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  1. Article ; Online: Psi promotes Drosophila wing growth via direct transcriptional activation of cell cycle targets and repression of growth inhibitors.

    Zaytseva, Olga / Mitchell, Naomi C / Muckle, Damien / Delandre, Caroline / Nie, Zuqin / Werner, Janis K / Lis, John T / Eyras, Eduardo / Hannan, Ross D / Levens, David L / Marshall, Owen J / Quinn, Leonie M

    Development (Cambridge, England)

    2023  Volume 150, Issue 2

    Abstract: The first characterised FUSE Binding Protein family member, FUBP1, binds single-stranded DNA to activate MYC transcription. Psi, the sole FUBP protein in Drosophila, binds RNA to regulate P-element and mRNA splicing. Our previous work revealed pro-growth ...

    Abstract The first characterised FUSE Binding Protein family member, FUBP1, binds single-stranded DNA to activate MYC transcription. Psi, the sole FUBP protein in Drosophila, binds RNA to regulate P-element and mRNA splicing. Our previous work revealed pro-growth functions for Psi, which depend, in part, on transcriptional activation of Myc. Genome-wide functions for FUBP family proteins in transcriptional control remain obscure. Here, through the first genome-wide binding and expression profiles obtained for a FUBP family protein, we demonstrate that, in addition to being required to activate Myc to promote cell growth, Psi also directly binds and activates stg to couple growth and cell division. Thus, Psi knockdown results in reduced cell division in the wing imaginal disc. In addition to activating these pro-proliferative targets, Psi directly represses transcription of the growth inhibitor tolkin (tok, a metallopeptidase implicated in TGFβ signalling). We further demonstrate tok overexpression inhibits proliferation, while tok loss of function increases mitosis alone and suppresses impaired cell division caused by Psi knockdown. Thus, Psi orchestrates growth through concurrent transcriptional activation of the pro-proliferative genes Myc and stg, in combination with repression of the growth inhibitor tok.
    MeSH term(s) Animals ; Cell Division ; Cell Proliferation ; Drosophila/metabolism ; Drosophila Proteins/metabolism ; Proto-Oncogene Proteins c-myc/metabolism ; RNA-Binding Proteins/metabolism ; Transcriptional Activation
    Chemical Substances Drosophila Proteins ; Proto-Oncogene Proteins c-myc ; PSI protein, Drosophila ; RNA-Binding Proteins
    Language English
    Publishing date 2023-01-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 90607-4
    ISSN 1477-9129 ; 0950-1991
    ISSN (online) 1477-9129
    ISSN 0950-1991
    DOI 10.1242/dev.201563
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  2. Article ; Online: In Vivo Chemical Probing for G-Quadruplex Formation.

    Kouzine, Fedor / Wojtowicz, Damian / Yamane, Arito / Casellas, Rafael / Przytycka, Teresa M / Levens, David L

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 2035, Page(s) 369–382

    Abstract: While DNA inside the cells is predominantly canonical right-handed double helix, guanine-rich DNAs have potential to fold into four-stranded structures that contain stacks of G-quartets (G4 DNA quadruplex). Genome sequencing has revealed G4 sequences ... ...

    Abstract While DNA inside the cells is predominantly canonical right-handed double helix, guanine-rich DNAs have potential to fold into four-stranded structures that contain stacks of G-quartets (G4 DNA quadruplex). Genome sequencing has revealed G4 sequences tend to localize at the gene control regions, especially in the promoters of oncogenes. A growing body of evidence indicates that G4 DNA quadruplexes might have important regulatory roles in genome function, highlighting the need for techniques to detect genome-wide folding of DNA into this structure. Potassium permanganate in vivo treatment of cells results in oxidizing of nucleotides in single-stranded DNA regions that accompany G4 DNA quadruplexes formation, providing an excellent probe for the conformational state of DNA inside the living cells. Here, we describe a permanganate-based methodology to detect G4 DNA quadruplex, genome-wide. This methodology combined with high-throughput sequencing provides a snapshot of the DNA conformation over the whole genome in vivo.
    MeSH term(s) Chromatin/chemistry ; G-Quadruplexes ; Genomics ; Manganese Compounds/chemistry ; Oxides/chemistry
    Chemical Substances Chromatin ; Manganese Compounds ; Oxides ; permanganic acid (14333-13-2)
    Language English
    Publishing date 2019-08-23
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9666-7_23
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  3. Article ; Online: Transcriptional repression of Myc underlies the tumour suppressor function of AGO1 in

    Zaytseva, Olga / Mitchell, Naomi C / Guo, Linna / Marshall, Owen J / Parsons, Linda M / Hannan, Ross D / Levens, David L / Quinn, Leonie M

    Development (Cambridge, England)

    2020  Volume 147, Issue 11

    Abstract: Here, we report novel tumour suppressor activity for ... ...

