | - Dorte Bohla
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Ikram Ullah
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, 35037 Marburg, Germany
| | - Igor Mačinković
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, 35037 Marburg, Germany
| | - Alexander Brehm
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, 35037 Marburg, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
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Avva SVSP, Hart CM. Characterization of the Drosophila BEAF-32A and BEAF-32B Insulator Proteins. PLoS One 2016; 11:e0162906. [PMID: 27622635 PMCID: PMC5021357 DOI: 10.1371/journal.pone.0162906] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022] Open
Abstract
Data implicate the Drosophila 32 kDa Boundary Element-Associated Factors BEAF-32A and BEAF-32B in both chromatin domain insulator element function and promoter function. They might also function as an epigenetic memory by remaining bound to mitotic chromosomes. Both proteins are made from the same gene. They differ in their N-terminal 80 amino acids, which contain single DNA-binding BED fingers. The remaining 200 amino acids are identical in the two proteins. The structure and function of the middle region of 120 amino acids is unknown, while the C-terminal region of 80 amino acids has a putative leucine zipper and a BESS domain and mediates BEAF-BEAF interactions. Here we report a further characterization of BEAF. We show that the BESS domain alone is sufficient to mediate BEAF-BEAF interactions, although the presence of the putative leucine zipper on at least one protein strengthens the interactions. BEAF-32B is sufficient to rescue a null BEAF mutation in flies. Using mutant BEAF-32B rescue transgenes, we show that the middle region and the BESS domain are essential. In contrast, the last 40 amino acids of the middle region, which is poorly conserved among Drosophila species, is dispensable. Deleting the putative leucine zipper results in a hypomorphic mutant BEAF-32B protein. Finally, we document the dynamics of BEAF-32A-EGFP and BEAF-32B-mRFP during mitosis in embryos. A subpopulation of both proteins appears to remain on mitotic chromosomes and also on the mitotic spindle, while much of the fluorescence is dispersed during mitosis. Differences in the dynamics of the two proteins are observed in syncytial embryos, and both proteins show differences between syncytial and later embryos. This characterization of BEAF lays a foundation for future studies into molecular mechanisms of BEAF function.
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Affiliation(s)
- S. V. Satya Prakash Avva
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Craig M. Hart
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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Lee H, Cho DY, Whitworth C, Eisman R, Phelps M, Roote J, Kaufman T, Cook K, Russell S, Przytycka T, Oliver B. Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PLoS Genet 2016; 12:e1006295. [PMID: 27599372 PMCID: PMC5012587 DOI: 10.1371/journal.pgen.1006295] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 08/10/2016] [Indexed: 11/18/2022] Open
Abstract
Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies of the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of gene regulation due to altered nuclear architecture are rare. These rare cases include trans de-repression when deficiencies delete chromatin characterized as repressive in other studies. Generally, effects of breakpoints on expression are promoter proximal (~100bp) or in the gene body. Effects of deficiencies genome-wide are in genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds.
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Affiliation(s)
- Hangnoh Lee
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dong-Yeon Cho
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cale Whitworth
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Robert Eisman
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Melissa Phelps
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - John Roote
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Thomas Kaufman
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Kevin Cook
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Steven Russell
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Teresa Przytycka
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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7
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Kyrchanova O, Mogila V, Wolle D, Deshpande G, Parshikov A, Cléard F, Karch F, Schedl P, Georgiev P. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex. PLoS Genet 2016; 12:e1006188. [PMID: 27428541 PMCID: PMC4948906 DOI: 10.1371/journal.pgen.1006188] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/22/2016] [Indexed: 12/16/2022] Open
Abstract
Functionally autonomous regulatory domains direct the parasegment-specific expression of the Drosophila Bithorax complex (BX-C) homeotic genes. Autonomy is conferred by boundary/insulator elements that separate each regulatory domain from its neighbors. For six of the nine parasegment (PS) regulatory domains in the complex, at least one boundary is located between the domain and its target homeotic gene. Consequently, BX-C boundaries must not only block adventitious interactions between neighboring regulatory domains, but also be permissive (bypass) for regulatory interactions between the domains and their gene targets. To elucidate how the BX-C boundaries combine these two contradictory activities, we have used a boundary replacement strategy. We show that a 337 bp fragment spanning the Fab-8 boundary nuclease hypersensitive site and lacking all but 83 bp of the 625 bp Fab-8 PTS (promoter targeting sequence) fully rescues a Fab-7 deletion. It blocks crosstalk between the iab-6 and iab-7 regulatory domains, and has bypass activity that enables the two downstream domains, iab-5 and iab-6, to regulate Abdominal-B (Abd-B) transcription in spite of two intervening boundary elements. Fab-8 has two dCTCF sites and we show that they are necessary both for blocking and bypass activity. However, CTCF sites on their own are not sufficient for bypass. While multimerized dCTCF (or Su(Hw)) sites have blocking activity, they fail to support bypass. Moreover, this bypass defect is not rescued by the full length PTS. Finally, we show that orientation is critical for the proper functioning the Fab-8 replacement. Though the inverted Fab-8 boundary still blocks crosstalk, it disrupts the topology of the Abd-B regulatory domains and does not support bypass. Importantly, altering the orientation of the Fab-8 dCTCF sites is not sufficient to disrupt bypass, indicating that orientation dependence is conferred by other factors. Boundary elements in the Bithorax complex have two seemingly contradictory activities. They must block crosstalk between neighboring regulatory domains, but at the same time be permissive (insulator bypass) for regulatory interactions between the domains and the BX-C homeotic genes. We have used a replacement strategy to investigate how they carry out these two functions. We show that a 337 bp fragment spanning the Fab-8 boundary nuclease hypersensitive site is sufficient to fully rescue a Fab-7 boundary deletion. It blocks crosstalk and supports bypass. As has been observed in transgene assays, blocking activity requires the Fab-8 dCTCF sites, while full bypass activity requires the dCTCF sites plus a small part of PTS. In transgene assays, bypass activity typically depends on the orientation of the two insulators relative to each other. A similar orientation dependence is observed for the Fab-8 replacement in BX-C. When the orientation of the Fab-8 boundary is reversed, bypass activity is lost, while blocking is unaffected. Interestingly, unlike what has been observed in mammals, reversing the orientation of only the Fab-8 dCTCF sites does not affect boundary function. This finding indicates that other Fab-8 factors must play a critical role in determining orientation. Taken together, our findings argue that carrying out the paradoxical functions of the BX-C boundaries does not require any unusual or special properties; rather BX-C boundaries utilize generic blocking and insulator bypass activities that are appropriately adapted to their regulatory context. Thus making them a good model for studying the functional properties of boundaries/insulators in their native setting.
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Affiliation(s)
- Olga Kyrchanova
- Department of Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (OK); (PG)
| | - Vladic Mogila
- Department of Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Wolle
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Girish Deshpande
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Alexander Parshikov
- Department of Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Fabienne Cléard
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Francois Karch
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Paul Schedl
- Department of Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Pavel Georgiev
- Department of Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (OK); (PG)
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8
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Kyrchanova O, Mogila V, Wolle D, Magbanua JP, White R, Georgiev P, Schedl P. The boundary paradox in the Bithorax complex. Mech Dev 2015; 138 Pt 2:122-132. [PMID: 26215349 PMCID: PMC4890074 DOI: 10.1016/j.mod.2015.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 02/08/2023]
Abstract
The parasegment-specific expression of the three Drosophila Bithorax complex homeotic genes is orchestrated by nine functionally autonomous regulatory domains. Functional autonomy depends upon special elements called boundaries or insulators that are located between each domain. The boundaries ensure the independent activity of each domain by blocking adventitious interactions with initiators, enhancers and silencers in the neighboring domains. However, this blocking activity poses a regulatory paradox--the Bithorax boundaries are also able to insulate promoters from regulatory interactions with enhancers and silencers and six of the nine Bithorax regulatory domains are separated from their target genes by at least one boundary element. Here we consider several mechanisms that have been suggested for how the Bithorax regulatory domains are able to bypass intervening boundary elements and direct the appropriate parasegment-specific temporal and spatial expression of their target gene.
