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Jores T, Mueth NA, Tonnies J, Char SN, Liu B, Grillo-Alvarado V, Abbitt S, Anand A, Deschamps S, Diehn S, Gordon-Kamm B, Jiao S, Munkvold K, Snowgren H, Sardesai N, Fields S, Yang B, Cuperus JT, Queitsch C. Small DNA elements that act as both insulators and silencers in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612883. [PMID: 39345455 PMCID: PMC11429706 DOI: 10.1101/2024.09.13.612883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Insulators are cis -regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments of eight large insulators to identify more than 100 fragments that block enhancer activity. The short fragments can be combined to generate more powerful insulators that abolish the capacity of the strong viral 35S enhancer to activate the 35S minimal promoter. Unexpectedly, when tested upstream of weak enhancers, these fragments act as silencers and repress transcription. Thus, these elements are capable of both insulating or repressing transcription dependent upon regulatory context. We validate our findings in stable transgenic Arabidopsis , maize, and rice plants. The short elements identified here should be useful building blocks for plant biotechnology efforts.
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Bing X, Ke W, Fujioka M, Kurbidaeva A, Levitt S, Levine M, Schedl P, Jaynes JB. Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. eLife 2024; 13:RP94070. [PMID: 39110499 PMCID: PMC11305675 DOI: 10.7554/elife.94070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Two different models have been proposed to explain how the endpoints of chromatin looped domains ('TADs') in eukaryotic chromosomes are determined. In the first, a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop. In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of MicroC to analyze how TADs are organized, and experimental manipulations of the even skipped TAD boundary, homie, to test the predictions of the 'loop-extrusion' and the 'boundary-pairing' models. Our findings are incompatible with the loop-extrusion model, and instead suggest that the endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their partners, either head-to-head or head-to-tail, with varying degrees of specificity. Although our experiments do not address how partners find each other, the mechanism is unlikely to require loop extrusion.
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Affiliation(s)
- Xinyang Bing
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Wenfan Ke
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Amina Kurbidaeva
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Sarah Levitt
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Mike Levine
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
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Ke W, Fujioka M, Schedl P, Jaynes JB. Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties. eLife 2024; 13:RP94114. [PMID: 39110491 PMCID: PMC11305674 DOI: 10.7554/elife.94114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT orientation), and homie forward (same orientation as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: in MicroC experiments, the eve TAD is a 'volcano' triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the 'new' eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve triangle peak is converted to a pair of 'clouds' of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.
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Affiliation(s)
- Wenfan Ke
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Laspisa D, Illa-Berenguer E, Bang S, Schmitz RJ, Parrott W, Wallace J. Mining the Utricularia gibba genome for insulator-like elements for genetic engineering. FRONTIERS IN PLANT SCIENCE 2023; 14:1279231. [PMID: 38023853 PMCID: PMC10663240 DOI: 10.3389/fpls.2023.1279231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Introduction Gene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal. Methods To identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity. Results We identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller. Discussion Given the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.
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Affiliation(s)
- Daniel Laspisa
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Jason Wallace
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Simmons JR, An R, Amankwaa B, Zayac S, Kemp J, Labrador M. Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila. PLoS Genet 2022; 18:e1010396. [PMID: 36197938 PMCID: PMC9576066 DOI: 10.1371/journal.pgen.1010396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/17/2022] [Accepted: 08/24/2022] [Indexed: 11/27/2022] Open
Abstract
Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.