    Abstract Here, we report novel tumour suppressor activity for the
    MeSH term(s) Animals ; Animals, Genetically Modified/metabolism ; Argonaute Proteins/antagonists & inhibitors ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; DNA-Binding Proteins/antagonists & inhibitors ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Drosophila/growth & development ; Drosophila/metabolism ; Drosophila Proteins/antagonists & inhibitors ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Larva/metabolism ; MicroRNAs/metabolism ; Mutagenesis, Site-Directed ; Promoter Regions, Genetic ; RNA Interference ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; RNA, Messenger/metabolism ; RNA-Binding Proteins/antagonists & inhibitors ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Ribosomes/metabolism ; Transcription Factors/antagonists & inhibitors ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic ; Wings, Animal/growth & development ; Wings, Animal/physiology
    Chemical Substances AGO1 protein, Drosophila ; Argonaute Proteins ; DNA-Binding Proteins ; Drosophila Proteins ; MicroRNAs ; Myc protein, Drosophila ; PSI protein, Drosophila ; RNA, Messenger ; RNA-Binding Proteins ; Transcription Factors ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2020-06-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 90607-4
    ISSN 1477-9129 ; 0950-1991
    ISSN (online) 1477-9129
    ISSN 0950-1991
    DOI 10.1242/dev.190231
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  4. Article: MAIT cells drive chronic inflammation in a genetically diverse murine model of spontaneous colitis.

    Loh, Liyen / Orlicky, David / Spengler, Andrea / Levens, Cassandra / Celli, Sofia / Domenico, Joanne / Klarquist, Jared / Onyiah, Joseph / Matsuda, Jennifer / Kuhn, Kristine / Gapin, Laurent

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Background & aims: Lymphocytes that produce IL-17 can confer protective immunity during infections by pathogens, yet their involvement in inflammatory diseases is a subject of debate. Although these cells may perpetuate inflammation, resulting in tissue ...

    Abstract Background & aims: Lymphocytes that produce IL-17 can confer protective immunity during infections by pathogens, yet their involvement in inflammatory diseases is a subject of debate. Although these cells may perpetuate inflammation, resulting in tissue damage, they are also capable of contributing directly or indirectly to tissue repair, thus necessitating more detailed investigation. Mucosal-Associated-Invariant-T (MAIT) cells are innate-like T cells, acquiring a type III phenotype in the thymus. Here, we dissected the role of MAIT cells
    Methods: Multiparameter spectral flow cytometry and scRNAseq were used to characterize MAIT and immune cell dynamics and transcriptomic signatures respectively, in the collaborative-cross strain, CC011/Unc and CC011/Unc-
    Results: In contrast to many conventional mouse laboratory strains, the CC011 strain harbors a high baseline population of MAIT cells. We observed an age-related increase in colonic MAIT cells, Th17 cells, regulatory T cells, and neutrophils, which paralleled the development of spontaneous colitis. This progression manifested histological traits reminiscent of human IBD. The transcriptomic analysis of colonic MAIT cells from CC011 revealed an activation profile consistent with an inflammatory milieu, marked by an enhanced type-III response. Notably, IL-17A was abundantly secreted by MAIT cells in the colons of afflicted mice. Conversely, in the MAIT cell-deficient CC011-Traj33-/- mice, there was a notable absence of significant colonic histopathology. Furthermore, myeloperoxidase staining indicated a substantial decrease in colonic neutrophils.
    Conclusions: Our findings suggest that MAIT cells play a pivotal role in modulating the severity of intestinal pathology, potentially orchestrating the inflammatory process by driving the accumulation of neutrophils within the colonic environment.
    Language English
    Publishing date 2023-12-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.29.569225
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  5. Article ; Online: The Use of Psoralen Photobinding to Study Transcription-Induced Supercoiling.