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Affiliation(s)
- Olga Kyrchanova
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladic Mogila
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia; Nikolaev V.A. Sukhomlinsky National University, Department of Biology, Ukraine
| | - Daniel Wolle
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jose Paolo Magbanua
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia; Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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9
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Functional role of dimerization and CP190 interacting domains of CTCF protein in Drosophila melanogaster. BMC Biol 2015; 13:63. [PMID: 26248466 PMCID: PMC4528719 DOI: 10.1186/s12915-015-0168-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/15/2015] [Indexed: 12/22/2022] Open
Abstract
Background Insulators play a central role in gene regulation, chromosomal architecture and genome function in higher eukaryotes. To learn more about how insulators carry out their diverse functions, we have begun an analysis of the Drosophila CTCF (dCTCF). CTCF is one of the few insulator proteins known to be conserved from flies to man. Results In the studies reported here we have focused on the identification and characterization of two dCTCF protein interaction modules. The first mediates dCTCF multimerization, while the second mediates dCTCF–CP190 interactions. The multimerization domain maps in the N-terminus of the dCTCF protein and likely mediates the formation of tetrameric complexes. The CP190 interaction module encompasses a sequence ~200 amino acids long that spans the C-terminal and mediates interactions with the N-terminal BTB domain of the CP190 protein. Transgene rescue experiments showed that a dCTCF protein lacking sequences critical for CP190 interactions was almost as effective as wild type in rescuing the phenotypic effects of a dCTCF null allele. The mutation did, however, affect CP190 recruitment to specific Drosophila insulator elements and had a modest effect on dCTCF chromatin association. A protein lacking the N-terminal dCTCF multimerization domain incompletely rescued the zygotic and maternal effect lethality of the null and did not rescue the defects in Abd-B regulation evident in surviving adult dCTCF mutant flies. Finally, we show that elimination of maternally contributed dCTCF at the onset of embryogenesis has quite different effects on development and Abd-B regulation than is observed when the homozygous mutant animals develop in the presence of maternally derived dCTCF activity. Conclusions Our results indicate that dCTCF–CP190 interactions are less critical for the in vivo functions of the dCTCF protein than the N-terminal dCTCF–dCTCF interaction domain. We also show that the phenotypic consequences of dCTCF mutations differ depending upon when and how dCTCF activity is lost. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0168-7) contains supplementary material, which is available to authorized users.
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10
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Srivastava S, Dhawan J, Mishra RK. Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters. Mech Dev 2015; 138 Pt 2:160-169. [PMID: 26254900 DOI: 10.1016/j.mod.2015.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 01/07/2023]
Abstract
Hox gene expression imparts segment identity to body structures along the anterior-posterior axis and is tightly governed by higher order chromatin mechanisms. Chromatin regulatory features of the homeotic complex are best defined in Drosophila melanogaster, where multiple cis-regulatory elements have been identified that ensure collinear Hox gene expression patterns in accordance with their genomic organization. Recent studies focused on delineating the epigenetic features of the vertebrate Hox clusters have helped reveal their dynamic chromatin organization and its impact on gene expression. Enrichment for the 'activating' H3K4me3 and 'repressive' H3K27me3 histone modifications is a particularly strong read-out for transcriptional status and correlates well with the evidence for chromatin loop domain structures and stage specific topological changes at these loci. However, it is not clear how such distinct domains are imposed and regulated independent of each other. Comparative analysis of the chromatin structure and organization of the homeotic gene clusters in fly and mammals is increasingly revealing the functional conservation of chromatin mediated mechanisms. Here we discuss the case for interspersed boundary elements existing within mammalian Hox clusters along with their possible roles and mechanisms of action. Recent studies suggest a role for factors other than the well characterized vertebrate boundary factor CTCF, such as the GAGA binding factor (GAF), in maintaining chromatin domains at the Hox loci. We also present data demonstrating how such regulatory elements may be involved in organizing higher order structure and demarcating active domains of gene expression at the mammalian Hox clusters.
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Affiliation(s)
- Surabhi Srivastava
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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11
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Le Gall A, Valeri A, Nollmann M. Roles of chromatin insulators in the formation of long-range contacts. Nucleus 2015; 6:118-22. [PMID: 25781057 DOI: 10.1080/19491034.2015.1010962] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromatin insulators are factors involved in higher-order, genome-wide organization of chromatin, and play key roles in regulating transcriptional programs. In this review, we discuss recent studies on the diverse composition of insulator complexes, and on the mechanism by which they establish long-range DNA interactions. Particularly, we describe new biophysical methods that allow for the study of the composition of large molecular complexes, and for defining the factors potentially required to establish long-range DNA contacts.
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Affiliation(s)
- Antoine Le Gall
- a Centre de Biochimie Structurale ; CNRS UMR5048; INSERM U1054; Université de Montpellier ; Montpellier , France
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12
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Ozdemir A, Ma L, White KP, Stathopoulos A. Su(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos. Dev Cell 2015; 31:100-13. [PMID: 25313963 DOI: 10.1016/j.devcel.2014.08.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 06/10/2014] [Accepted: 08/05/2014] [Indexed: 12/22/2022]
Abstract
In Drosophila embryos, a nuclear gradient of the Dorsal (Dl) transcription factor directs differential gene expression along the dorsoventral (DV) axis, translating it into distinct domains that specify future mesodermal, neural, and ectodermal territories. However, the mechanisms used to differentially position gene expression boundaries along this axis are not fully understood. Here, using a combination of approaches, including mutant phenotype analyses and chromatin immunoprecipitation, we show that the transcription factor Suppressor of Hairless, Su(H), helps define dorsal boundaries for many genes expressed along the DV axis. Synthetic reporter constructs also provide molecular evidence that Su(H) binding sites support repression and act to counterbalance activation through Dl and the ubiquitous activator Zelda. Our study highlights a role for broadly expressed repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory modules as important elements controlling spatial domains of gene expression to facilitate flexible positioning of boundaries across the entire DV axis.
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Affiliation(s)
- Anil Ozdemir
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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13
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Librado P, Rozas J. Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes. Genome Biol Evol 2014; 5:2096-108. [PMID: 24148943 PMCID: PMC3845639 DOI: 10.1093/gbe/evt158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Animal olfactory systems have a critical role for the survival and reproduction of individuals. In insects, the odorant-binding proteins (OBPs) are encoded by a moderately sized gene family, and mediate the first steps of the olfactory processing. Most OBPs are organized in clusters of a few paralogs, which are conserved over time. Currently, the biological mechanism explaining the close physical proximity among OBPs is not yet established. Here, we conducted a comprehensive study aiming to gain insights into the mechanisms underlying the OBP genomic organization. We found that the OBP clusters are embedded within large conserved arrangements. These organizations also include other non-OBP genes, which often encode proteins integral to plasma membrane. Moreover, the conservation degree of such large clusters is related to the following: 1) the promoter architecture of the confined genes, 2) a characteristic transcriptional environment, and 3) the chromatin conformation of the chromosomal region. Our results suggest that chromatin domains may restrict the location of OBP genes to regions having the appropriate transcriptional environment, leading to the OBP cluster structure. However, the appropriate transcriptional environment for OBP and the other neighbor genes is not dominated by reduced levels of expression noise. Indeed, the stochastic fluctuations in the OBP transcript abundance may have a critical role in the combinatorial nature of the olfactory coding process.
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Affiliation(s)
- Pablo Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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14
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Vogelmann J, Le Gall A, Dejardin S, Allemand F, Gamot A, Labesse G, Cuvier O, Nègre N, Cohen-Gonsaud M, Margeat E, Nöllmann M. Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila genome. PLoS Genet 2014; 10:e1004544. [PMID: 25165871 PMCID: PMC4148193 DOI: 10.1371/journal.pgen.1004544] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 06/17/2014] [Indexed: 11/18/2022] Open
Abstract
Chromatin insulators are genetic elements implicated in the organization of chromatin and the regulation of transcription. In Drosophila, different insulator types were characterized by their locus-specific composition of insulator proteins and co-factors. Insulators mediate specific long-range DNA contacts required for the three dimensional organization of the interphase nucleus and for transcription regulation, but the mechanisms underlying the formation of these contacts is currently unknown. Here, we investigate the molecular associations between different components of insulator complexes (BEAF32, CP190 and Chromator) by biochemical and biophysical means, and develop a novel single-molecule assay to determine what factors are necessary and essential for the formation of long-range DNA interactions. We show that BEAF32 is able to bind DNA specifically and with high affinity, but not to bridge long-range interactions (LRI). In contrast, we show that CP190 and Chromator are able to mediate LRI between specifically-bound BEAF32 nucleoprotein complexes in vitro. This ability of CP190 and Chromator to establish LRI requires specific contacts between BEAF32 and their C-terminal domains, and dimerization through their N-terminal domains. In particular, the BTB/POZ domains of CP190 form a strict homodimer, and its C-terminal domain interacts with several insulator binding proteins. We propose a general model for insulator function in which BEAF32/dCTCF/Su(HW) provide DNA specificity (first layer proteins) whereas CP190/Chromator are responsible for the physical interactions required for long-range contacts (second layer). This network of organized, multi-layer interactions could explain the different activities of insulators as chromatin barriers, enhancer blockers, and transcriptional regulators, and suggest a general mechanism for how insulators may shape the organization of higher-order chromatin during cell division.
