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Huang Z, Cui W, Ratnayake I, Tawil R, Pfeifer GP. SMCHD1 maintains heterochromatin and genome compartments in human myoblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602392. [PMID: 39026812 PMCID: PMC11257445 DOI: 10.1101/2024.07.07.602392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Mammalian genomes are subdivided into euchromatic A compartments that contain mostly active chromatin, and inactive, heterochromatic B compartments. However, it is unknown how A and B genome compartments are established and maintained. Here we studied SMCHD1, an SMC-like protein in human male myoblasts. SMCHD1 colocalizes with Lamin B1 and the heterochromatin mark H3K9me3. Loss of SMCHD1 leads to extensive heterochromatin depletion at the nuclear lamina and acquisition of active chromatin states along all chromosomes. In absence of SMCHD1, long range intra-chromosomal and inter-chromosomal contacts between B compartments are lost while many new TADs and loops are formed. Inactivation of SMCHD1 promotes numerous B to A compartment transitions accompanied by activation of silenced genes. SMCHD1 functions as an anchor for heterochromatin domains ensuring that these domains are inaccessible to epigenome modification enzymes that typically operate in active chromatin. Therefore, A compartments are formed by default when not prevented by SMCHD1.
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2
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Stanković D, Tain LS, Uhlirova M. Xrp1 governs the stress response program to spliceosome dysfunction. Nucleic Acids Res 2024; 52:2093-2111. [PMID: 38303573 PMCID: PMC10954486 DOI: 10.1093/nar/gkae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
Co-transcriptional processing of nascent pre-mRNAs by the spliceosome is vital to regulating gene expression and maintaining genome integrity. Here, we show that the deficiency of functional U5 small nuclear ribonucleoprotein particles (snRNPs) in Drosophila imaginal cells causes extensive transcriptome remodeling and accumulation of highly mutagenic R-loops, triggering a robust stress response and cell cycle arrest. Despite compromised proliferative capacity, the U5 snRNP-deficient cells increased protein translation and cell size, causing intra-organ growth disbalance before being gradually eliminated via apoptosis. We identify the Xrp1-Irbp18 heterodimer as the primary driver of transcriptional and cellular stress program downstream of U5 snRNP malfunction. Knockdown of Xrp1 or Irbp18 in U5 snRNP-deficient cells attenuated JNK and p53 activity, restored normal cell cycle progression and growth, and inhibited cell death. Reducing Xrp1-Irbp18, however, did not rescue the splicing defects, highlighting the requirement of accurate splicing for cellular and tissue homeostasis. Our work provides novel insights into the crosstalk between splicing and the DNA damage response and defines the Xrp1-Irbp18 heterodimer as a critical sensor of spliceosome malfunction and mediator of the stress-induced cellular senescence program.
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Affiliation(s)
- Dimitrije Stanković
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Luke S Tain
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
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3
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Xu C, Ramos TB, Marshall OJ, Doe CQ. Notch signaling and Bsh homeodomain activity are integrated to diversify Drosophila lamina neuron types. eLife 2024; 12:RP90136. [PMID: 38193901 PMCID: PMC10945509 DOI: 10.7554/elife.90136] [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] [Indexed: 01/10/2024] Open
Abstract
Notch signaling is an evolutionarily conserved pathway for specifying binary neuronal fates, yet how it specifies different fates in different contexts remains elusive. In our accompanying paper, using the Drosophila lamina neuron types (L1-L5) as a model, we show that the primary homeodomain transcription factor (HDTF) Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates. Here we test the hypothesis that Notch signaling enables Bsh to differentially specify L4 and L5 fates. We show asymmetric Notch signaling between newborn L4 and L5 neurons, but they are not siblings; rather, Notch signaling in L4 is due to Delta expression in adjacent L1 neurons. While Notch signaling and Bsh expression are mutually independent, Notch is necessary and sufficient for Bsh to specify L4 fate over L5. The NotchON L4, compared to NotchOFF L5, has a distinct open chromatin landscape which allows Bsh to bind distinct genomic loci, leading to L4-specific identity gene transcription. We propose a novel model in which Notch signaling is integrated with the primary HDTF activity to diversify neuron types by directly or indirectly generating a distinct open chromatin landscape that constrains the pool of genes that a primary HDTF can activate.
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Affiliation(s)
- Chundi Xu
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Tyler B Ramos
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Owen J Marshall
- Menzies Institute for Medical Research, University of TasmaniaHobartAustralia
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
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4
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Friedman CE, Cheetham SW, Negi S, Mills RJ, Ogawa M, Redd MA, Chiu HS, Shen S, Sun Y, Mizikovsky D, Bouveret R, Chen X, Voges HK, Paterson S, De Angelis JE, Andersen SB, Cao Y, Wu Y, Jafrani YMA, Yoon S, Faulkner GJ, Smith KA, Porrello E, Harvey RP, Hogan BM, Nguyen Q, Zeng J, Kikuchi K, Hudson JE, Palpant NJ. HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Dev Cell 2024; 59:91-107.e6. [PMID: 38091997 DOI: 10.1016/j.devcel.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
Genomic regulation of cardiomyocyte differentiation is central to heart development and function. This study uses genetic loss-of-function human-induced pluripotent stem cell-derived cardiomyocytes to evaluate the genomic regulatory basis of the non-DNA-binding homeodomain protein HOPX. We show that HOPX interacts with and controls cardiac genes and enhancer networks associated with diverse aspects of heart development. Using perturbation studies in vitro, we define how upstream cell growth and proliferation control HOPX transcription to regulate cardiac gene programs. We then use cell, organoid, and zebrafish regeneration models to demonstrate that HOPX-regulated gene programs control cardiomyocyte function in development and disease. Collectively, this study mechanistically links cell signaling pathways as upstream regulators of HOPX transcription to control gene programs underpinning cardiomyocyte identity and function.
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Affiliation(s)
- Clayton E Friedman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sumedha Negi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Masahito Ogawa
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Meredith A Redd
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Romaric Bouveret
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Holly K Voges
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Scott Paterson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jessica E De Angelis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yohaann M A Jafrani
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sohye Yoon
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Kelly A Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Enzo Porrello
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Benjamin M Hogan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kazu Kikuchi
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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5
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Xu C, Ramos TB, Rogers EM, Reiser MB, Doe CQ. Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity. eLife 2024; 12:RP90133. [PMID: 38180023 PMCID: PMC10942767 DOI: 10.7554/elife.90133] [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] [Indexed: 01/06/2024] Open
Abstract
How our brain generates diverse neuron types that assemble into precise neural circuits remains unclear. Using Drosophila lamina neuron types (L1-L5), we show that the primary homeodomain transcription factor (HDTF) brain-specific homeobox (Bsh) is initiated in progenitors and maintained in L4/L5 neurons to adulthood. Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates while repressing the HDTF Zfh1 to prevent ectopic L1/L3 fates (control: L1-L5; Bsh-knockdown: L1-L3), thereby generating lamina neuronal diversity for normal visual sensitivity. Subsequently, in L4 neurons, Bsh and Ap function in a feed-forward loop to activate the synapse recognition molecule DIP-β, thereby bridging neuronal fate decision to synaptic connectivity. Expression of a Bsh:Dam, specifically in L4, reveals Bsh binding to the DIP-β locus and additional candidate L4 functional identity genes. We propose that HDTFs function hierarchically to coordinate neuronal molecular identity, circuit formation, and function. Hierarchical HDTFs may represent a conserved mechanism for linking neuronal diversity to circuit assembly and function.