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Affiliation(s)
- James R. Simmons
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ran An
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Bright Amankwaa
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Shannon Zayac
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Justin Kemp
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Zhou R, Tian K, Huang J, Duan W, Fu H, Feng Y, Wang H, Jiang Y, Li Y, Wang R, Hu J, Ma H, Qi Z, Ji X. CTCF DNA binding domain undergoes dynamic and selective protein–protein interactions. iScience 2022; 25:105011. [PMID: 36117989 PMCID: PMC9474293 DOI: 10.1016/j.isci.2022.105011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/13/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
CTCF is a predominant insulator protein required for three-dimensional chromatin organization. However, the roles of its insulation of enhancers in a 3D nuclear organization have not been fully explained. Here, we found that the CTCF DNA-binding domain (DBD) forms dynamic self-interacting clusters. Strikingly, CTCF DBD clusters were found to incorporate other insulator proteins but are not coenriched with transcriptional activators in the nucleus. This property is not observed in other domains of CTCF or the DBDs of other transcription factors. Moreover, endogenous CTCF shows a phenotype consistent with the DBD by forming small protein clusters and interacting with CTCF motif arrays that have fewer transcriptional activators bound. Our results reveal an interesting phenomenon in which CTCF DBD interacts with insulator proteins and selectively localizes to nuclear positions with lower concentrations of transcriptional activators, providing insights into the insulation function of CTCF. The CTCF DNA-binding domain forms protein clusters in vivo and in vitro CTCF DBD clusters colocalize with insulator proteins but not with activators Arginine residues of CTCF DBD are frequently mutated in cancers Multiple transcription factor DBDs form protein clusters
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Schmitz RJ, Grotewold E, Stam M. Cis-regulatory sequences in plants: Their importance, discovery, and future challenges. THE PLANT CELL 2022; 34:718-741. [PMID: 34918159 PMCID: PMC8824567 DOI: 10.1093/plcell/koab281] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 05/19/2023]
Abstract
The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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9
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Liu H, Jiang L, Wen Z, Yang Y, Singer SD, Bennett D, Xu W, Su Z, Yu Z, Cohn J, Chae H, Que Q, Liu Y, Liu C, Liu Z. Rice RS2-9, which is bound by transcription factor OSH1, blocks enhancer-promoter interactions in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:541-554. [PMID: 34773305 PMCID: PMC9303810 DOI: 10.1111/tpj.15574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/02/2021] [Indexed: 05/13/2023]
Abstract
Insulators characterized in Drosophila and mammals have been shown to play a key role in the restriction of promiscuous enhancer-promoter interactions, as well as reshaping the topological landscape of chromosomes. Yet the role of insulators in plants remains poorly understood, in large part because of a lack of well-characterized insulators and binding factor(s). In this study, we isolated a 1.2-kb RS2-9 insulator from the Oryza sativa (rice) genome that can, when interposed between an enhancer and promoter, efficiently block the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and Nicotiana tabacum (tobacco). In the rice genome, the genes flanking RS2-9 exhibit an absence of mutual transcriptional interactions, as well as a lack of histone modification spread. We further determined that O. sativa Homeobox 1 (OSH1) bound two regions of RS2-9, as well as over 50 000 additional sites in the rice genome, the majority of which resided in intergenic regions. Mutation of one of the two OSH1-binding sites in RS2-9 impaired insulation activity by up to 60%, whereas the mutation of both binding sites virtually abolished insulator function. We also demonstrated that OSH1 binding sites were associated with 72% of the boundaries of topologically associated domains (TADs) identified in the rice genome, which is comparable to the 77% of TAD boundaries bound by the insulator CCCTC-binding factor (CTCF) in mammals. Taken together, our findings indicate that OSH1-RS2-9 acts as a true insulator in plants, and highlight a potential role for OSH1 in gene insulation and topological organization in plant genomes.
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Affiliation(s)
- Huawei Liu
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Li Jiang
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Zhifeng Wen
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of HorticultureFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Yingjun Yang
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- Forestry CollegeHenan University of Science and TechnologyLuoyang471023China
| | - Stacy D. Singer
- Agriculture and Agri‐Food CanadaLethbridge Research and Development CentreLethbridgeAlbertaT1J 4B1Canada
| | - Dennis Bennett
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Zhifang Yu
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Jonathan Cohn
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Hyunsook Chae
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Qiudeng Que
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Yue Liu
- College of HorticultureQingdao Agricultural UniversityQingdao266109China
| | - Chang Liu
- Department of EpigeneticsUniversity of HohenheimStuttgart70599Germany
| | - Zongrang Liu
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
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10
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Papanikolaou E, Bosio A. The Promise and the Hope of Gene Therapy. Front Genome Ed 2021; 3:618346. [PMID: 34713249 PMCID: PMC8525363 DOI: 10.3389/fgeed.2021.618346] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/19/2021] [Indexed: 12/26/2022] Open
Abstract
It has been over 30 years since visionary scientists came up with the term "Gene Therapy," suggesting that for certain indications, mostly monogenic diseases, substitution of the missing or mutated gene with the normal allele via gene addition could provide long-lasting therapeutic effect to the affected patients and consequently improve their quality of life. This notion has recently become a reality for certain diseases such as hemoglobinopathies and immunodeficiencies and other monogenic diseases. However, the therapeutic wave of gene therapies was not only applied in this context but was more broadly employed to treat cancer with the advent of CAR-T cell therapies. This review will summarize the gradual advent of gene therapies from bench to bedside with a main focus on hemopoietic stem cell gene therapy and genome editing and will provide some useful insights into the future of genetic therapies and their gradual integration in the everyday clinical practice.