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Affiliation(s)
- Jutta Vogelmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Antoine Le Gall
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Stephanie Dejardin
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Frederic Allemand
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Adrien Gamot
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université de Toulouse, Toulouse; France
| | - Gilles Labesse
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Olivier Cuvier
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS and Université de Toulouse, Toulouse; France
| | - Nicolas Nègre
- Laboratoire Diversité, Génomes & Interactions Microorganismes-Insectes, INRA UMR1333, Université de Montpellier 2, Montpellier, France
| | - Martin Cohen-Gonsaud
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Emmanuel Margeat
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
| | - Marcelo Nöllmann
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, Montpellier, France
- Institut National de la Santé et la Recherche Médicale, Unité 1054, Montpellier, France
- Universités Montpellier I et II, Montpellier, France
- * E-mail:
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15
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Lhoumaud P, Hennion M, Gamot A, Cuddapah S, Queille S, Liang J, Micas G, Morillon P, Urbach S, Bouchez O, Severac D, Emberly E, Zhao K, Cuvier O. Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes. EMBO J 2014; 33:1599-613. [PMID: 24916307 DOI: 10.15252/embj.201385965] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chromosomal domains in Drosophila are marked by the insulator-binding proteins (IBPs) dCTCF/Beaf32 and cofactors that participate in regulating long-range interactions. Chromosomal borders are further enriched in specific histone modifications, yet the role of histone modifiers and nucleosome dynamics in this context remains largely unknown. Here, we show that IBP depletion impairs nucleosome dynamics specifically at the promoters and coding sequence of genes flanked by IBP binding sites. Biochemical purification identifies the H3K36 histone methyltransferase NSD/dMes-4 as a novel IBP cofactor, which specifically co-regulates the chromatin accessibility of hundreds of genes flanked by dCTCF/Beaf32. NSD/dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-dependent H3K36 trimethylation, nucleosome positioning, and RNA splicing. Our results unveil a model for how IBPs regulate nucleosome dynamics and gene expression through NSD/dMes-4, which may regulate H3K27me3 spreading. Our data uncover how IBPs dynamically regulate chromatin organization depending on distinct cofactors.
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Affiliation(s)
- Priscillia Lhoumaud
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Magali Hennion
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Adrien Gamot
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Suresh Cuddapah
- Systems Biology Center, National Heart, Lung and Blood Institute National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sophie Queille
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Jun Liang
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Gael Micas
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Pauline Morillon
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Serge Urbach
- Mass-Spectrometry Facility, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Olivier Bouchez
- UMR444-Laboratoire de Génétique Cellulaire & GeT-PlaGe, INRA Genotoul, Auzeville, Toulouse, France
| | - Dany Severac
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Eldon Emberly
- Physics Department, Simon Fraser University (SFU), Burnaby, BC, Canada
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute National Institutes of Health (NIH), Bethesda, MD, USA
| | - Olivier Cuvier
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
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16
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Cuartero S, Fresán U, Reina O, Planet E, Espinàs ML. Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function. EMBO J 2014; 33:637-47. [PMID: 24502977 DOI: 10.1002/embj.201386001] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Insulators are DNA-protein complexes that play a central role in chromatin organization and regulation of gene expression. In Drosophila different proteins, dCTCF, Su(Hw), and BEAF bind to specific subsets of insulators most of them having in common CP190. It has been shown that there are a number of CP190-binding sites that are not shared with any other known insulator protein, suggesting that other proteins could cooperate with CP190 to regulate insulator activity. Here we report on the identification of two previously uncharacterized proteins as CP190-interacting proteins, that we have named Ibf1 and Ibf2. These proteins localize at insulator bodies and associate with chromatin at CP190-binding sites throughout the genome. We also show that Ibf1 and Ibf2 are DNA-binding proteins that form hetero-oligomers that mediate CP190 binding to chromatin. Moreover, Ibf1 and Ibf2 are necessary for insulator activity in enhancer-blocking assays and Ibf2 null mutation cause a homeotic phenotype. Taken together our data reveal a novel pathway of CP190 recruitment to chromatin that is required for insulator activity.
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Affiliation(s)
- Sergi Cuartero
- Institute of Molecular Biology of Barcelona IBMB-CSIC, and Institute for Research in Biomedicine IRB, Barcelona, Spain
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17
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Cléard F, Karch F, Maeda RK. DamID as an approach to studying long-distance chromatin interactions. Methods Mol Biol 2014; 1196:279-89. [PMID: 25151170 DOI: 10.1007/978-1-4939-1242-1_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
How transcription is controlled by distally located cis-regulatory elements is an active area of research in biology. As such, there have been many techniques developed to probe these long-distance chromatin interactions. Here, we focus on one such method, called DamID (van Steensel and Henikoff, Nat Biotechnol 18(4):424-428, 2000). While other methods like 3C (Dekker et al., Science 295(5558):1306-1311, 2002), 4C (Simonis et al., Nat Genet 38(11):1348-1354, 2006; Zhao et al., Nat Genet 38(11):1341-1347, 2006), and 5C (Dostie et al., Genome Res 16(10):1299-1309, 2006) are undoubtedly powerful, the DamID method can offer some advantages over these methods if the genetic locus can be easily modified. The lack of tissue fixation, the low amounts of starting material required to perform the experiment, and the relatively modest hardware requirements make DamID experiments an interesting alternative to consider when examining long-distance chromatin interactions.
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Affiliation(s)
- Fabienne Cléard
- Department of Genetics and Evolution, University of Geneva, 30 quai E. Ansermet, 1211, Geneva-4, Switzerland
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18
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Fujioka M, Sun G, Jaynes JB. The Drosophila eve insulator Homie promotes eve expression and protects the adjacent gene from repression by polycomb spreading. PLoS Genet 2013; 9:e1003883. [PMID: 24204298 PMCID: PMC3814318 DOI: 10.1371/journal.pgen.1003883] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/29/2013] [Indexed: 12/18/2022] Open
Abstract
Insulators can block the action of enhancers on promoters and the spreading of repressive chromatin, as well as facilitating specific enhancer-promoter interactions. However, recent studies have called into question whether the activities ascribed to insulators in model transgene assays actually reflect their functions in the genome. The Drosophila even skipped (eve) gene is a Polycomb (Pc) domain with a Pc-group response element (PRE) at one end, flanked by an insulator, an arrangement also seen in other genes. Here, we show that this insulator has three major functions. It blocks the spreading of the eve Pc domain, preventing repression of the adjacent gene, TER94. It prevents activation of TER94 by eve regulatory DNA. It also facilitates normal eve expression. When Homie is deleted in the context of a large transgene that mimics both eve and TER94 regulation, TER94 is repressed. This repression depends on the eve PRE. Ubiquitous TER94 expression is “replaced” by expression in an eve pattern when Homie is deleted, and this effect is reversed when the PRE is also removed. Repression of TER94 is attributable to spreading of the eve Pc domain into the TER94 locus, accompanied by an increase in histone H3 trimethylation at lysine 27. Other PREs can functionally replace the eve PRE, and other insulators can block PRE-dependent repression in this context. The full activity of the eve promoter is also dependent on Homie, and other insulators can promote normal eve enhancer-promoter communication. Our data suggest that this is not due to preventing promoter competition, but is likely the result of the insulator organizing a chromosomal conformation favorable to normal enhancer-promoter interactions. Thus, insulator activities in a native context include enhancer blocking and enhancer-promoter facilitation, as well as preventing the spread of repressive chromatin. Insulators are specialized DNA elements that can separate the genome into functional units. Most of the current thinking about these elements comes from studies done with model transgenes. Studies of insulators within the specialized Hox gene complexes have suggested that model transgenes can reflect the normal functions of these elements in their native context. However, recent genome-wide studies have called this into question. This work analyzes the native function of an insulator that resides between the Drosophila genes eve and TER94, which are expressed in very different patterns. Also, the eve gene is a Polycomb (Pc) domain, a specialized type of chromatin that is found in many places throughout the genome. We show that this insulator has three major functions. It blocks the spreading of the eve Pc domain, preventing repression of TER94. It prevents activation of TER94 by eve regulatory DNA. It also facilitates normal eve expression. Each of these activities are consistent with those seen with model transgenes, and other known insulators can provide these functions in this context. This work provides a novel and convincing example of the normal role of insulators in regulating the eukaryotic genome, as well as providing insights into their mechanisms of action.
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Affiliation(s)
- Miki Fujioka
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Guizhi Sun
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - James B. Jaynes
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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19
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Variation in meiotic recombination frequencies between allelic transgenes inserted at different sites in the Drosophila melanogaster genome. G3-GENES GENOMES GENETICS 2013; 3:1419-27. [PMID: 23797104 PMCID: PMC3737181 DOI: 10.1534/g3.113.006411] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Meiotic crossovers are distributed nonrandomly across the genome. Classic studies in Drosophila suggest that the position of a gene along a chromosome arm can affect the outcome of the recombination process, with proximity to the centromere being associated with lower crossing over. To examine this phenomenon molecularly, we developed an assay that measures meiotic crossovers and noncrossover gene conversions between allelic transgenes inserted into different genomic positions. To facilitate collecting a large number of virgin females, we developed a useful genetic system that kills males and undesired classes of females. We found that the recombination frequency at a site in the middle of the X chromosome, where crossovers are normally frequent, was similar to the frequency at the centromere-proximal end of the euchromatin, where crossovers are normally infrequent. In contrast, we recovered no recombinants--crossovers or noncrossovers--at a site on chromosome 4 and at a site toward the distal end of the X chromosome. These results suggest that local sequence or chromatin features have a stronger impact on recombination rates in this transgene assay than position along the chromosome arm.