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Affiliation(s)
- Chundi Xu
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Tyler B Ramos
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Edward M Rogers
- Janelia Research Campus, Howard Hughes Medical Institute, Helix DriveAshburnUnited States
| | - Michael B Reiser
- Janelia Research Campus, Howard Hughes Medical Institute, Helix DriveAshburnUnited States
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
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6
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Zhao X, Yang X, Lv P, Xu Y, Wang X, Zhao Z, Du J. Polycomb regulates circadian rhythms in Drosophila in clock neurons. Life Sci Alliance 2024; 7:e202302140. [PMID: 37914396 PMCID: PMC10620068 DOI: 10.26508/lsa.202302140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Circadian rhythms are essential physiological feature for most living organisms. Previous studies have shown that epigenetic regulation plays a crucial role. There is a knowledge gap in the chromatin state of some key clock neuron clusters. In this study, we show that circadian rhythm is affected by the epigenetic regulator Polycomb (Pc) within the Drosophila clock neurons. To investigate the molecular mechanisms underlying the roles of Pc in these clock neuron clusters, we use targeted DamID (TaDa) to identify genes significantly bound by Pc in the neurons marked by C929-Gal4 (including l-LNvs cluster), R6-Gal4 (including s-LNvs cluster), R18H11-Gal4 (including DN1 cluster), and DVpdf-Gal4, pdf-Gal80 (including LNds cluster). It shows that Pc binds to the genes involved in the circadian rhythm pathways, arguing a direct role for Pc in regulating circadian rhythms through specific clock genes. This study shows the identification of Pc targets in the clock neuron clusters, providing potential resource for understanding the regulatory mechanisms of circadian rhythms by the PcG complex. Thus, this study provided an example for epigenetic regulation of adult behavior.
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Affiliation(s)
- Xianguo Zhao
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xingzhuo Yang
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Pengfei Lv
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuetong Xu
- https://ror.org/04v3ywz14 Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Xiangfeng Wang
- https://ror.org/04v3ywz14 Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Zhangwu Zhao
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Juan Du
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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7
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Josserand M, Rubanova N, Stefanutti M, Roumeliotis S, Espenel M, Marshall OJ, Servant N, Gervais L, Bardin AJ. Chromatin state transitions in the Drosophila intestinal lineage identify principles of cell-type specification. Dev Cell 2023; 58:3048-3063.e6. [PMID: 38056452 DOI: 10.1016/j.devcel.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/20/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
Tissue homeostasis relies on rewiring of stem cell transcriptional programs into those of differentiated cells. Here, we investigate changes in chromatin occurring in a bipotent adult stem cells. Combining mapping of chromatin-associated factors with statistical modeling, we identify genome-wide transitions during differentiation in the adult Drosophila intestinal stem cell (ISC) lineage. Active, stem-cell-enriched genes transition to a repressive heterochromatin protein-1-enriched state more prominently in enteroendocrine cells (EEs) than in enterocytes (ECs), in which the histone H1-enriched Black state is preeminent. In contrast, terminal differentiation genes associated with metabolic functions follow a common path from a repressive, primed, histone H1-enriched Black state in ISCs to active chromatin states in EE and EC cells. Furthermore, we find that lineage priming has an important function in adult ISCs, and we identify histone H1 as a mediator of this process. These data define underlying principles of chromatin changes during adult multipotent stem cell differentiation.
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Affiliation(s)
- Manon Josserand
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France
| | - Natalia Rubanova
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France; Institut Curie Bioinformatics Core Facility, PSL Research University, INSERM U900, MINES ParisTech, Paris 75005, France
| | - Marine Stefanutti
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France
| | - Spyridon Roumeliotis
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France
| | - Marion Espenel
- Institut Curie, PSL University, ICGex Next-Generation Sequencing Platform, 75005 Paris, France
| | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7000, Australia
| | - Nicolas Servant
- Institut Curie Bioinformatics Core Facility, PSL Research University, INSERM U900, MINES ParisTech, Paris 75005, France
| | - Louis Gervais
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France.
| | - Allison J Bardin
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France.
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Rogers MF, Marshall OJ, Secombe J. KDM5-mediated activation of genes required for mitochondrial biology is necessary for viability in Drosophila. Development 2023; 150:dev202024. [PMID: 37800333 PMCID: PMC10651110 DOI: 10.1242/dev.202024] [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: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Histone-modifying proteins play important roles in the precise regulation of the transcriptional programs that coordinate development. KDM5 family proteins interact with chromatin through demethylation of H3K4me3 as well as demethylase-independent mechanisms that remain less understood. To gain fundamental insights into the transcriptional activities of KDM5 proteins, we examined the essential roles of the single Drosophila Kdm5 ortholog during development. KDM5 performs crucial functions in the larval neuroendocrine prothoracic gland, providing a model to study its role in regulating key gene expression programs. Integrating genome binding and transcriptomic data, we identify that KDM5 regulates the expression of genes required for the function and maintenance of mitochondria, and we find that loss of KDM5 causes morphological changes to mitochondria. This is key to the developmental functions of KDM5, as expression of the mitochondrial biogenesis transcription factor Ets97D, homolog of GABPα, is able to suppress the altered mitochondrial morphology as well as the lethality of Kdm5 null animals. Together, these data establish KDM5-mediated cellular functions that are important for normal development and could contribute to KDM5-linked disorders when dysregulated.
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Affiliation(s)
- Michael F. Rogers
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Owen J. Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart TAS 7000, Australia
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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9
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Brener A, Lorber D, Reuveny A, Toledano H, Porat-Kuperstein L, Lebenthal Y, Weizman E, Olender T, Volk T. Sedentary Behavior Impacts on the Epigenome and Transcriptome: Lessons from Muscle Inactivation in Drosophila Larvae. Cells 2023; 12:2333. [PMID: 37830547 PMCID: PMC10571804 DOI: 10.3390/cells12192333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
The biological mechanisms linking sedentary lifestyles and metabolic derangements are incompletely understood. In this study, temporal muscle inactivation in Drosophila larvae carrying a temperature-sensitive mutation in the shibire (shi1) gene was induced to mimic sedentary behavior during early life and study its transcriptional outcome. Our findings indicated a significant change in the epigenetic profile, as well as the genomic profile, of RNA Pol II binding in the inactive muscles relative to control, within a relatively short time period. Whole-genome analysis of RNA-Pol II binding to DNA by muscle-specific targeted DamID (TaDa) protocol revealed that muscle inactivity altered Pol II binding in 121 out of 2010 genes (6%), with a three-fold enrichment of genes coding for lncRNAs. The suppressed protein-coding genes included genes associated with longevity, DNA repair, muscle function, and ubiquitin-dependent proteostasis. Moreover, inducing muscle inactivation exerted a multi-level impact upon chromatin modifications, triggering an altered epigenetic balance of active versus inactive marks. The downregulated genes in the inactive muscles included genes essential for muscle structure and function, carbohydrate metabolism, longevity, and others. Given the multiple analogous genes in Drosophila for many human genes, extrapolating our findings to humans may hold promise for establishing a molecular link between sedentary behavior and metabolic diseases.
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Affiliation(s)
- Avivit Brener
- Pediatric Endocrinology and Diabetes Institute, Dana-Dwek Children’s Hospital, Tel Aviv Sourasky Medical Center, Affiliated with the Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (A.B.); (Y.L.)
| | - Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (D.L.); (A.R.); (T.O.)
| | - Adriana Reuveny
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (D.L.); (A.R.); (T.O.)
| | - Hila Toledano
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel; (H.T.); (L.P.-K.)
| | - Lilach Porat-Kuperstein
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel; (H.T.); (L.P.-K.)
| | - Yael Lebenthal
- Pediatric Endocrinology and Diabetes Institute, Dana-Dwek Children’s Hospital, Tel Aviv Sourasky Medical Center, Affiliated with the Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (A.B.); (Y.L.)
| | - Eviatar Weizman
- G-INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (D.L.); (A.R.); (T.O.)
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel; (D.L.); (A.R.); (T.O.)
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10
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de la Cruz-Ruiz P, Rodríguez-Palero MJ, Askjaer P, Artal-Sanz M. Tissue-specific chromatin-binding patterns of Caenorhabditis elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression. Genetics 2023; 224:iyad081. [PMID: 37119802 PMCID: PMC10324947 DOI: 10.1093/genetics/iyad081] [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: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
Heterochromatin is characterized by an enrichment of repetitive elements and low gene density and is often maintained in a repressed state across cell division and differentiation. The silencing is mainly regulated by repressive histone marks such as H3K9 and H3K27 methylated forms and the heterochromatin protein 1 (HP1) family. Here, we analyzed in a tissue-specific manner the binding profile of the two HP1 homologs in Caenorhabditis elegans, HPL-1 and HPL-2, at the L4 developmental stage. We identified the genome-wide binding profile of intestinal and hypodermal HPL-2 and intestinal HPL-1 and compared them with heterochromatin marks and other features. HPL-2 associated preferentially to the distal arms of autosomes and correlated positively with the methylated forms of H3K9 and H3K27. HPL-1 was also enriched in regions containing H3K9me3 and H3K27me3 but exhibited a more even distribution between autosome arms and centers. HPL-2 showed a differential tissue-specific enrichment for repetitive elements conversely with HPL-1, which exhibited a poor association. Finally, we found a significant intersection of genomic regions bound by the BLMP-1/PRDM1 transcription factor and intestinal HPL-1, suggesting a corepressive role during cell differentiation. Our study uncovers both shared and singular properties of conserved HP1 proteins, providing information about genomic binding preferences in relation to their role as heterochromatic markers.