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Affiliation(s)
- Eleni Papanikolaou
- Department of Molecular Technologies and Stem Cell Therapy, Miltenyi Biotec, Bergisch Gladbach, Germany.,Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Bosio
- Department of Molecular Technologies and Stem Cell Therapy, Miltenyi Biotec, Bergisch Gladbach, Germany
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11
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Kurbidaeva A, Purugganan M. Insulators in Plants: Progress and Open Questions. Genes (Basel) 2021; 12:genes12091422. [PMID: 34573404 PMCID: PMC8470105 DOI: 10.3390/genes12091422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
The genomes of higher eukaryotes are partitioned into topologically associated domains or TADs, and insulators (also known as boundary elements) are the key elements responsible for their formation and maintenance. Insulators were first identified and extensively studied in Drosophila as well as mammalian genomes, and have also been described in yeast and plants. In addition, many insulator proteins are known in Drosophila, and some have been investigated in mammals. However, much less is known about this important class of non-coding DNA elements in plant genomes. In this review, we take a detailed look at known plant insulators across different species and provide an overview of potential determinants of plant insulator functions, including cis-elements and boundary proteins. We also discuss methods previously used in attempts to identify plant insulators, provide a perspective on their importance for research and biotechnology, and discuss areas of potential future research.
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12
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Hsu SJ, Stow EC, Simmons JR, Wallace HA, Lopez AM, Stroud S, Labrador M. Mutations in the insulator protein Suppressor of Hairy wing induce genome instability. Chromosoma 2020; 129:255-274. [PMID: 33140220 DOI: 10.1007/s00412-020-00743-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
Insulator proteins orchestrate the three-dimensional organization of the genome. Insulators function by facilitating communications between regulatory sequences and gene promoters, allowing accurate gene transcription regulation during embryo development and cell differentiation. However, the role of insulator proteins beyond genome organization and transcription regulation remains unclear. Suppressor of Hairy wing [Su(Hw)] is a Drosophila insulator protein that plays an important function in female oogenesis. Here we find that su(Hw) has an unsuspected role in genome stability during cell differentiation. We show that su(Hw) mutant developing egg chambers have poorly formed microtubule organization centers (MTOCs) in the germarium and display mislocalization of the anterior/posterior axis specification factor gurken in later oogenesis stages. Additionally, eggshells from partially rescued su(Hw) mutant female germline exhibit dorsoventral patterning defects. These phenotypes are very similar to phenotypes found in the important class of spindle mutants or in piRNA pathway mutants in Drosophila, in which defects generally result from the failure of germ cells to repair DNA damage. Similarities between mutations in su(Hw) and spindle and piRNA mutants are further supported by an excess of DNA damage in nurse cells, and because Gurken localization defects are partially rescued by mutations in the ATR (mei-41) and Chk1 (grapes) DNA damage response genes. Finally, we also show that su(Hw) mutants produce an elevated number of chromosome breaks in dividing neuroblasts from larval brains. Together, these findings suggest that Su(Hw) is necessary for the maintenance of genome integrity during Drosophila development, in both germline and dividing somatic cells.
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Affiliation(s)
- Shih-Jui Hsu
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Emily C Stow
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - James R Simmons
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Heather A Wallace
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Andrea Mancheno Lopez
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Shannon Stroud
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, 37996, USA.