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20
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Kyrchanova O, Leman D, Parshikov A, Fedotova A, Studitsky V, Maksimenko O, Georgiev P. New properties of Drosophila scs and scs' insulators. PLoS One 2013; 8:e62690. [PMID: 23638134 PMCID: PMC3634774 DOI: 10.1371/journal.pone.0062690] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/25/2013] [Indexed: 11/18/2022] Open
Abstract
Insulators are defined as a class of regulatory elements that delimit independent transcriptional domains within eukaryotic genomes. The first insulators to be identified were scs and scs', which flank the domain including two heat shock 70 genes. Zw5 and BEAF bind to scs and scs', respectively, and are responsible for the interaction between these insulators. Using the regulatory regions of yellow and white reporter genes, we have found that the interaction between scs and scs' improves the enhancer-blocking activity of the weak scs' insulator. The sequences of scs and scs' insulators include the promoters of genes that are strongly active in S2 cells but not in the eyes, in which the enhancer-blocking activity of these insulators has been extensively examined. Only the promoter of the Cad87A gene located at the end of the scs insulator drives white expression in the eyes, and the white enhancer can slightly stimulate this promoter. The scs insulator contains polyadenylation signals that may be important for preventing transcription through the insulator. As shown previously, scs and scs' can insulate transcription of the white transgene from the enhancing effects of the surrounding genome, a phenomenon known as the chromosomal position effect (CPE). After analyzing many independent transgenic lines, we have concluded that transgenes carrying the scs insulator are rarely inserted into genomic regions that stimulate the white reporter expression in the eyes.
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Affiliation(s)
- Olga Kyrchanova
- Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Leman
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Parshikov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Fedotova
- Group of Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vasily Studitsky
- School of Biology, Moscow State University, Moscow, Russia
- Department of Pharmacology, UMDNJ–Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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21
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Srivastava S, Puri D, Garapati HS, Dhawan J, Mishra RK. Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters. Epigenetics Chromatin 2013; 6:8. [PMID: 23607454 PMCID: PMC3639804 DOI: 10.1186/1756-8935-6-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 04/02/2013] [Indexed: 11/10/2022] Open
Abstract
Background Hox genes impart segment identity to body structures along the anterior-posterior axis and are crucial for the proper development of all organisms. Multiple regulatory elements, best defined in Drosophila melanogaster, ensure that Hox expression patterns follow the spatial and temporal colinearity reflected in their tight genomic organization. However, the precise mechanisms that regulate colinear patterns of Hox gene expression remain unclear, especially in higher vertebrates where it is not fully determined how the distinct activation domains of the tightly clustered Hox genes are defined independently of each other. Here, we report the identification of a large number of novel cis-elements at mammalian Hox clusters that can help in regulating their precise expression pattern. Results We have identified DNA elements at all four murine Hox clusters that show poor association with histone H3 in chromatin immunoprecipitation (ChIP)-chip tiling arrays. The majority of these elements lie in the intergenic regions segregating adjacent Hox genes; we demonstrate that they possess efficient enhancer-blocking activity in mammalian cells. Further, we find that these histone-free intergenic regions bear GA repeat motifs and associate with the vertebrate homolog of the GAGA binding boundary factor. This suggests that they can act as GAGA factor-dependent chromatin boundaries that create independent domains, insulating each Hox gene from the influence of neighboring regulatory elements. Conclusions Our results reveal a large number of potential regulatory elements throughout the murine Hox clusters. We further demarcate the precise location of several novel cis-elements bearing chromatin boundary activity that appear to segregate successive Hox genes. This reflects a pattern reminiscent of the organization of homeotic genes in Drosophila, where such regulatory elements have been characterized. Our findings thus provide new insights into the regulatory processes and evolutionarily conserved epigenetic mechanisms that control homeotic gene expression.
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Affiliation(s)
- Surabhi Srivastava
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, India.
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22
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Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP. Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic Acids Res 2013; 41:2963-80. [PMID: 23358822 PMCID: PMC3597698 DOI: 10.1093/nar/gkt037] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin insulators are functionally conserved DNA-protein complexes situated throughout the genome that organize independent transcriptional domains. Previous work implicated RNA as an important cofactor in chromatin insulator activity, although the precise mechanisms are not yet understood. Here we identify the exosome, the highly conserved major cellular 3' to 5' RNA degradation machinery, as a physical interactor of CP190-dependent chromatin insulator complexes in Drosophila. Genome-wide profiling of exosome by ChIP-seq in two different embryonic cell lines reveals extensive and specific overlap with the CP190, BEAF-32 and CTCF insulator proteins. Colocalization occurs mainly at promoters but also boundary elements such as Mcp, Fab-8, scs and scs', which overlaps with a promoter. Surprisingly, exosome associates primarily with promoters but not gene bodies of active genes, arguing against simple cotranscriptional recruitment to RNA substrates. Similar to insulator proteins, exosome is also significantly enriched at divergently transcribed promoters. Directed ChIP of exosome in cell lines depleted of insulator proteins shows that CTCF is required specifically for exosome association at Mcp and Fab-8 but not other sites, suggesting that alternate mechanisms must also contribute to exosome chromatin recruitment. Taken together, our results reveal a novel positive relationship between exosome and chromatin insulators throughout the genome.
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Affiliation(s)
- Su Jun Lim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
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23
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Ahanger SH, Shouche YS, Mishra RK. Functional sub-division of the Drosophila genome via chromatin looping: the emerging importance of CP190. Nucleus 2013; 4:115-22. [PMID: 23333867 DOI: 10.4161/nucl.23389] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Insulators help in organizing the eukaryotic genomes into physically and functionally autonomous regions through the formation of chromatin loops. Recent findings in Drosophila and vertebrates suggest that insulators anchor multiple loci through long-distance interactions which may be mechanistically linked to insulator function. Important to such processes in Drosophila is CP190, a common co-factor of insulator complexes. CP190 is also known to associate with the nuclear matrix, components of the RNAi machinery, active promoters and borders of the repressive chromatin domains. Although CP190 plays a pivotal role in insulator function in Drosophila, vertebrates lack a probable functional equivalent of CP190 and employ CTCF as the major factor to carry out insulator function/chromatin looping. In this review, we discuss the emerging role of CP190 in tethering genome, specifically in the perspective of insulator function in Drosophila. Future studies aiming genome-wide role of CP190 in chromatin looping is likely to give important insights into the mechanism of genome organization.
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Nakayama T, Shimojima T, Hirose S. The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions. Development 2012; 139:4582-90. [PMID: 23136390 DOI: 10.1242/dev.083246] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Establishment and maintenance of epigenetic memories are essential for development. Replacement of canonical histone H3 by its variant H3.3 has been implicated in cellular memory. Drosophila sequence-specific DNA-binding protein GAGA factor and a chromatin factor FACT direct H3.3 replacement in conjunction with H3.3-specific chaperone HIRA at chromatin boundaries to counteract the spreading of silent chromatin. However, little is known about which ATP-driven chromatin remodeling factor is responsible for the H3.3 replacement at chromatin boundaries. Here, we report that GAGA factor associates with the Polybromo-associated Brm (PBAP) remodeling complex, which consists of many Trithorax group proteins, and recruits this complex to chromatin boundaries d1 (which is downstream of w), the Fab-7 DNase-hypersensitive site (HS) 1 of Abd-B and the bxd region of Ubx. Trl-encoding GAGA factor, brm and polybromo/bap180 mutations compromise the H3.3 replacement and boundary functions in a synergistic manner. Furthermore, Polybromo is necessary for generation of the DNase HS at d1, and HIRA functions to restore the alteration. Taken together, we propose that FACT and PBAP complexes are recruited to chromatin boundaries in a GAGA factor-dependent manner, and are needed for H3.3 replacement to execute boundary functions. Our results provide new insight into the function of the trithorax group during development.
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Affiliation(s)
- Takahiro Nakayama
- Department of Developmental Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan
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25
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Wood AM, Van Bortle K, Ramos E, Takenaka N, Rohrbaugh M, Jones BC, Jones KC, Corces VG. Regulation of chromatin organization and inducible gene expression by a Drosophila insulator. Mol Cell 2011; 44:29-38. [PMID: 21981916 DOI: 10.1016/j.molcel.2011.07.035] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 06/02/2011] [Accepted: 07/29/2011] [Indexed: 11/19/2022]
Abstract
Insulators are multiprotein-DNA complexes thought to affect gene expression by mediating inter- and intrachromosomal interactions. Drosophila insulators contain specific DNA-binding proteins plus common components, such as CP190, that facilitate these interactions. Here, we examine changes in the distribution of Drosophila insulator proteins during the heat-shock and ecdysone responses. We find that CP190 recruitment to insulator sites is the main regulatable step in controlling insulator function during heat shock. In contrast, both CP190 and DNA-binding protein recruitment are regulated during the ecdysone response. CP190 is necessary to stabilize specific chromatin loops and for proper activation of transcription of genes regulated by this hormone. These findings suggest that cells may regulate recruitment of insulator proteins to DNA to activate insulator activity at specific sites and create distinct patterns of nuclear organization that are necessary to achieve proper gene expression in response to different stimuli.