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Affiliation(s)
- Patricia de la Cruz-Ruiz
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
| | - María Jesús Rodríguez-Palero
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Peter Askjaer
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
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11
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Sgammeglia N, Widmer YF, Kaldun JC, Fritsch C, Bruggmann R, Sprecher SG. Memory phase-specific genes in the Mushroom Bodies identified using CrebB-target DamID. PLoS Genet 2023; 19:e1010802. [PMID: 37307281 DOI: 10.1371/journal.pgen.1010802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/29/2023] [Indexed: 06/14/2023] Open
Abstract
The formation of long-term memories requires changes in the transcriptional program and de novo protein synthesis. One of the critical regulators for long-term memory (LTM) formation and maintenance is the transcription factor CREB. Genetic studies have dissected the requirement of CREB activity within memory circuits, however less is known about the genetic mechanisms acting downstream of CREB and how they may contribute defining LTM phases. To better understand the downstream mechanisms, we here used a targeted DamID approach (TaDa). We generated a CREB-Dam fusion protein using the fruit fly Drosophila melanogaster as model. Expressing CREB-Dam in the mushroom bodies (MBs), a brain center implicated in olfactory memory formation, we identified genes that are differentially expressed between paired and unpaired appetitive training paradigm. Of those genes we selected candidates for an RNAi screen in which we identified genes causing increased or decreased LTM.
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Affiliation(s)
- Noemi Sgammeglia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Yves F Widmer
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jenifer C Kaldun
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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12
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Zuñiga-Hernandez J, Meneses C, Bastias M, Allende ML, Glavic A. Drosophila DAxud1 Has a Repressive Transcription Activity on Hsp70 and Other Heat Shock Genes. Int J Mol Sci 2023; 24:ijms24087485. [PMID: 37108646 PMCID: PMC10138878 DOI: 10.3390/ijms24087485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Drosophila melanogaster DAxud1 is a transcription factor that belongs to the Cysteine Serine Rich Nuclear Protein (CSRNP) family, conserved in metazoans, with a transcriptional transactivation activity. According to previous studies, this protein promotes apoptosis and Wnt signaling-mediated neural crest differentiation in vertebrates. However, no analysis has been conducted to determine what other genes it might control, especially in connection with cell survival and apoptosis. To partly answer this question, this work analyzes the role of Drosophila DAxud1 using Targeted-DamID-seq (TaDa-seq), which allows whole genome screening to determine in which regions it is most frequently found. This analysis confirmed the presence of DAxud1 in groups of pro-apoptotic and Wnt pathway genes, as previously described; furthermore, stress resistance genes that coding heat shock protein (HSP) family genes were found as hsp70, hsp67, and hsp26. The enrichment of DAxud1 also identified a DNA-binding motif (AYATACATAYATA) that is frequently found in the promoters of these genes. Surprisingly, the following analyses demonstrated that DAxud1 exerts a repressive role on these genes, which are necessary for cell survival. This is coupled with the pro-apoptotic and cell cycle arrest roles of DAxud1, in which repression of hsp70 complements the maintenance of tissue homeostasis through cell survival modulation.
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Affiliation(s)
- Jorge Zuñiga-Hernandez
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
| | - Claudio Meneses
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
- Millennium Nucleus Development of Super Adaptable Plants (MN-SAP), Santiago 8331150, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Macarena Bastias
- Centro de Biotecnología vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370035, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
| | - Alvaro Glavic
- Millennium Institute Center for Genome Regulation (CGR), Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile
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13
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Li Mow Chee F, Beernaert B, Griffith BGC, Loftus AEP, Kumar Y, Wills JC, Lee M, Valli J, Wheeler AP, Armstrong JD, Parsons M, Leigh IM, Proby CM, von Kriegsheim A, Bickmore WA, Frame MC, Byron A. Mena regulates nesprin-2 to control actin-nuclear lamina associations, trans-nuclear membrane signalling and gene expression. Nat Commun 2023; 14:1602. [PMID: 36959177 PMCID: PMC10036544 DOI: 10.1038/s41467-023-37021-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/21/2023] [Indexed: 03/25/2023] Open
Abstract
Interactions between cells and the extracellular matrix, mediated by integrin adhesion complexes, play key roles in fundamental cellular processes, including the sensing and transduction of mechanical cues. Here, we investigate systems-level changes in the integrin adhesome in patient-derived cutaneous squamous cell carcinoma cells and identify the actin regulatory protein Mena as a key node in the adhesion complex network. Mena is connected within a subnetwork of actin-binding proteins to the LINC complex component nesprin-2, with which it interacts and co-localises at the nuclear envelope. Moreover, Mena potentiates the interactions of nesprin-2 with the actin cytoskeleton and the nuclear lamina. CRISPR-mediated Mena depletion causes altered nuclear morphology, reduces tyrosine phosphorylation of the nuclear membrane protein emerin and downregulates expression of the immunomodulatory gene PTX3 via the recruitment of its enhancer to the nuclear periphery. We uncover an unexpected role for Mena at the nuclear membrane, where it controls nuclear architecture, chromatin repositioning and gene expression. Our findings identify an adhesion protein that regulates gene transcription via direct signalling across the nuclear envelope.
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Affiliation(s)
- Frederic Li Mow Chee
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Bruno Beernaert
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, OX3 7DQ, UK
| | - Billie G C Griffith
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Alexander E P Loftus
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Yatendra Kumar
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Jimi C Wills
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Martin Lee
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Jessica Valli
- Edinburgh Super Resolution Imaging Consortium, Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Ann P Wheeler
- Advanced Imaging Resource, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - J Douglas Armstrong
- Simons Initiative for the Developing Brain, School of Informatics, University of Edinburgh, Edinburgh, EH8 9LE, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
| | - Irene M Leigh
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
- Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Charlotte M Proby
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Alex von Kriegsheim
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Margaret C Frame
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Adam Byron
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK.
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, UK.
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14
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Sung H, Vaziri A, Wilinski D, Woerner RKR, Freddolino PL, Dus M. Nutrigenomic regulation of sensory plasticity. eLife 2023; 12:e83979. [PMID: 36951889 PMCID: PMC10036121 DOI: 10.7554/elife.83979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/10/2023] [Indexed: 03/24/2023] Open
Abstract
Diet profoundly influences brain physiology, but how metabolic information is transmuted into neural activity and behavior changes remains elusive. Here, we show that the metabolic enzyme O-GlcNAc Transferase (OGT) moonlights on the chromatin of the D. melanogaster gustatory neurons to instruct changes in chromatin accessibility and transcription that underlie sensory adaptations to a high-sugar diet. OGT works synergistically with the Mitogen Activated Kinase/Extracellular signal Regulated Kinase (MAPK/ERK) rolled and its effector stripe (also known as EGR2 or Krox20) to integrate activity information. OGT also cooperates with the epigenetic silencer Polycomb Repressive Complex 2.1 (PRC2.1) to decrease chromatin accessibility and repress transcription in the high-sugar diet. This integration of nutritional and activity information changes the taste neurons' responses to sugar and the flies' ability to sense sweetness. Our findings reveal how nutrigenomic signaling generates neural activity and behavior in response to dietary changes in the sensory neurons.