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13
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Dong P, Tu X, Liang Z, Kang BH, Zhong S. Plant and animal chromatin three-dimensional organization: similar structures but different functions. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5119-5128. [PMID: 32374833 DOI: 10.1093/jxb/eraa220] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
Chromatin is the main carrier of genetic information and is non-randomly distributed within the nucleus. Next-generation sequence-based chromatin conformation capture technologies have enabled us to directly examine its three-dimensional organization at an unprecedented scale and resolution. In the best-studied mammalian models, chromatin folding can be broken down into three hierarchical levels, compartment, domains, and loops, which play important roles in transcriptional regulation. Although similar structures have now been identified in plants, they might not possess exactly the same functions as the mammalian ones. Here, we review recent Hi-C studies in plants, compare plant chromatin structures with their mammalian counterparts, and discuss the differences between plants with different genome sizes.
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Affiliation(s)
- Pengfei Dong
- The South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoyu Tu
- The South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zizheng Liang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Byung-Ho Kang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Silin Zhong
- The South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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14
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Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
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Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
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15
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Stam M, Tark-Dame M, Fransz P. 3D genome organization: a role for phase separation and loop extrusion? CURRENT OPINION IN PLANT BIOLOGY 2019; 48:36-46. [PMID: 31035031 DOI: 10.1016/j.pbi.2019.03.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/08/2019] [Accepted: 03/20/2019] [Indexed: 05/21/2023]
Abstract
In eukaryotes, genomic information is encoded in chromosomes, which occupy distinct territories within the nucleus. Inside these territories, chromosomes are folded in a hierarchical set of topological structures, called compartments, topologically associated domains and loops. Phase separation and loop extrusion are the mechanisms indicated to mediate the 3D organization of the genome, and gene activity and epigenetic marks determine the activity level of the formed chromatin domains. The main difference between plants and animals may be the absence of canonical insulator elements in plants. Comparison across plant species indicates that the identification of chromatin domains is affected by genome size, gene density, and the linear distribution of genes and transposable elements.
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Affiliation(s)
- Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Mariliis Tark-Dame
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands
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16
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Kouprina N, Petrov N, Molina O, Liskovykh M, Pesenti E, Ohzeki JI, Masumoto H, Earnshaw WC, Larionov V. Human Artificial Chromosome with Regulated Centromere: A Tool for Genome and Cancer Studies. ACS Synth Biol 2018; 7:1974-1989. [PMID: 30075081 PMCID: PMC6154217 DOI: 10.1021/acssynbio.8b00230] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since their description in the late 1990s, Human Artificial Chromosomes (HACs) bearing functional kinetochores have been considered as promising systems for gene delivery and expression. More recently a HAC assembled from a synthetic alphoid DNA array has been exploited in studies of centromeric chromatin and in assessing the impact of different epigenetic modifications on kinetochore structure and function in human cells. This HAC was termed the alphoidtetO-HAC, as the synthetic monomers each contained a tetO sequence in place of the CENP-B box that can be targeted specifically with tetR-fusion proteins. Studies in which the kinetochore chromatin of the alphoidtetO-HAC was specifically modified, revealed that heterochromatin is incompatible with centromere function and that centromeric transcription is important for centromere assembly and maintenance. In addition, the alphoidtetO-HAC was modified to carry large gene inserts that are expressed in target cells under conditions that recapitulate the physiological regulation of endogenous loci. Importantly, the phenotypes arising from stable gene expression can be reversed when cells are "cured" of the HAC by inactivating its kinetochore in proliferating cell populations, a feature that provides a control for phenotypic changes attributed to expression of HAC-encoded genes. AlphoidtetO-HAC-based technology has also been used to develop new drug screening and assessment strategies to manipulate the CIN phenotype in cancer cells. In summary, the alphoidtetO-HAC is proving to be a versatile tool for studying human chromosome transactions and structure as well as for genome and cancer studies.