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Affiliation(s)
- Ashley M Wood
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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26
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Raab JR, Chiu J, Zhu J, Katzman S, Kurukuti S, Wade PA, Haussler D, Kamakaka RT. Human tRNA genes function as chromatin insulators. EMBO J 2011; 31:330-50. [PMID: 22085927 DOI: 10.1038/emboj.2011.406] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 10/07/2011] [Indexed: 11/09/2022] Open
Abstract
Insulators help separate active chromatin domains from silenced ones. In yeast, gene promoters act as insulators to block the spread of Sir and HP1 mediated silencing while in metazoans most insulators are multipartite autonomous entities. tDNAs are repetitive sequences dispersed throughout the human genome and we now show that some of these tDNAs can function as insulators in human cells. Using computational methods, we identified putative human tDNA insulators. Using silencer blocking, transgene protection and repressor blocking assays we show that some of these tDNA-containing fragments can function as barrier insulators in human cells. We find that these elements also have the ability to block enhancers from activating RNA pol II transcribed promoters. Characterization of a putative tDNA insulator in human cells reveals that the site possesses chromatin signatures similar to those observed at other better-characterized eukaryotic insulators. Enhanced 4C analysis demonstrates that the tDNA insulator makes long-range chromatin contacts with other tDNAs and ETC sites but not with intervening or flanking RNA pol II transcribed genes.
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Affiliation(s)
- Jesse R Raab
- Department of MCD Biology, University of California, Santa Cruz, CA, USA
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27
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Erokhin M, Davydova A, Kyrchanova O, Parshikov A, Georgiev P, Chetverina D. Insulators form gene loops by interacting with promoters in Drosophila. Development 2011; 138:4097-106. [PMID: 21862564 DOI: 10.1242/dev.062836] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chromatin insulators are regulatory elements involved in the modulation of enhancer-promoter communication. The 1A2 and Wari insulators are located immediately downstream of the Drosophila yellow and white genes, respectively. Using an assay based on the yeast GAL4 activator, we have found that both insulators are able to interact with their target promoters in transgenic lines, forming gene loops. The existence of an insulator-promoter loop is confirmed by the fact that insulator proteins could be detected on the promoter only in the presence of an insulator in the transgene. The upstream promoter regions, which are required for long-distance stimulation by enhancers, are not essential for promoter-insulator interactions. Both insulators support basal activity of the yellow and white promoters in eyes. Thus, the ability of insulators to interact with promoters might play an important role in the regulation of basal gene transcription.
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Affiliation(s)
- Maksim Erokhin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334 Russia
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28
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Vogelmann J, Valeri A, Guillou E, Cuvier O, Nollmann M. Roles of chromatin insulator proteins in higher-order chromatin organization and transcription regulation. Nucleus 2011; 2:358-69. [PMID: 21983085 DOI: 10.4161/nucl.2.5.17860] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Eukaryotic chromosomes are condensed into several hierarchical levels of complexity: DNA is wrapped around core histones to form nucleosomes, nucleosomes form a higher-order structure called chromatin, and chromatin is subsequently compartmentalized in part by the combination of multiple specific or unspecific long-range contacts. The conformation of chromatin at these three levels greatly influences DNA metabolism and transcription. One class of chromatin regulatory proteins called insulator factors may organize chromatin both locally, by setting up barriers between heterochromatin and euchromatin, and globally by establishing platforms for long-range interactions. Here, we review recent data revealing a global role of insulator proteins in the regulation of transcription through the formation of clusters of long-range interactions that impact different levels of chromatin organization.
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Affiliation(s)
- Jutta Vogelmann
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique and Institut National de la Santé et la Recherche Médicale, 29 rue de Navacelles, 34090, Montpellier, France
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29
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Nikolaev LG, Akopov SB, Didych DA, Sverdlov ED. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity. Curr Genomics 2011; 10:294-302. [PMID: 20119526 PMCID: PMC2729993 DOI: 10.2174/138920209788921038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/15/2009] [Accepted: 06/18/2009] [Indexed: 11/24/2022] Open
Abstract
The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s).
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Affiliation(s)
- L G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, 117997, Moscow, Russia
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A barrier-only boundary element delimits the formation of facultative heterochromatin in Drosophila melanogaster and vertebrates. Mol Cell Biol 2011; 31:2729-41. [PMID: 21518956 DOI: 10.1128/mcb.05165-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Formation of facultative heterochromatin at specific genomic loci is fundamentally important in defining cellular properties such as differentiation potential and responsiveness to developmental, physiological, and environmental stimuli. By the nature of their formation, heterochromatin and repressive histone marks propagate until the chain reaction is broken. While certain active promoters can block propagation of heterochromatin, there are also specialized DNA elements, referred to as chromatin barriers, that serve to demarcate the boundary of facultative heterochromatin formation. In this study, we identified a chromatin barrier that specifically limits the formation of repressive chromatin to a distal enhancer region so that repressive histone modifications cannot reach the promoter and promoter-proximal enhancer regions of reaper. Unlike all of the known boundary elements identified for Drosophila melanogaster, this IRER (irradiation-responsive enhancer region) left barrier (ILB) does not exhibit enhancer-blocking activity. Not only has the ILB been conserved in different Drosophila species, it can also function as an effective chromatin barrier in vertebrate cells. This suggests that the mechanism by which it functions to spatially restrict the formation of repressive chromatin marked by trimethylated H3K27 has also been conserved widely during evolution.
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31
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Maeda RK, Karch F. Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions. Curr Opin Genet Dev 2011; 21:187-93. [PMID: 21349696 DOI: 10.1016/j.gde.2011.01.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/18/2011] [Indexed: 11/19/2022]
Abstract
In higher eukaryotes, individual genes are often intermingled with other genes and spread out across tens to hundreds of kilobases, even though only small portions of their sequence are devoted to protein coding. Yet, in this seemingly extended and tangled mess, the cell is able to precisely regulate gene expression in both time and space. Over the past few decades, numerous elements, like enhancers, silencers and insulators have been found that shed some light on how the precise control of gene expression is achieved. Through these discoveries, an additive model of gene expression was envisioned, where the addition of the patterning details imparted by regulatory elements would create the final pattern of gene expression. Although many genes can be described using this model, recent work in the Drosophila bithorax complex suggests that this model may be somewhat simplistic and, in fact, regulatory elements sometimes seem to communicate with each other to form a functional hierarchy that is far from additive.
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Affiliation(s)
- Robert K Maeda
- Department of Zoology and Animal Biology and NCCR Frontiers in Genetics, University of Geneva, 30 quai E. Ansermet, 1211 Geneva-4, Switzerland
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32
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Initiator elements function to determine the activity state of BX-C enhancers. PLoS Genet 2010; 6:e1001260. [PMID: 21203501 PMCID: PMC3009686 DOI: 10.1371/journal.pgen.1001260] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 11/23/2010] [Indexed: 11/19/2022] Open
Abstract
A >300 kb cis-regulatory region is required for the proper expression of the three bithorax complex (BX-C) homeotic genes. Based on genetic and transgenic analysis, a model has been proposed in which the numerous BX-C cis-regulatory elements are spatially restricted through the activation or repression of parasegment-specific chromatin domains. Particular early embryonic enhancers, called initiators, have been proposed to control this complex process. Here, in order to better understand the process of domain activation, we have undertaken a systematic in situ dissection of the iab-6 cis-regulatory domain using a new method, called InSIRT. Using this method, we create and genetically characterize mutations affecting iab-6 function, including mutations specifically modifying the iab-6 initiator. Through our mutagenesis of the iab-6 initiator, we provide strong evidence that initiators function not to directly control homeotic gene expression but rather as domain control centers to determine the activity state of the enhancers and silencers within a cis-regulatory domain. Understanding how genes become activated is one of the primary areas of research in modern biology. In order to decipher the DNA components required for this process, scientists have traditionally turned to transgenic reporter assays, where DNA elements are removed from their native environment and placed next to a simplified reporter gene to monitor transcriptional activation. Although this approach is powerful, it can result in artifacts stemming from the channelization of regulatory element activities into predetermined classes. In this manuscript, we investigate the biological role of elements from the Drosophila bithorax complex, called initiators. In transgenic assays, these elements have been categorized as enhancers. However, genetic analysis suggests that, in situ, these elements perform a far more complex function. Here, using a new method to repeatedly target a genetic locus for mutagenesis, we show that initiators function as control elements that coordinate the activity of nearby enhancers and silencers. Overall, our study highlights how gene expression can be controlled through a hierarchical arrangement of cis-regulatory elements.