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Affiliation(s)
- Hayeon Sung
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
| | - Anoumid Vaziri
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of MichiganAnn ArborUnited States
| | - Daniel Wilinski
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
| | - Riley KR Woerner
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
| | - Peter L Freddolino
- Department of Biological Chemistry, The University of Michigan Medical SchoolAnn ArborUnited States
- Department of Computational Medicine and Bioinformatics, The University of Michigan Medical SchoolAnn ArborUnited States
| | - Monica Dus
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of MichiganAnn ArborUnited States
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of MichiganAnn ArborUnited States
- The Michigan Neuroscience InstituteAnn ArborUnited States
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15
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Amiad Pavlov D, Unnikannan CP, Lorber D, Bajpai G, Olender T, Stoops E, Reuveny A, Safran S, Volk T. The LINC Complex Inhibits Excessive Chromatin Repression. Cells 2023; 12:cells12060932. [PMID: 36980273 PMCID: PMC10047284 DOI: 10.3390/cells12060932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex transduces nuclear mechanical inputs suggested to control chromatin organization and gene expression; however, the underlying mechanism is currently unclear. We show here that the LINC complex is needed to minimize chromatin repression in muscle tissue, where the nuclei are exposed to significant mechanical inputs during muscle contraction. To this end, the genomic binding profiles of Polycomb, Heterochromatin Protein1 (HP1a) repressors, and of RNA-Pol II were studied in Drosophila larval muscles lacking functional LINC complex. A significant increase in the binding of Polycomb and parallel reduction of RNA-Pol-II binding to a set of muscle genes was observed. Consistently, enhanced tri-methylated H3K9 and H3K27 repressive modifications and reduced chromatin activation by H3K9 acetylation were found. Furthermore, larger tri-methylated H3K27me3 repressive clusters, and chromatin redistribution from the nuclear periphery towards nuclear center, were detected in live LINC mutant larval muscles. Computer simulation indicated that the observed dissociation of the chromatin from the nuclear envelope promotes growth of tri-methylated H3K27 repressive clusters. Thus, we suggest that by promoting chromatin-nuclear envelope binding, the LINC complex restricts the size of repressive H3K27 tri-methylated clusters, thereby limiting the binding of Polycomb transcription repressor, directing robust transcription in muscle fibers.
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Affiliation(s)
- Daria Amiad Pavlov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elizabeth Stoops
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adriana Reuveny
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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16
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Zaytseva O, Mitchell NC, Muckle D, Delandre C, Nie Z, Werner JK, Lis JT, Eyras E, Hannan RD, Levens DL, Marshall OJ, Quinn LM. Psi promotes Drosophila wing growth via direct transcriptional activation of cell cycle targets and repression of growth inhibitors. Development 2023; 150:286725. [PMID: 36692218 PMCID: PMC10110491 DOI: 10.1242/dev.201563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/25/2023]
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.
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Affiliation(s)
- Olga Zaytseva
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Naomi C Mitchell
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Damien Muckle
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Zuqin Nie
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - John T Lis
- Cornell University, Ithaca, NY 14850, USA
| | - Eduardo Eyras
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Ross D Hannan
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | | | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Leonie M Quinn
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
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17
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Lim K, Donovan APA, Tang W, Sun D, He P, Pett JP, Teichmann SA, Marioni JC, Meyer KB, Brand AH, Rawlins EL. Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease. Cell Stem Cell 2023; 30:20-37.e9. [PMID: 36493780 DOI: 10.1016/j.stem.2022.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 10/02/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022]
Abstract
Variation in lung alveolar development is strongly linked to disease susceptibility. However, underlying cellular and molecular mechanisms are difficult to study in humans. We have identified an alveolar-fated epithelial progenitor in human fetal lungs, which we grow as self-organizing organoids that model key aspects of cell lineage commitment. Using this system, we have functionally validated cell-cell interactions in the developing human alveolar niche, showing that Wnt signaling from differentiating fibroblasts promotes alveolar-type-2 cell identity, whereas myofibroblasts secrete the Wnt inhibitor, NOTUM, providing spatial patterning. We identify a Wnt-NKX2.1 axis controlling alveolar differentiation. Moreover, we show that differential binding of NKX2.1 coordinates alveolar maturation, allowing us to model the effects of human genetic variation in NKX2.1 on alveolar differentiation. Our organoid system recapitulates key aspects of human fetal lung stem cell biology allowing mechanistic experiments to determine the cellular and molecular regulation of human development and disease.
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Affiliation(s)
- Kyungtae Lim
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Alex P A Donovan
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Walfred Tang
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Dawei Sun
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Peng He
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - John C Marioni
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | | | - Andrea H Brand
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Emma L Rawlins
- Wellcome Trust, CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK; Wellcome Trust, MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK.
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18
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Sun D, Llora Batlle O, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA, Marioni JC, Jackson SP, Brand AH, Rawlins EL. SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. EMBO J 2022; 41:e111338. [PMID: 36121125 PMCID: PMC9627674 DOI: 10.15252/embj.2022111338] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022] Open
Abstract
The balance between self-renewal and differentiation in human foetal lung epithelial progenitors controls the size and function of the adult organ. Moreover, progenitor cell gene regulation networks are employed by both regenerating and malignant lung cells, where modulators of their effects could potentially be of therapeutic value. Details of the molecular networks controlling human lung progenitor self-renewal remain unknown. We performed the first CRISPRi screen in primary human lung organoids to identify transcription factors controlling progenitor self-renewal. We show that SOX9 promotes proliferation of lung progenitors and inhibits precocious airway differentiation. Moreover, by identifying direct transcriptional targets using Targeted DamID, we place SOX9 at the centre of a transcriptional network, which amplifies WNT and RTK signalling to stabilise the progenitor cell state. In addition, the proof-of-principle CRISPRi screen and Targeted DamID tools establish a new workflow for using primary human organoids to elucidate detailed functional mechanisms underlying normal development and disease.
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Affiliation(s)
- Dawei Sun
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Oriol Llora Batlle
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Jelle van den Ameele
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Present address:
Department of Clinical Neurosciences and MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - John C Thomas
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Peng He
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Kyungtae Lim
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Walfred Tang
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Chufan Xu
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Present address:
Department of Anaesthesiology and Surgical Intensive Care Unit, Xinhua HospitalShanghai Jiaotong University School of MedicineShanghaiChina
| | | | - Sarah A Teichmann
- Wellcome Sanger InstituteCambridgeUK
- Department of Physics/Cavendish LaboratoryUniversity of CambridgeCambridgeUK
| | - John C Marioni
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Stephen P Jackson
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Andrea H Brand
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
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19
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Fragoso-Luna A, Romero-Bueno R, Eibl M, Ayuso C, Muñoz-Jiménez C, Benes V, Cases I, Askjaer P. Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in Caenorhabditis elegans. Genetics 2022; 223:6793861. [PMID: 36321973 PMCID: PMC9836023 DOI: 10.1093/genetics/iyac166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 11/05/2022] Open
Abstract
Control of gene expression in specific tissues and/or at certain stages of development allows the study and manipulation of gene function with high precision. Site-specific genome recombination by the flippase (FLP) and cyclization recombination (Cre) enzymes has proved particularly relevant. Joint efforts of many research groups have led to the creation of efficient FLP and Cre drivers to regulate gene expression in a variety of tissues in Caenorhabditis elegans. Here, we extend this toolkit by the addition of FLP lines that drive recombination specifically in distal tip cells, the somatic gonad, coelomocytes, and the epithelial P lineage. In some cases, recombination-mediated gene knockouts do not completely deplete protein levels due to persistence of long-lived proteins. To overcome this, we developed a spatiotemporally regulated degradation system for green fluorescent fusion proteins based on FLP-mediated recombination. Using 2 stable nuclear pore proteins, MEL-28/ELYS and NPP-2/NUP85 as examples, we report the benefit of combining tissue-specific gene knockout and protein degradation to achieve complete protein depletion. We also demonstrate that FLP-mediated recombination can be utilized to identify transcriptomes in a C. elegans tissue of interest. We have adapted RNA polymerase DamID for the FLP toolbox and by focusing on a well-characterized tissue, the hypodermis, we show that the vast majority of genes identified by RNA polymerase DamID are known to be expressed in this tissue. These tools allow combining FLP activity for simultaneous gene inactivation and transcriptomic profiling, thus enabling the inquiry of gene function in various complex biological processes.
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Affiliation(s)
| | | | | | - Cristina Ayuso
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Junta de Andalucía, 41013 Sevilla, Spain
| | - Celia Muñoz-Jiménez
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Junta de Andalucía, 41013 Sevilla, Spain
| | | | - Ildefonso Cases
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Pablo de Olavide, Junta de Andalucía, 41013 Sevilla, Spain
| | - Peter Askjaer
- Corresponding author: Andalusian Centre for Developmental Biology, Gene Regulation and Morphogenesis, CSIC—Universidad Pablo de Olavide, Carretera de Utrera, km 1, 41013 Seville, Spain.