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Affiliation(s)
- Natalay Kouprina
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States,E-mail: . Tel: +1-240-760-7325
| | - Nikolai Petrov
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States
| | - Oscar Molina
- Josep
Carreras Leukaemia Research Institute, School of Medicine, University
of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Mikhail Liskovykh
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States
| | - Elisa Pesenti
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Jun-ichirou Ohzeki
- Laboratory
of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818d Japan
| | - Hiroshi Masumoto
- Laboratory
of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818d Japan,E-mail: . Tel: +81-438-52-395
| | - William C. Earnshaw
- Wellcome
Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland,E-mail: . Tel: +44-(0)131-650-7101
| | - Vladimir Larionov
- Developmental
Therapeutics Branch, National Cancer Institute,
NIH, Bethesda, Maryland 20892, United
States,E-mail: . Tel: +1-240-760-7325
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17
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Thean LF, Wong YH, Lo M, Loi C, Chew MH, Tang CL, Cheah PY. Chromosome 19q13 disruption alters expressions of CYP2A7, MIA and MIA-RAB4B lncRNA and contributes to FAP-like phenotype in APC mutation-negative familial colorectal cancer patients. PLoS One 2017; 12:e0173772. [PMID: 28306719 PMCID: PMC5357012 DOI: 10.1371/journal.pone.0173772] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/27/2017] [Indexed: 12/28/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal-dominantly inherited form of colorectal cancer (CRC) caused by mutation in the adenomatous polyposis coli (APC) gene. Our ability to exhaustively screen for APC mutations identify microsatellite-stable and APC-mutation negative familial CRC patients, enabling us to search for novel genes. We performed genome-wide scan on two affected siblings of one family and 88 ethnicity- and gender-matched healthy controls to identify deletions shared by the siblings. Combined loss of heterozygosity, copy number and allelic-specific copy number analysis uncovered 5 shared deletions. Long-range polymerase chain reaction (PCR) confirmed chromosome 19q13 deletion, which was subsequently found in one other family. The 32 kb deleted region harbors the CYP2A7 gene and was enriched with enhancer, repressor and insulator sites. The wildtype allele was lost in the polyps of the proband. Further, real-time RT-PCR assays showed that expressions of MIA and MIA-RAB4B located 35 kb upstream of the deletion, were up-regulated in the polyps compared to the matched mucosa of the proband. MIA-RAB4B, the read-through long non-coding RNA (lncRNA), RAB4B, PIM2 and TAOK1 share common binding site of a microRNA, miR-24, in their 3'UTRs. PIM2 and TAOK1, two target oncogenes of miR-24, were co-ordinately up-regulated with MIA-RAB4B in the polyps, suggesting that MIA-RAB4B could function as competitive endogenous RNA to titrate miR-24 away from its other targets. The data suggest that the 19.13 deletion disrupted chromatin boundary, leading to altered expression of several genes and lncRNA, could contribute to colorectal cancer via novel genetic and epigenetic mechanisms.
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Affiliation(s)
- Lai Fun Thean
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Yu Hui Wong
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Michelle Lo
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Carol Loi
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Min Hoe Chew
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Choong Leong Tang
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore
- * E-mail:
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18
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Pauli T, Vedder L, Dowling D, Petersen M, Meusemann K, Donath A, Peters RS, Podsiadlowski L, Mayer C, Liu S, Zhou X, Heger P, Wiehe T, Hering L, Mayer G, Misof B, Niehuis O. Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins. BMC Genomics 2016; 17:861. [PMID: 27809783 PMCID: PMC5094011 DOI: 10.1186/s12864-016-3205-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/25/2016] [Indexed: 01/19/2023] Open
Abstract
Background Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods. Results Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number of IBPs. Specifically, of the known twelve insect IBPs, at least three (i.e., CP190, Su(Hw), and CTCF) already existed prior to the evolution of insects. Furthermore we found GAF orthologs in early branching insect orders, including Zygentoma (silverfish and firebrats) and Diplura (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of Neoptera, while Pita is likely an evolutionary novelty of holometabolous insects. Zw5 appears to be restricted to schizophoran flies, whereas BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus Drosophila. Selection models indicate that insect IBPs evolved under neutral or purifying selection. Conclusions Our results suggest that a substantial number of IBPs either pre-date the evolution of insects or evolved early during insect evolution. This suggests an evolutionary history of insulator binding proteins in insects different to that previously thought. Moreover, our study demonstrates the versatility of the 1KITE transcriptomic data for comparative analyses in insects and other arthropods. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Pauli
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.