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33
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Cabianca DS, Gabellini D. The cell biology of disease: FSHD: copy number variations on the theme of muscular dystrophy. J Cell Biol 2010; 191:1049-60. [PMID: 21149563 PMCID: PMC3002039 DOI: 10.1083/jcb.201007028] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/08/2010] [Indexed: 01/17/2023] Open
Abstract
In humans, copy number variations (CNVs) are a common source of phenotypic diversity and disease susceptibility. Facioscapulohumeral muscular dystrophy (FSHD) is an important genetic disease caused by CNVs. It is an autosomal-dominant myopathy caused by a reduction in the copy number of the D4Z4 macrosatellite repeat located at chromosome 4q35. Interestingly, the reduction of D4Z4 copy number is not sufficient by itself to cause FSHD. A number of epigenetic events appear to affect the severity of the disease, its rate of progression, and the distribution of muscle weakness. Indeed, recent findings suggest that virtually all levels of epigenetic regulation, from DNA methylation to higher order chromosomal architecture, are altered at the disease locus, causing the de-regulation of 4q35 gene expression and ultimately FSHD.
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Affiliation(s)
- Daphne Selvaggia Cabianca
- International PhD Program in Cellular and Molecular Biology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Division of Regenerative Medicine, San Raffaele Scientific Institute, DIBIT 1, 2A3-49, 20132 Milan, Italy
| | - Davide Gabellini
- Division of Regenerative Medicine, San Raffaele Scientific Institute, DIBIT 1, 2A3-49, 20132 Milan, Italy
- Dulbecco Telethon Institute, 20132 Milan, Italy
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34
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Kyrchanova O, Ivlieva T, Toshchakov S, Parshikov A, Maksimenko O, Georgiev P. Selective interactions of boundaries with upstream region of Abd-B promoter in Drosophila bithorax complex and role of dCTCF in this process. Nucleic Acids Res 2010; 39:3042-52. [PMID: 21149269 PMCID: PMC3082887 DOI: 10.1093/nar/gkq1248] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of the genes Ubx, abd-A, and Abd-B of the bithorax complex depends on its cis-regulatory region, which is divided into discrete functional domains (iab). Boundary/insulator elements, named Mcp, Fab-6, Fab-7 and Fab-8 (PTS/F8), have been identified at the borders of the iab domains. Recently, binding sites for a Drosophila homolog of the vertebrate insulator protein CTCF have been identified in Mcp, Fab-6 and Fab-8 and also in several regions that correspond to predicted boundaries, Fab-3 and Fab-4 in particular. Taking into account the inability of the yeast GAL4 activator to stimulate the white promoter when the activator and the promoter are separated by a 5-kb yellow gene, we have tested functional interactions between the boundaries. The results show that all dCTCF-containing boundaries interact with each other. However, inactivation of dCTCF binding sites in Mcp, Fab-6 and PTS/F8 only partially reduces their ability to interact, suggesting the presence of additional protein(s) supporting distant interactions between the boundaries. Interestingly, only Fab-6, Fab-7 (which contains no dCTCF binding sites) and PTS/F8 interact with the upstream region of the Abd-B promoter. Thus, the boundaries might be involved in supporting the specific interactions between iab enhancers and promoters of the bithorax complex.
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Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow 119334, Russia
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35
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When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol 2010; 350:239-54. [PMID: 21130761 DOI: 10.1016/j.ydbio.2010.11.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 11/11/2010] [Accepted: 11/22/2010] [Indexed: 01/22/2023]
Abstract
A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found. Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project.
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36
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Raab JR, Kamakaka RT. Insulators and promoters: closer than we think. Nat Rev Genet 2010; 11:439-46. [PMID: 20442713 DOI: 10.1038/nrg2765] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Insulators prevent promiscuous gene regulation by restricting the action of enhancers and silencers. Recent studies have revealed a number of similarities between insulators and promoters, including binding of specific transcription factors, chromatin-modification signatures and localization to specific subnuclear positions. We propose that enhancer-blockers and silencing barrier-insulators might have evolved as specialized derivatives of promoters and that the two types of element use related mechanisms to mediate their distinct functions. These insights can help to reconcile different models of insulator action.
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Affiliation(s)
- Jesse R Raab
- Department of Molecular Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA
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37
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Erokhin M, Parshikov A, Georgiev P, Chetverina D. E(y)2/Sus1 is required for blocking PRE silencing by the Wari insulator in Drosophila melanogaster. Chromosoma 2010; 119:243-53. [PMID: 20082086 DOI: 10.1007/s00412-009-0253-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/07/2009] [Accepted: 12/08/2009] [Indexed: 11/29/2022]
Abstract
Chromatin insulators affect interactions between promoters and enhancers/silencers and function as barriers to the spread of repressive chromatin. Recently, we have found an insulator, named Wari, located on the 3' side of the white gene. Here, we show that the previously identified 368-bp core of this insulator is sufficient for blocking Polycomb response element-mediated silencing. Although Wari does not contain binding sites for known insulator proteins, the E(y)2 and CP190 proteins bind to Wari as well as to the Su(Hw)-containing insulators in vivo. It may well be that these proteins are recruited to the insulator by as yet unidentified DNA-binding protein. Partial inactivation of E(y)2 in a weak e(y)2 ( u1 ) mutation impairs only the anti-silencing but not the enhancer-blocking activity of the Wari insulator. Thus, the E(y)2 protein in different Drosophila insulators serves to protect gene expression from silencing.
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Affiliation(s)
- Maksim Erokhin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
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38
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Maeda RK, Karch F. Cis-regulation in the Drosophila Bithorax Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:17-40. [PMID: 20795320 DOI: 10.1007/978-1-4419-6673-5_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The discovery of the first homeotic mutation by Calvin Bridges in 1915 profoundly influenced the way we think about developmental processes. Although many mutations modify or deform morphological structures, homeotic mutations cause a spectacular phenotype in which a morphological structure develops like a copy of a structure that is normally found elsewhere on an organism's body plan. This is best illustrated in Drosophila where homeotic mutations were first discovered. For example, Antennapedia mutants have legs developing on their head instead of antennae. Because a mutation in a single gene creates such complete structures, homeotic genes were proposed to be key "selector genes" regulating the initiation of a developmental program. According to this model, once a specific developmental program is initiated (i.e., antenna or leg), it can be executed by downstream "realizator genes" independent of its location along the body axis. Consistent with this idea, homeotic genes have been shown to encode transcription factor proteins that control the activity of the many downstream targets to "realize" a developmental program. Here, we will review the first and perhaps, best characterized homeotic complex, the Bithorax Complex (BX-C).
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Affiliation(s)
- Robert K Maeda
- NCCR Frontiers in Genetics, University of Geneva, 30 quai E. Ansermet, 1211 Geneva-4, Switzerland
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39
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Kheradmand Kia S, Solaimani Kartalaei P, Farahbakhshian E, Pourfarzad F, von Lindern M, Verrijzer CP. EZH2-dependent chromatin looping controls INK4a and INK4b, but not ARF, during human progenitor cell differentiation and cellular senescence. Epigenetics Chromatin 2009; 2:16. [PMID: 19954516 PMCID: PMC3225837 DOI: 10.1186/1756-8935-2-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 12/02/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The INK4b-ARF-INK4a tumour suppressor locus controls the balance between progenitor cell renewal and cancer. In this study, we investigated how higher-order chromatin structure modulates differential expression of the human INK4b-ARF-INK4a locus during progenitor cell differentiation, cellular ageing and senescence of cancer cells. RESULTS We found that INK4b and INK4a, but not ARF, are upregulated following the differentiation of haematopoietic progenitor cells, in ageing fibroblasts and in senescing malignant rhabdoid tumour cells. To investigate the underlying molecular mechanism we analysed binding of polycomb group (PcG) repressive complexes (PRCs) and the spatial organization of the INK4b-ARF-INK4a locus. In agreement with differential derepression, PcG protein binding across the locus is discontinuous. As we described earlier, PcG repressors bind the INK4a promoter, but not ARF. Here, we identified a second peak of PcG binding that is located approximately 3 kb upstream of the INK4b promoter. During progenitor cell differentiation and ageing, PcG silencer EZH2 attenuates, causing loss of PRC binding and transcriptional activation of INK4b and INK4a. The expression pattern of the locus is reflected by its organization in space. In the repressed state, the PRC-binding regions are in close proximity, while the intervening chromatin harbouring ARF loops out. Down regulation of EZH2 causes release of the approximately 35 kb repressive chromatin loop and induction of both INK4a and INK4b, whereas ARF expression remains unaltered. CONCLUSION PcG silencers bind and coordinately regulate INK4b and INK4a, but not ARF, during a variety of physiological processes. Developmentally regulated EZH2 levels are one of the factors that can determine the higher order chromatin structure and expression pattern of the INK4b-ARF-INK4a locus, coupling human progenitor cell differentiation to proliferation control. Our results revealed a chromatin looping mechanism of long-range control and argue against models involving homogeneous spreading of PcG silencers across the INK4b-ARF-INK4a locus.