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20
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Tang JLY, Krautz R, Llorà-Batlle O, Hakes AE, Fox PM, Brand AH. In vivo, genome-wide profiling of endogenously tagged chromatin-binding proteins with spatial and temporal resolution using NanoDam in Drosophila. STAR Protoc 2022; 3:101788. [PMID: 36345375 PMCID: PMC9636480 DOI: 10.1016/j.xpro.2022.101788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
NanoDam is a technique for genome-wide profiling of the binding targets of any endogenously tagged chromatin-binding protein in vivo, without the need for antibodies, crosslinking, or immunoprecipitation. Here, we explain the procedure for NanoDam experiments in Drosophila, starting from a genetic cross, to the generation of sequencing libraries and, finally, bioinformatic analysis. This protocol can be readily adapted for use in other model systems after simple modifications. For complete details on the use and execution of this protocol, please refer to Tang et al. (2022).
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Affiliation(s)
- Jocelyn L Y Tang
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Robert Krautz
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Oriol Llorà-Batlle
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Anna E Hakes
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Paul M Fox
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Andrea H Brand
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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21
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Fox PM, Tang JLY, Brand AH. The Drosophila homologue of CTIP1 (Bcl11a) and CTIP2 (Bcl11b) regulates neural stem cell temporal patterning. Development 2022; 149:dev200677. [PMID: 36069896 PMCID: PMC9482335 DOI: 10.1242/dev.200677] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/03/2022] [Indexed: 11/07/2023]
Abstract
In the developing nervous system, neural stem cells (NSCs) use temporal patterning to generate a wide variety of different neuronal subtypes. In Drosophila, the temporal transcription factors, Hunchback, Kruppel, Pdm and Castor, are sequentially expressed by NSCs to regulate temporal identity during neurogenesis. Here, we identify a new temporal transcription factor that regulates the transition from the Pdm to Castor temporal windows. This factor, which we call Chronophage (or 'time-eater'), is homologous to mammalian CTIP1 (Bcl11a) and CTIP2 (Bcl11b). We show that Chronophage binds upstream of the castor gene and regulates its expression. Consistent with Chronophage promoting a temporal switch, chronophage mutants generate an excess of Pdm-specified neurons and are delayed in generating neurons associated with the Castor temporal window. In addition to promoting the Pdm to Castor transition, Chronophage also represses the production of neurons generated during the earlier Hunchback and Kruppel temporal windows. Genetic interactions with Hunchback and Kruppel indicate that Chronophage regulates NSC competence to generate Hunchback- and Kruppel-specified neurons. Taken together, our results suggest that Chronophage has a conserved role in temporal patterning and neuronal subtype specification.
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Affiliation(s)
| | | | - Andrea H. Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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22
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Ray A, Li X. A Notch-dependent transcriptional mechanism controls expression of temporal patterning factors in Drosophila medulla. eLife 2022; 11:e75879. [PMID: 36040415 PMCID: PMC9427115 DOI: 10.7554/elife.75879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
Temporal patterning is an important mechanism for generating a great diversity of neuron subtypes from a seemingly homogenous progenitor pool in both vertebrates and invertebrates. Drosophila neuroblasts are temporally patterned by sequentially expressed Temporal Transcription Factors (TTFs). These TTFs are proposed to form a transcriptional cascade based on mutant phenotypes, although direct transcriptional regulation between TTFs has not been verified in most cases. Furthermore, it is not known how the temporal transitions are coupled with the generation of the appropriate number of neurons at each stage. We use neuroblasts of the Drosophila optic lobe medulla to address these questions and show that the expression of TTFs Sloppy-paired 1/2 (Slp1/2) is directly regulated at the transcriptional level by two other TTFs and the cell-cycle dependent Notch signaling through two cis-regulatory elements. We also show that supplying constitutively active Notch can rescue the delayed transition into the Slp stage in cell cycle arrested neuroblasts. Our findings reveal a novel Notch-pathway dependent mechanism through which the cell cycle progression regulates the timing of a temporal transition within a TTF transcriptional cascade.
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Affiliation(s)
- Alokananda Ray
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Xin Li
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
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23
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Tang JLY, Hakes AE, Krautz R, Suzuki T, Contreras EG, Fox PM, Brand AH. NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system. Dev Cell 2022; 57:1193-1207.e7. [PMID: 35483359 PMCID: PMC9616798 DOI: 10.1016/j.devcel.2022.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/08/2022] [Accepted: 04/05/2022] [Indexed: 11/24/2022]
Abstract
Temporal patterning of neural progenitors is an evolutionarily conserved strategy for generating neuronal diversity. Type II neural stem cells in the Drosophila central brain produce transit-amplifying intermediate neural progenitors (INPs) that exhibit temporal patterning. However, the known temporal factors cannot account for the neuronal diversity in the adult brain. To search for missing factors, we developed NanoDam, which enables rapid genome-wide profiling of endogenously tagged proteins in vivo with a single genetic cross. Mapping the targets of known temporal transcription factors with NanoDam revealed that Homeobrain and Scarecrow (ARX and NKX2.1 orthologs) are also temporal factors. We show that Homeobrain and Scarecrow define middle-aged and late INP temporal windows and play a role in cellular longevity. Strikingly, Homeobrain and Scarecrow have conserved functions as temporal factors in the developing visual system. NanoDam enables rapid cell-type-specific genome-wide profiling with temporal resolution and is easily adapted for use in higher organisms.
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Affiliation(s)
- Jocelyn L Y Tang
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Anna E Hakes
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Robert Krautz
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Takumi Suzuki
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Esteban G Contreras
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Paul M Fox
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Andrea H Brand
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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24
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Reduced chromatin accessibility correlates with resistance to Notch activation. Nat Commun 2022; 13:2210. [PMID: 35468895 PMCID: PMC9039071 DOI: 10.1038/s41467-022-29834-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/18/2022] [Indexed: 11/08/2022] Open
Abstract
The Notch signalling pathway is a master regulator of cell fate transitions in development and disease. In the brain, Notch promotes neural stem cell (NSC) proliferation, regulates neuronal migration and maturation and can act as an oncogene or tumour suppressor. How NOTCH and its transcription factor RBPJ activate distinct gene regulatory networks in closely related cell types in vivo remains to be determined. Here we use Targeted DamID (TaDa), requiring only thousands of cells, to identify NOTCH and RBPJ binding in NSCs and their progeny in the mouse embryonic cerebral cortex in vivo. We find that NOTCH and RBPJ associate with a broad network of NSC genes. Repression of NSC-specific Notch target genes in intermediate progenitors and neurons correlates with decreased chromatin accessibility, suggesting that chromatin compaction may contribute to restricting NOTCH-mediated transactivation.
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25
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Microbes affect gut epithelial cell composition through immune-dependent regulation of intestinal stem cell differentiation. Cell Rep 2022; 38:110572. [PMID: 35354023 PMCID: PMC9078081 DOI: 10.1016/j.celrep.2022.110572] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/14/2021] [Accepted: 03/03/2022] [Indexed: 12/29/2022] Open
Abstract
Gut microbes play important roles in host physiology; however, the mechanisms underlying their impact remain poorly characterized. Here, we demonstrate that microbes not only influence gut physiology but also alter its epithelial composition. The microbiota and pathogens both influence intestinal stem cell (ISC) differentiation. Intriguingly, while the microbiota promotes ISC differentiation into enterocytes (EC), pathogens stimulate enteroendocrine cell (EE) fate and long-term accumulation of EEs in the midgut epithelium. Importantly, the evolutionarily conserved Drosophila NFKB (Relish) pushes stem cell lineage specification toward ECs by directly regulating differentiation factors. Conversely, the JAK-STAT pathway promotes EE fate in response to infectious damage. We propose a model in which the balance of microbial pattern recognition pathways, such as Imd-Relish, and damage response pathways, such as JAK-STAT, influence ISC differentiation, epithelial composition, and gut physiology.