| | - Lucia Vedder
- University of Tübingen, Geschwister-Scholl-Platz, 72074, Tübingen, Germany
| | - Daniel Dowling
- Johannes Gutenberg University Mainz, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Malte Petersen
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Karen Meusemann
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.,Department for Evolutionary Biology and Ecology (Institut for Biology I, Zoology), University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany.,Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Acton, ACT, 2601, Australia
| | - Alexander Donath
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Ralph S Peters
- Zoological Research Museum Alexander Koenig, Arthropod Department, Adenauerallee 160, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- University of Bonn, Institute of Evolutionary Biology and Ecology, An der Immenburg 1, 53121, Bonn, Germany
| | - Christoph Mayer
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Peter Heger
- University of Cologne, Cologne Biocenter, Institute for Genetics, Zülpicher Straße 47a, 50674, Köln, Germany
| | - Thomas Wiehe
- University of Cologne, Cologne Biocenter, Institute for Genetics, Zülpicher Straße 47a, 50674, Köln, Germany
| | - Lars Hering
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Georg Mayer
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Bernhard Misof
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Oliver Niehuis
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.
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19
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Baiamonte E, Spinelli G, Maggio A, Acuto S, Cavalieri V. The Sea Urchin sns5 Chromatin Insulator Shapes the Chromatin Architecture of a Lentivirus Vector Integrated in the Mammalian Genome. Nucleic Acid Ther 2016; 26:318-326. [PMID: 27248156 DOI: 10.1089/nat.2016.0614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lentivirus vectors are presently the favorite vehicles for therapeutic gene transfer in hematopoietic cells. Nonetheless, these vectors integrate randomly throughout the genome, exhibiting variegation of transgene expression due to the spreading of heterochromatin into the vector sequences. Moreover, the cis-regulatory elements harbored by the vector could disturb the proper transcription of resident genes neighboring the integration site. The incorporation of chromatin insulators in flanking position to the transferred unit can alleviate both the above-mentioned dangerous effects, due to the insulator-specific barrier and enhancer-blocking activities. In this study, we report the valuable properties of the sea urchin-derived sns5 insulator in improving the expression efficiency of a lentivirus vector integrated in the mammalian erythroid genome. We show that these results neither reflect an intrinsic sns5 enhancer activity nor rely on the recruitment of the erythroid-specific GATA-1 factor to sns5. Furthermore, by using the Chromosome Conformation Capture technology, we report that a single copy of the sns5-insulated vector is specifically organized into an independent chromatin loop at the provirus locus. Our results not only provide new clues concerning the molecular mechanism of sns5 function in the erythroid genome but also reassure the use of sns5 to improve the performance of gene therapy vectors.
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Affiliation(s)
- Elena Baiamonte
- 1 Campus of Haematology Franco e Piera Cutino, Villa Sofia-Cervello Hospital , Palermo, Italy
| | - Giovanni Spinelli
- 2 Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo , Palermo, Italy
| | - Aurelio Maggio
- 1 Campus of Haematology Franco e Piera Cutino, Villa Sofia-Cervello Hospital , Palermo, Italy
| | - Santina Acuto
- 1 Campus of Haematology Franco e Piera Cutino, Villa Sofia-Cervello Hospital , Palermo, Italy
| | - Vincenzo Cavalieri
- 2 Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo , Palermo, Italy
- 3 Mediterranean Center for Human Health Advanced Biotechnologies (CHAB), University of Palermo , Palermo, Italy
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20
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Razin SV, Gavrilov AA, Ulyanov SV. Transcription-controlling regulatory elements of the eukaryotic genome. Mol Biol 2015. [DOI: 10.1134/s0026893315020119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Del Vecchio D. Modularity, context-dependence, and insulation in engineered biological circuits. Trends Biotechnol 2015; 33:111-9. [DOI: 10.1016/j.tibtech.2014.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/06/2014] [Accepted: 11/19/2014] [Indexed: 01/21/2023]
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