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Affiliation(s)
- Sima Kheradmand Kia
- Department of Biochemistry, Center for Biomedical Genetics, Erasmus University Medical Center, PO Box 1738, 3000 DR Rotterdam, The Netherlands.
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40
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Fujioka M, Wu X, Jaynes JB. A chromatin insulator mediates transgene homing and very long-range enhancer-promoter communication. Development 2009; 136:3077-87. [PMID: 19675129 PMCID: PMC2730365 DOI: 10.1242/dev.036467] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2009] [Indexed: 12/11/2022]
Abstract
Insulator sequences help to organize the genome into discrete functional regions by preventing inappropriate cross-regulation. This is thought to be mediated in part through associations with other insulators located elsewhere in the genome. Enhancers that normally drive Drosophila even skipped (eve) expression are located closer to the TER94 transcription start site than to that of eve. We discovered that the region between these genes has enhancer-blocking activity, and that this insulator region also mediates homing of P-element transgenes to the eve-TER94 genomic neighborhood. Localization of these activities to within 0.6 kb failed to separate them. Importantly, homed transgenic promoters respond to endogenous eve enhancers from great distances, and this long-range communication depends on the homing/insulator region, which we call Homie. We also find that the eve promoter contributes to long-distance communication. However, even the basal hsp70 promoter can communicate with eve enhancers across distances of several megabases, when the communication is mediated by Homie. These studies show that, while Homie blocks enhancer-promoter communication at short range, it facilitates long-range communication between distant genomic regions, possibly by organizing a large chromosomal loop between endogenous and transgenic Homies.
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Affiliation(s)
- Miki Fujioka
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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41
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Abstract
Enhancers act over many kilobase pairs to activate target promoters, but their activity is constrained by insulator elements that prevent indiscriminate activation of nearby genes. In the July 1, 2009, issue of Genes & Development, Chopra and colleagues (pp. 1505-1509) report that promoters containing a stalled Pol II are activated by enhancers, but these promoters also serve as insulators that block enhancers from reaching more distal genes. This new class of insulators provide critical clues to regulatory mechanisms.
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Affiliation(s)
- Leighton J. Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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Chopra VS, Cande J, Hong JW, Levine M. Stalled Hox promoters as chromosomal boundaries. Genes Dev 2009; 23:1505-9. [PMID: 19515973 DOI: 10.1101/gad.1807309] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Many developmental control genes contain stalled RNA Polymerase II (Pol II) in the early Drosophila embryo, including four of the eight Hox genes. Here, we present evidence that the stalled Hox promoters possess an intrinsic insulator activity. The enhancer-blocking activities of these promoters are dependent on general transcription factors that inhibit Pol II elongation, including components of the DSIF and NELF complexes. The activities of conventional insulators are also impaired in embryos containing reduced levels of DSIF and NELF. Thus, promoter-proximal stalling factors might help promote insulator-promoter interactions. We propose that stalled promoters help organize gene complexes within chromosomal loop domains.
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Affiliation(s)
- Vivek S Chopra
- Department of Molecular and Cellular Biology, Division of Genetics, Genomics, and Development, University of California at Berkeley, Berkeley, California 94720, USA.
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43
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Bushey AM, Ramos E, Corces VG. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev 2009; 23:1338-50. [PMID: 19443682 DOI: 10.1101/gad.1798209] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Insulators are protein-bound DNA elements that are thought to play a role in chromatin organization and the regulation of gene expression by mediating intra- and interchromosomal interactions. Suppressor of Hair-wing [Su(Hw)] and Drosophila CTCF (dCTCF) insulators are found at distinct loci throughout the Drosophila melanogaster genome and function by recruiting an additional protein, Centrosomal Protein 190 (CP190). We performed chromatin immunoprecipitation (ChIP) and microarray analysis (ChIP-chip) experiments with whole-genome tiling arrays to compare Su(Hw), dCTCF, boundary element-associated factor (BEAF), and CP190 localization on DNA in two different cell lines and found evidence that BEAF is a third subclass of CP190-containing insulators. The DNA-binding proteins Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line-specific localization sites for all three DNA-binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. These findings suggest a model in which insulator subclasses may have distinct functions that together organize the genome in a cell type-specific manner, resulting in differential regulation of gene expression.
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Affiliation(s)
- Ashley M Bushey
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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Abstract
Cornelia de Lange syndrome (CdLS) is genetically heterogeneous and is usually sporadic, occurring approximately once per 10,000 births. CdLS individuals display diverse and variable deficits in growth, mental development, limbs, and organs. In the past few years it has been shown that CdLS is caused by gene mutations affecting proteins involved in sister chromatid cohesion. Studies in model organisms, and more recently in human cells, have revealed, somewhat unexpectedly, that the developmental deficits in CdLS likely arise from changes in gene expression. The mechanisms by which cohesion factors regulate gene expression remain to be elucidated, but current data suggest that they likely regulate transcription in multiple ways.
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Affiliation(s)
- Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 South Grand Boulevard, Saint Louis, MO 63104, USA.
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45
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Emberly E, Blattes R, Schuettengruber B, Hennion M, Jiang N, Hart CM, Käs E, Cuvier O. BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites. PLoS Biol 2009; 6:2896-910. [PMID: 19108610 PMCID: PMC2605929 DOI: 10.1371/journal.pbio.0060327] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 11/11/2008] [Indexed: 12/25/2022] Open
Abstract
Chromatin insulators/boundary elements share the ability to insulate a transgene from its chromosomal context by blocking promiscuous enhancer–promoter interactions and heterochromatin spreading. Several insulating factors target different DNA consensus sequences, defining distinct subfamilies of insulators. Whether each of these families and factors might possess unique cellular functions is of particular interest. Here, we combined chromatin immunoprecipitations and computational approaches to break down the binding signature of the Drosophila boundary element–associated factor (BEAF) subfamily. We identify a dual-core BEAF binding signature at 1,720 sites genome-wide, defined by five to six BEAF binding motifs bracketing 200 bp AT-rich nuclease-resistant spacers. Dual-cores are tightly linked to hundreds of genes highly enriched in cell-cycle and chromosome organization/segregation annotations. siRNA depletion of BEAF from cells leads to cell-cycle and chromosome segregation defects. Quantitative RT-PCR analyses in BEAF-depleted cells show that BEAF controls the expression of dual core–associated genes, including key cell-cycle and chromosome segregation regulators. beaf mutants that impair its insulating function by preventing proper interactions of BEAF complexes with the dual-cores produce similar effects in embryos. Chromatin immunoprecipitations show that BEAF regulates transcriptional activity by restricting the deposition of methylated histone H3K9 marks in dual-cores. Our results reveal a novel role for BEAF chromatin dual-cores in regulating a distinct set of genes involved in chromosome organization/segregation and the cell cycle. The genome of eukaryotes is packaged in chromatin, which consists of DNA, histones, and accessory proteins. This leads to a general repression of genes, particularly for those exposed to mostly condensed, heterochromatin regions. DNA sequences called chromatin insulators/boundary elements are able to insulate a gene from its chromosomal context by blocking promiscuous heterochromatin spreading. No common feature has been identified among the insulators/boundary elements known so far. Rather, distinct subfamilies of insulators harbor different DNA consensus sequences targeted by different DNA-binding factors, which confer their insulating activity. Determining whether distinct subfamilies possess distinct cellular functions is important for understanding genome regulation. Here, using Drosophila, we have combined computational and experimental approaches to address the function of the boundary element-associated factor (BEAF) subfamily of insulators. We identify hundreds of BEAF dual-cores that are defined by a particular arrangement of DNA sequence motifs bracketing nucleosome binding sequences, and that mark the genomic BEAF binding sites. BEAF dual-cores are close to hundreds of genes that regulate chromosome organization/segregation and the cell cycle. Since BEAF acts by restricting the deposition of repressing epigenetic histone marks, which affects the accessibility of chromatin, its depletion affects the expression of cell-cycle genes. Our data reveal a new role for BEAF in regulating the cell cycle through its binding to highly conserved chromatin dual-cores. Chromatin Dual-Cores define new potent nucleosome-associatedcis-regulatory elements that regulate the accessibility of promoters of genes controlling chromosome organization/segregation and the cell cycle.