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26
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Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains. Nat Commun 2022; 13:1483. [PMID: 35304483 PMCID: PMC8933459 DOI: 10.1038/s41467-022-29146-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/28/2022] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic chromosomes are folded into hierarchical domains, forming functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks contributing to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for the identification of nucleolar associated domains (NADs). Here we have established DamID- and HiC-based methodologies to generate accurate genome-wide maps of NADs in embryonic stem cells (ESCs) and neural progenitor cells (NPCs), revealing layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs show higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation into NPCs, chromosomes around the nucleolus acquire a more compact, rigid architecture with neural genes moving away from nucleoli and becoming unlocked for later activation. Further, histone modifications and the interaction strength within A and B compartments of NADs and LADs in ESCs set the choice to associate with NL or nucleoli upon dissociation from their respective compartments during differentiation. The methodologies here developed will make possible to include the nucleolar contribution in nuclear space and genome function in diverse biological systems.
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27
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Katsanos D, Barkoulas M. Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate. SCIENCE ADVANCES 2022; 8:eabk3141. [PMID: 35119932 PMCID: PMC8816332 DOI: 10.1126/sciadv.abk3141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they display complex patterns of expression and binding to their targets, hence, tissue specificity is required in the characterization of transcription factor-target interactions. We introduce here targeted DamID (TaDa) as a method for tissue-specific transcription factor target identification in intact Caenorhabditis elegans animals. We use TaDa to recover targets in the epidermis for two factors, the HES1 homolog LIN-22, and the NR5A1/2 nuclear hormone receptor NHR-25. We demonstrate a direct link between LIN-22 and the Wnt signaling pathway through repression of the Frizzled receptor lin-17. We report a direct role for NHR-25 in promoting cell differentiation via repressing the expression of stem cell-promoting GATA factors. Our results expand our understanding of the epidermal gene network and highlight the potential of TaDa to dissect the architecture of tissue-specific gene regulatory networks.
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28
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Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier KI, De Rop FV, González-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, De Waegeneer M, Christiaens V, Southall T, Aerts S. Decoding gene regulation in the fly brain. Nature 2022; 601:630-636. [PMID: 34987221 DOI: 10.1038/s41586-021-04262-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1-6, three-dimensional morphological classification7 and electron microscopy mapping of the connectome8,9 have revealed an immense diversity of neuronal and glial cell types that underlie an array of functional and behavioural traits in the fly. The identities of these cell types are controlled by gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. Here, to characterize GRNs at the cell-type level in the fly brain, we profiled the chromatin accessibility of 240,919 single cells spanning 9 developmental timepoints and integrated these data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which 70,000 are linked to developmental trajectories involving neurogenesis, reprogramming and maturation. For 40 cell types, uniquely accessible regions were associated with their expressed transcription factors and downstream target genes through a combination of motif discovery, network inference and deep learning, creating enhancer GRNs. The enhancer architectures revealed by DeepFlyBrain lead to a better understanding of neuronal regulatory diversity and can be used to design genetic driver lines for cell types at specific timepoints, facilitating their characterization and manipulation.
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Affiliation(s)
- Jasper Janssens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joy N Ismail
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London, UK
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Florian V De Rop
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marc Dionne
- Department of Life Sciences, Imperial College London, London, UK
| | - Krista Grimes
- Department of Life Sciences, Imperial College London, London, UK
| | - Xiao Jiang Quan
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Dafni Papasokrati
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tony Southall
- Department of Life Sciences, Imperial College London, London, UK
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Human Genetics, KU Leuven, Leuven, Belgium.
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29
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Marshall OJ, Delandre C. Profiling Protein-DNA Interactions Cell-Type-Specifically with Targeted DamID. Methods Mol Biol 2022; 2458:195-213. [PMID: 35103969 DOI: 10.1007/978-1-0716-2140-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Targeted DamID (TaDa) is a means of profiling the binding of any DNA-associated protein cell-type specifically, including transcription factors, RNA polymerase, and chromatin-modifying proteins. The technique is highly sensitive, highly reproducible, requires no mechanical disruption, cell isolation or antibody purification, and can be performed by anyone with basic molecular biology knowledge. Here, we describe the TaDa method and downstream bioinformatics data processing.
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Affiliation(s)
- Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
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30
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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31
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de la Cruz Ruiz P, Romero-Bueno R, Askjaer P. Analysis of Nuclear Pore Complexes in Caenorhabditis elegans by Live Imaging and Functional Genomics. Methods Mol Biol 2022; 2502:161-182. [PMID: 35412238 DOI: 10.1007/978-1-0716-2337-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nuclear pore complexes (NPCs) are essential to communication of macromolecules between the cell nucleus and the surrounding cytoplasm. RNA synthesized in the nucleus is exported through NPCs to function in the cytoplasm, whereas transcription factors and other proteins are selectively and actively imported. In addition, many NPC constituents, known as nuclear pore proteins (nucleoporins or nups), also play critical roles in other processes, such as genome organization, gene expression, and kinetochore function. Thanks to its genetic amenability and transparent body, the nematode Caenorhabditis elegans is an attractive model to study NPC dynamics. We provide here an overview of available genome engineered strains and FLP/Frt-based tools to study tissue-specific functions of individual nucleoporins. We also present protocols for live imaging of fluorescently tagged nucleoporins in intact tissues of embryos, larvae, and adult and for analysis of interactions between nucleoporins and chromatin by DamID.
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Affiliation(s)
- Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Raquel Romero-Bueno
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain.
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32
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Wade AA, van den Ameele J, Cheetham SW, Yakob R, Brand AH, Nord AS. In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain. iScience 2021; 24:103234. [PMID: 34746699 PMCID: PMC8551073 DOI: 10.1016/j.isci.2021.103234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/11/2021] [Accepted: 10/04/2021] [Indexed: 01/15/2023] Open
Abstract
Genetic studies of autism have revealed causal roles for chromatin remodeling gene mutations. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with significant de novo mutation rates in sporadic autism. However, relationships between CHD8 genomic function and autism-relevant biology remain poorly elucidated. Published studies utilizing ChIP-seq to map CHD8 protein-DNA interactions have high variability, consistent with technical challenges and limitations associated with this method. Thus, complementary approaches are needed to establish CHD8 genomic targets and regulatory functions in developing brain. We used in utero CHD8 Targeted DamID followed by sequencing (TaDa-seq) to characterize CHD8 binding in embryonic mouse cortex. CHD8 TaDa-seq reproduced interaction patterns observed from ChIP-seq and further highlighted CHD8 distal interactions associated with neuronal loci. This study establishes TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provides insights into the regulatory targets of CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.
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Affiliation(s)
- A. Ayanna Wade
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Jelle van den Ameele
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Seth W. Cheetham
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Rebecca Yakob
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Andrea H. Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Alex S. Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
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33
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Lucas T, Hafer TL, Zhang HG, Molotkova N, Kohwi M. Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo. Dev Cell 2021; 56:2649-2663.e6. [PMID: 34529940 PMCID: PMC8629127 DOI: 10.1016/j.devcel.2021.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/24/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023]
Abstract
The nuclear lamina is typically associated with transcriptional silencing, and peripheral relocation of genes highly correlates with repression. However, the DNA sequences and proteins regulating gene-lamina interactions are largely unknown. Exploiting the developmentally timed hunchback gene movement to the lamina in Drosophila neuroblasts, we identified a 250 bp intronic element (IE) both necessary and sufficient for relocation. The IE can target a reporter transgene to the lamina and silence it. Endogenously, however, hunchback is already repressed prior to relocation. Instead, IE-mediated relocation confers a heritably silenced gene state refractory to activation in descendent neurons, which terminates neuroblast competence to specify early-born identity. Surprisingly, we found that the Polycomb group chromatin factors bind the IE and are required for lamina relocation, revealing a nuclear architectural role distinct from their well-known function in transcriptional repression. Together, our results uncover in vivo mechanisms underlying neuroblast competence and lamina association in heritable gene silencing. In Drosophila neuroblasts, relocation of the hunchback gene locus to the nuclear lamina confers heritable silencing in daughter neurons. Lucas et al. identify a genomic element necessary and sufficient for hunchback gene movement in vivo. Polycomb proteins target this element for lamina relocation, thereby regulating competence, but not hunchback expression.
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Affiliation(s)
- Tanguy Lucas
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Terry L Hafer
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Harrison G Zhang
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Natalia Molotkova
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Minoree Kohwi
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA.