    Kouzine, Fedor / Baranello, Laura / Levens, David

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1703, Page(s) 95–108

    Abstract: Proteins manipulating intracellular DNA necessarily impart torsional stress, which redistributes across the DNA. Overtwisting and undertwisting of the double helix result in the manifestation of positive and negative DNA supercoiling. A growing body of ... ...

    Abstract Proteins manipulating intracellular DNA necessarily impart torsional stress, which redistributes across the DNA. Overtwisting and undertwisting of the double helix result in the manifestation of positive and negative DNA supercoiling. A growing body of evidence indicates that DNA topology is an important player in the key regulatory steps of genome function, highlighting the need for biochemical techniques to detect dynamic changes in the DNA structure. Psoralen binding to DNA in vivo is proportional to the level of supercoiling, providing an excellent probe for the topological state of nuclear DNA. Here we describe a psoralen-based methodology to detect transcription-induced DNA supercoiling genome-wide. The DNA samples generated with this approach can be hybridized to microarray platforms or high-throughput sequenced to provide a topological snapshot of the whole genome.
    MeSH term(s) Cell Line ; DNA, Superhelical/chemistry ; DNA, Superhelical/genetics ; Ficusin/pharmacology ; Genome, Human ; Humans ; Models, Molecular ; Nucleic Acid Conformation ; Photosensitizing Agents/pharmacology ; Transcription, Genetic
    Chemical Substances DNA, Superhelical ; Photosensitizing Agents ; Ficusin (KTZ7ZCN2EX)
    Language English
    Publishing date 2017-11-20
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7459-7_7
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  6. Article: Reconstructing MYC.

    Levens, David L

    Genes & development

    2003  Volume 17, Issue 9, Page(s) 1071–1077

    MeSH term(s) Animals ; Gene Expression Profiling ; Gene Expression Regulation/physiology ; Genes, myc/physiology ; Humans ; Precipitin Tests ; RNA, Messenger/metabolism
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2003-05-01
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.1095203
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  7. Article: Controlling gene expression by DNA mechanics: emerging insights and challenges.

    Levens, David / Baranello, Laura / Kouzine, Fedor

    Biophysical reviews

    2016  Volume 8, Issue 3, Page(s) 259–268

    Abstract: Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in ... ...

    Abstract Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
    Language English
    Publishing date 2016-08-20
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-016-0216-8
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  8. Article: Controlling gene expression by DNA mechanics: emerging insights and challenges.

    Levens, David / Baranello, Laura / Kouzine, Fedor

    Biophysical reviews

    2016  Volume 8, Issue Suppl 1, Page(s) 23–32

    Abstract: Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in ... ...

    Abstract Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions. The double helix is a fiber that responds to flexural and torsional stress, which if accumulated, can affect promoter output as well as change DNA and chromatin structure. The relationship between DNA mechanics and the control of early transcription initiation events has been under-investigated. Genomic techniques to display topological stress and conformational variation in DNA across the mammalian genome provide an exciting new insight on the role of DNA mechanics in the early stages of the transcription cycle. Without understanding how torsional and flexural stresses are generated, transmitted, and dissipated, no model of transcription will be complete and accurate.
    Language English
    Publishing date 2016-11-14
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-016-0243-5
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  9. Article: N

    Candish, Lisa / Levens, Alison / Lupton, David W

    Chemical science

    2015  Volume 6, Issue 4, Page(s) 2366–2370

    Abstract: ... ...

    Abstract N
    Language English
    Publishing date 2015-01-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/c4sc03726j
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  10. Article ; Online: Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation.

    Shaheen, Cynthia / Hastie, Cameron / Metera, Kimberly / Scott, Shane / Zhang, Zhi / Chen, Sitong / Gu, Gracia / Weber, Lisa / Munsky, Brian / Kouzine, Fedor / Levens, David / Benham, Craig / Leslie, Sabrina

    Nucleic acids research

    2022  Volume 50, Issue 5, Page(s) 2754–2764

    Abstract: Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform ... ...

    Abstract Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
    MeSH term(s) DNA/genetics ; DNA, Superhelical/genetics ; Kinetics ; Nucleic Acid Conformation ; Plasmids/genetics ; Single Molecule Imaging
    Chemical Substances DNA, Superhelical ; DNA (9007-49-2)
    Language English
    Publishing date 2022-02-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac101
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