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Affiliation(s)
- Eldon Emberly
- Physics Department, Simon Fraser University, Burnaby, British Columbia, Canada
- * To whom correspondence should be addressed. E-mail: (EE); (OC)
| | - Roxane Blattes
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
| | - Bernd Schuettengruber
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Magali Hennion
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
- Institut de Genetique Humaine, Department of Genome Dynamics, CNRS, Montpelier, France
| | - Nan Jiang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Craig M Hart
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Lousiana, United States of America
| | - Emmanuel Käs
- CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, France
| | - Olivier Cuvier
- Institut de Genetique Humaine, Department of Genome Dynamics, CNRS, Montpelier, France
- * To whom correspondence should be addressed. E-mail: (EE); (OC)
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46
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Abstract
In his 1978 seminal paper, Ed Lewis described a series of mutations that affect the segmental identities of the segments forming the posterior two-thirds of the Drosophila body plan. In each class of mutations, particular segments developed like copies of a more-anterior segment. Genetic mapping of the different classes of mutations led to the discovery that their arrangement along the chromosome paralleled the body segments they affect along the anteroposterior axis of the fly. As all these mutations mapped to the same cytological location, he named this chromosomal locus after its founding mutation. Thus the first homeotic gene (Hox) cluster became known as the bithorax complex (BX-C). Even before the sequencing of the BX-C, the fact that these similar mutations grouped together in a cluster, lead Ed Lewis to propose that the homeotic genes arose through a gene duplication mechanism and that these clusters would be conserved through evolution. With the identification of the homeobox in the early 1980s, Lewis' first prediction was confirmed. The two cloned Drosophila homeotic genes, Antennapedia and Ultrabithorax, were indeed related genes. Using the homeobox as an entry point, homologous genes have since been cloned in many other species. Today, Hox clusters have been discovered in almost all metazoan phyla, confirming Lewis' second prediction. Remarkably, these homologous Hox genes are also arranged in clusters with their order within each cluster reflecting the anterior boundary of their domain of expression along the anterior-posterior axis of the animal. This correlation between the genomic organization and the activity along the anteroposterior body axis is known as the principle of "colinearity." The description of the BX-C inspired decades of developmental and evolutionary biology. And although this first Hox cluster led to the identification of many important features common to all Hox gene clusters, it now turns out that the fly Hox clusters are rather exceptional when compared with the Hox clusters of other animals. In this chapter, we will review the history and salient features of bithorax molecular genetics, in part, emphasizing its unique features relative to the other Hox clusters.
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Affiliation(s)
- Robert K Maeda
- Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland
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Abstract
The cohesin complex, discovered through its role in sister chromatid cohesion, also plays roles in gene expression and development in organisms from yeast to human. This review highlights what has been learned about the gene control and developmental functions of cohesin and the Nipped-B (NIPBL/Scc2) cohesin loading factor in Drosophila. The Drosophila studies have provided unique insights into the aetiology of Cornelia de Lange syndrome (CdLS), which is caused by mutations affecting sister chromatid cohesion proteins in humans. In vivo experiments with Drosophila show that cohesin and Nipped-B have dosage-sensitive effects on the functions of many evolutionarily conserved genes and developmental pathways. Genome-wide studies with Drosophila cultured cells show that Nipped-B and cohesin co-localize on chromosomes, and bind preferentially, but not exclusively, to many actively transcribed genes and their regulatory sequences, including many of the proposed in vivo target genes. In contrast, the cohesion factors are largely excluded from genes silenced by Polycomb group (PcG) proteins. Combined, the in vivo genetic data and the binding patterns of cohesin and Nipped-B in cultured cells are consistent with the hypothesis that they control the action of gene regulatory sequences, including transcriptional enhancers and insulators, and suggest that they might also help define active chromatin domains and influence transcriptional elongation.
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Affiliation(s)
- Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 South Grand Boulevard, Saint Louis, MO 63104, USA.
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Chen Q, Wang X, O’Neill FA, Walsh D, Kendler KS, Chen X. Is the histidine triad nucleotide-binding protein 1 (HINT1) gene a candidate for schizophrenia? Schizophr Res 2008; 106:200-7. [PMID: 18799291 PMCID: PMC2729541 DOI: 10.1016/j.schres.2008.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 07/31/2008] [Accepted: 08/01/2008] [Indexed: 02/05/2023]
Abstract
BACKGROUND : The histidine triad nucleotide-binding protein 1, HINT1, hydrolyzes adenosine 5'-monophosphoramidate substrates such as AMP-morpholidate. The human HINT1 gene is located on chromosome 5q31.2, a region implicated in linkage studies of schizophrenia. HINT1 had been shown to have different expression in postmortem brains between schizophrenia patients and unaffected controls. It was also found to be associated with the dysregulation of postsynaptic dopamine transmission, thus suggesting a potential role in several neuropsychiatric diseases. METHODS : In this work, we studied 8 SNPs around the HINT1 gene region using the Irish study of high density schizophrenia families (ISHDSF, 1350 subjects and 273 pedigrees) and the Irish case control study of schizophrenia (ICCSS, 655 affected subjects and 626 controls). The expression level of HINT1 was compared between the postmortem brain cDNAs from schizophrenic patients and unaffected controls provided by the Stanley Medical Research Institute. RESULTS : We found nominally significant differences in allele frequencies in several SNPs for both ISHDSF and ICCSS samples in sex-stratified analyses. However, the sex effect differed between the two samples. In expression studies, no significant difference in expression was observed between patients and controls. However, significant interactions amongst sex, diagnosis and rs3864283 genotypes were observed. CONCLUSION : Data from both association and expression studies suggested that variants at HINT1 may be associated with schizophrenia and the associations may be sex-specific. However, the markers showing associations were in high LD to the SPEC2/PDZ-GEF2/ACSL6 locus reported previously in the same samples. This made it difficult to separate the association signals amongst these genes. Other independent studies may be necessary to distinguish these candidate genes.
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Affiliation(s)
- Qi Chen
- Department of Psychiatry and Virginia Institute for Psychiatric and Behavior Genetics, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, VA 23298
| | - Xu Wang
- Department of Psychiatry and Virginia Institute for Psychiatric and Behavior Genetics, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, VA 23298
| | - Francis A. O’Neill
- The Department of Psychiatry, The Queens University, Belfast, Northern Ireland
| | | | - Kenneth S. Kendler
- Department of Psychiatry and Virginia Institute for Psychiatric and Behavior Genetics, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, VA 23298
| | - Xiangning Chen
- Department of Psychiatry and Virginia Institute for Psychiatric and Behavior Genetics, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, VA 23298,Corresponding author: X. Chen, , Telephone: 804 828 8124, Fax: 804 828 1471
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Iampietro C, Cléard F, Gyurkovics H, Maeda RK, Karch F. Boundary swapping in the Drosophila Bithorax complex. Development 2008; 135:3983-7. [PMID: 18987027 DOI: 10.1242/dev.025700] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although the boundary elements of the Drosophila Bithorax complex (BX-C) have properties similar to chromatin insulators, genetic substitution experiments have demonstrated that these elements do more than simply insulate adjacent cis-regulatory domains. Many BX-C boundaries lie between enhancers and their target promoter, and must modulate their activity to allow distal enhancers to communicate with their target promoter. Given this complex function, it is surprising that the numerous BX-C boundaries share little sequence identity. To determine the extent of the similarity between these elements, we tested whether different BX-C boundary elements can functionally substitute for one another. Using gene conversion, we exchanged the Fab-7 and Fab-8 boundaries within the BX-C. Although the Fab-8 boundary can only partially substitute for the Fab-7 boundary, we find that the Fab-7 boundary can almost completely replace the Fab-8 boundary. Our results suggest that although boundary elements are not completely interchangeable, there is a commonality to the mechanism by which boundaries function. This commonality allows different DNA-binding proteins to create functional boundaries.
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Affiliation(s)
- Carole Iampietro
- NCCR, Frontiers in Genetics, University of Geneva, Department of Zoology and Animal Biology, 30 Quai Ernest Ansermet, 1211 Geneva 11, Switzerland
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Pérez-Lluch S, Cuartero S, Azorín F, Espinàs ML. Characterization of new regulatory elements within the Drosophila bithorax complex. Nucleic Acids Res 2008; 36:6926-33. [PMID: 18978017 PMCID: PMC2588531 DOI: 10.1093/nar/gkn818] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The homeotic Abdominal-B (Abd-B) gene expression depends on a modular cis-regulatory region divided into discrete functional domains (iab) that control the expression of the gene in a particular segment of the fly. These domains contain regulatory elements implicated in both initiation and maintenance of homeotic gene expression and elements that separate the different domains. In this paper we have performed an extensive analysis of the iab-6 regulatory region, which regulates Abd-B expression at abdominal segment A6 (PS11), and we have characterized two new polycomb response elements (PREs) within this domain. We report that PREs at Abd-B cis-regulatory domains present a particular chromatin structure which is nuclease accessible all along Drosophila development and both in active and repressed states. We also show that one of these regions contains a dCTCF and CP190 dependent activity in transgenic enhancer-blocking assays, suggesting that it corresponds to the Fab-6 boundary element of the Drosophila bithorax complex.
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Affiliation(s)
- Sílvia Pérez-Lluch
- Institut de Biologia Molecular de Barcelona, CSIC, Institut de Recerca Biomedica de Barcelona, IRBB, Parc Científic de Barcelona, Barcelona, Spain
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