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34
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Gómez-Saldivar G, Glauser DA, Meister P. Tissue-specific DamID protocol using nanopore sequencing. J Biol Methods 2021; 8:e152. [PMID: 34514013 PMCID: PMC8411031 DOI: 10.14440/jbm.2021.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
DNA adenine methylation identification (DamID) is a powerful method to determine DNA binding profiles of proteins at a genomic scale. The method leverages the fusion between a protein of interest and the Dam methyltransferase of E. coli, which methylates proximal DNA in vivo. Here, we present an optimized procedure, which was developed for tissue-specific analyses in Caenorhabditis elegans and successfully used to footprint genes actively transcribed by RNA polymerases and to map transcription factor binding in gene regulatory regions. The present protocol details C. elegans-specific steps involved in the preparation of transgenic lines and genomic DNA samples, as well as broadly applicable steps for the DamID procedure, including the isolation of methylated DNA fragments, the preparation of multiplexed libraries, Nanopore sequencing, and data analysis. Two distinctive features of the approach are (i) the use of an efficient recombination-based strategy to selectively analyze rare cell types and (ii) the use of Nanopore sequencing, which streamlines the process. The method allows researchers to go from genomic DNA samples to sequencing results in less than a week, while being sensitive enough to report reliable DNA footprints in cell types as rare as 2 cells per animal.
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Affiliation(s)
| | | | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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35
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Katsanos D, Ferrando-Marco M, Razzaq I, Aughey G, Southall TD, Barkoulas M. Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID. Development 2021; 148:dev199452. [PMID: 34397094 PMCID: PMC7613258 DOI: 10.1242/dev.199452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/05/2021] [Indexed: 12/19/2022]
Abstract
The epidermis of Caenorhabditis elegans is an essential tissue for survival because it contributes to the formation of the cuticle barrier as well as facilitating developmental progression and animal growth. Most of the epidermis consists of the hyp7 hypodermal syncytium, the nuclei of which are largely generated by the seam cells, which exhibit stem cell-like behaviour during development. How seam cell progenitors differ transcriptionally from the differentiated hypodermis is poorly understood. Here, we introduce Targeted DamID (TaDa) in C. elegans as a method for identifying genes expressed within a tissue of interest without cell isolation. We show that TaDa signal enrichment profiles can be used to identify genes transcribed in the epidermis and use this method to resolve differences in gene expression between the seam cells and the hypodermis. Finally, we predict and functionally validate new transcription and chromatin factors acting in seam cell development. These findings provide insights into cell type-specific gene expression profiles likely associated with epidermal cell fate patterning.
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Affiliation(s)
- Dimitris Katsanos
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mar Ferrando-Marco
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Iqrah Razzaq
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Tony D. Southall
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Michalis Barkoulas
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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36
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Iwasaki YW, Sriswasdi S, Kinugasa Y, Adachi J, Horikoshi Y, Shibuya A, Iwasaki W, Tashiro S, Tomonaga T, Siomi H. Piwi-piRNA complexes induce stepwise changes in nuclear architecture at target loci. EMBO J 2021; 40:e108345. [PMID: 34337769 PMCID: PMC8441340 DOI: 10.15252/embj.2021108345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/04/2021] [Accepted: 07/09/2021] [Indexed: 12/25/2022] Open
Abstract
PIWI‐interacting RNAs (piRNAs) are germline‐specific small RNAs that form effector complexes with PIWI proteins (Piwi–piRNA complexes) and play critical roles for preserving genomic integrity by repressing transposable elements (TEs). Drosophila Piwi transcriptionally silences specific targets through heterochromatin formation and increases histone H3K9 methylation (H3K9me3) and histone H1 deposition at these loci, with nuclear RNA export factor variant Nxf2 serving as a co‐factor. Using ChEP and DamID‐seq, we now uncover a Piwi/Nxf2‐dependent target association with nuclear lamins. Hi‐C analysis of Piwi or Nxf2‐depleted cells reveals decreased intra‐TAD and increased inter‐TAD interactions in regions harboring Piwi–piRNA target TEs. Using a forced tethering system, we analyze the functional effects of Piwi–piRNA/Nxf2‐mediated recruitment of piRNA target regions to the nuclear periphery. Removal of active histone marks is followed by transcriptional silencing, chromatin conformational changes, and H3K9me3 and H1 association. Our data show that the Piwi–piRNA pathway can induce stepwise changes in nuclear architecture and chromatin state at target loci for transcriptional silencing.
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Affiliation(s)
- Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan.,Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan
| | - Sira Sriswasdi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yasuha Kinugasa
- Department of Cellular Biology, Research Institute for Radiation Biology Medicine, Hiroshima University, Hiroshima, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology Medicine, Hiroshima University, Hiroshima, Japan
| | - Aoi Shibuya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology Medicine, Hiroshima University, Hiroshima, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
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37
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The Serine Protease Homolog, Scarface, Is Sensitive to Nutrient Availability and Modulates the Development of the Drosophila Blood-Brain Barrier. J Neurosci 2021; 41:6430-6448. [PMID: 34210781 PMCID: PMC8318086 DOI: 10.1523/jneurosci.0452-20.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 02/08/2021] [Accepted: 03/14/2021] [Indexed: 01/21/2023] Open
Abstract
The adaptable transcriptional response to changes in food availability not only ensures animal survival but also lets embryonic development progress. Interestingly, the CNS is preferentially protected from periods of malnutrition, a phenomenon known as “brain sparing.” However, the mechanisms that mediate this response remain poorly understood. To get a better understanding of this, we used Drosophila melanogaster as a model, analyzing the transcriptional response of neural stem cells (neuroblasts) and glia of the blood–brain barrier (BBB) from larvae of both sexes during nutrient restriction using targeted DamID. We found differentially expressed genes in both neuroblasts and glia of the BBB, although the effect of nutrient deficiency was primarily observed in the BBB. We characterized the function of a nutritional sensitive gene expressed in the BBB, the serine protease homolog, scarface (scaf). Scaf is expressed in subperineurial glia in the BBB in response to nutrition. Tissue-specific knockdown of scaf increases subperineurial glia endoreplication and proliferation of perineurial glia in the blood–brain barrier. Furthermore, neuroblast proliferation is diminished on scaf knockdown in subperineurial glia. Interestingly, reexpression of Scaf in subperineurial glia is able to enhance neuroblast proliferation and brain growth of animals in starvation. Finally, we show that loss of scaf in the blood–brain barrier increases sensitivity to drugs in adulthood, suggesting a physiological impairment. We propose that Scaf integrates the nutrient status to modulate the balance between neurogenesis and growth of the BBB, preserving the proper equilibrium between the size of the barrier and the brain. SIGNIFICANCE STATEMENT The Drosophila BBB separates the CNS from the open circulatory system. The BBB glia are not only acting as a physical segregation of tissues but participate in the regulation of the metabolism and neurogenesis during development. Here we analyze the transcriptional response of the BBB glia to nutrient deprivation during larval development, a condition in which protective mechanisms are switched on in the brain. Our findings show that the gene scarface reduces growth in the BBB while promoting the proliferation of neural stem, assuring the balanced growth of the larval brain. Thus, Scarface would link animal nutrition with brain development, coordinating neurogenesis with the growth of the BBB.
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Dynamic adult tracheal plasticity drives stem cell adaptation to changes in intestinal homeostasis in Drosophila. Nat Cell Biol 2021; 23:485-496. [PMID: 33972729 PMCID: PMC7610788 DOI: 10.1038/s41556-021-00676-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022]
Abstract
Coordination of stem cell function by local and niche-derived signals is essential to preserve adult tissue homeostasis and organismal health. The vasculature is a prominent component of multiple stem cell niches. However, its role in adult intestinal homeostasis remains largely understudied. Here, we uncover a previously unrecognised crosstalk between adult intestinal stem cells (ISCs) in Drosophila and the vasculature-like tracheal system, which is essential for intestinal regeneration. Following damage to the intestinal epithelium, gut-derived reactive oxygen species (ROS) activate tracheal HIF-1α and bidirectional FGF/FGFR signalling, leading to reversible remodelling of gut-associated terminal tracheal cells and ISC proliferation following damage. Unexpectedly, ROS-induced adult tracheal plasticity involves downregulation of the tracheal specification factor trachealess (trh) and upregulation of IGF2 mRNA-binding protein (IGF2BP2/Imp). Our results reveal an intestine/vasculature inter-organ communication programme, which is essential to adapt stem cells response to the proliferative demands of the intestinal epithelium.
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39
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Hatch HAM, Belalcazar HM, Marshall OJ, Secombe J. A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. eLife 2021; 10:63886. [PMID: 33729157 PMCID: PMC7997662 DOI: 10.7554/elife.63886] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding their spatiotemporal requirements or neurodevelopmental contributions. Utilizing the mushroom body (MB), a major learning and memory center within the Drosophila brain, we demonstrate that KDM5 is required within ganglion mother cells and immature neurons for proper axogenesis. Moreover, the mechanism by which KDM5 functions in this context is independent of its canonical histone demethylase activity. Using in vivo transcriptional and binding analyses, we identify a network of genes directly regulated by KDM5 that are critical modulators of neurodevelopment. We find that KDM5 directly regulates the expression of prospero, a transcription factor that we demonstrate is essential for MB morphogenesis. Prospero functions downstream of KDM5 and binds to approximately half of KDM5-regulated genes. Together, our data provide evidence for a KDM5-Prospero transcriptional axis that is essential for proper MB development.
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Affiliation(s)
- Hayden AM Hatch
- Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine, Bronx, United States
| | - Helen M Belalcazar
- Department of Genetics Albert Einstein College of Medicine, Bronx, United States
| | - Owen J Marshall
- Menzies Institute for Medical Research University of Tasmania, Hobart, Australia
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine, Bronx, United States.,Department of Genetics Albert Einstein College of Medicine, Bronx, United States
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40
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Arguello JR, Abuin L, Armida J, Mika K, Chai PC, Benton R. Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. eLife 2021; 10:63036. [PMID: 33666172 PMCID: PMC7993999 DOI: 10.7554/elife.63036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Determining the molecular properties of neurons is essential to understand their development, function and evolution. Using Targeted DamID (TaDa), we characterize RNA polymerase II occupancy and chromatin accessibility in selected Ionotropic receptor (Ir)-expressing olfactory sensory neurons in Drosophila. Although individual populations represent a minute fraction of cells, TaDa is sufficiently sensitive and specific to identify the expected receptor genes. Unique Ir expression is not consistently associated with differences in chromatin accessibility, but rather to distinct transcription factor profiles. Genes that are heterogeneously expressed across populations are enriched for neurodevelopmental factors, and we identify functions for the POU-domain protein Pdm3 as a genetic switch of Ir neuron fate, and the atypical cadherin Flamingo in segregation of neurons into discrete glomeruli. Together this study reveals the effectiveness of TaDa in profiling rare neural populations, identifies new roles for a transcription factor and a neuronal guidance molecule, and provides valuable datasets for future exploration.
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Affiliation(s)
- J Roman Arguello
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland.,Department of Ecology and Evolution Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Liliane Abuin
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Jan Armida
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Kaan Mika
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Phing Chian Chai
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
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41
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Díaz-Torres A, Rosales-Nieves AE, Pearson JR, Santa-Cruz Mateos C, Marín-Menguiano M, Marshall OJ, Brand AH, González-Reyes A. Stem cell niche organization in the Drosophila ovary requires the ECM component Perlecan. Curr Biol 2021; 31:1744-1753.e5. [PMID: 33621481 PMCID: PMC8405445 DOI: 10.1016/j.cub.2021.01.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/10/2020] [Accepted: 01/20/2021] [Indexed: 12/26/2022]
Abstract
Stem cells reside in specialized microenvironments or niches that balance stem cell proliferation and differentiation.1,2 The extracellular matrix (ECM) is an essential component of most niches, because it controls niche homeostasis, provides physical support, and conveys extracellular signals.3, 4, 5, 6, 7, 8, 9, 10, 11 Basement membranes (BMs) are thin ECM sheets that are constituted mainly by Laminins, Perlecan, Collagen IV, and Entactin/Nidogen and surround epithelia and other tissues.12 Perlecans are secreted proteoglycans that interact with ECM proteins, ligands, receptors, and growth factors such as FGF, PDGF, VEGF, Hedgehog, and Wingless.13, 14, 15, 16, 17, 18 Thus, Perlecans have structural and signaling functions through the binding, storage, or sequestering of specific ligands. We have used the Drosophila ovary to assess the importance of Perlecan in the functioning of a stem cell niche. Ovarioles in the adult ovary are enveloped by an ECM sheath and possess a tapered structure at their anterior apex termed the germarium. The anterior tip of the germarium hosts the germline niche, where two to four germline stem cells (GSCs) reside together with a few somatic cells: terminal filament cells (TFCs), cap cells (CpCs), and escort cells (ECs).19 We report that niche architecture in the developing gonad requires trol, that niche cells secrete an isoform-specific Perlecan-rich interstitial matrix, and that DE-cadherin-dependent stem cell-niche adhesion necessitates trol. Hence, we provide evidence to support a structural role for Perlecan in germline niche establishment during larval stages and in the maintenance of a normal pool of stem cells in the adult niche. The Drosophila ovarian niche contains a Perlecan-rich interstitial matrix Niche cells express and secrete specific Perlecan isoforms Absence of trol results in aberrant niches containing fewer niche and stem cells trol regulates DE-cadherin levels in larval and adult niche cells
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Affiliation(s)
- Alfonsa Díaz-Torres
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide/JA, Carretera de Utrera km 1, 41013 Sevilla, Spain
| | - Alicia E Rosales-Nieves
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide/JA, Carretera de Utrera km 1, 41013 Sevilla, Spain
| | - John R Pearson
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide/JA, Carretera de Utrera km 1, 41013 Sevilla, Spain
| | - Carmen Santa-Cruz Mateos
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide/JA, Carretera de Utrera km 1, 41013 Sevilla, Spain
| | - Miriam Marín-Menguiano
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide/JA, Carretera de Utrera km 1, 41013 Sevilla, Spain
| | - Owen J Marshall
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 1QN, UK; Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS 7000, Australia
| | - Andrea H Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 1QN, UK
| | - Acaimo González-Reyes
- Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide/JA, Carretera de Utrera km 1, 41013 Sevilla, Spain.
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Aughey GN, Delandre C, McMullen JPD, Southall TD, Marshall OJ. FlyORF-TaDa allows rapid generation of new lines for in vivo cell-type-specific profiling of protein-DNA interactions in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2021; 11:6044134. [PMID: 33561239 PMCID: PMC8022459 DOI: 10.1093/g3journal/jkaa005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/07/2020] [Indexed: 12/01/2022]
Abstract
Targeted DamID (TaDa) is an increasingly popular method of generating cell-type-specific DNA-binding profiles in vivo. Although sensitive and versatile, TaDa requires the generation of new transgenic fly lines for every protein that is profiled, which is both time-consuming and costly. Here, we describe the FlyORF-TaDa system for converting an existing FlyORF library of inducible open reading frames (ORFs) to TaDa lines via a genetic cross, with recombinant progeny easily identifiable by eye color. Profiling the binding of the H3K36me3-associated chromatin protein MRG15 in larval neural stem cells using both FlyORF-TaDa and conventional TaDa demonstrates that new lines generated using this system provide accurate and highly reproducible DamID-binding profiles. Our data further show that MRG15 binds to a subset of active chromatin domains in vivo. Courtesy of the large coverage of the FlyORF library, the FlyORF-TaDa system enables the easy creation of TaDa lines for 74% of all transcription factors and chromatin-modifying proteins within the Drosophila genome.
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Affiliation(s)
- Gabriel N Aughey
- Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
| | - Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
| | - John P D McMullen
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
| | - Tony D Southall
- Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
| | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
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Maintenance of Cell Fate by the Polycomb Group Gene Sex Combs Extra Enables a Partial Epithelial Mesenchymal Transition in Drosophila. G3-GENES GENOMES GENETICS 2020; 10:4459-4471. [PMID: 33051260 PMCID: PMC7718746 DOI: 10.1534/g3.120.401785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Epigenetic silencing by Polycomb group (PcG) complexes can promote epithelial-mesenchymal transition (EMT) and stemness and is associated with malignancy of solid cancers. Here we report a role for Drosophila PcG repression in a partial EMT event that occurs during wing disc eversion, an early event during metamorphosis. In a screen for genes required for eversion we identified the PcG genes Sex combs extra (Sce) and Sex combs midleg (Scm). Depletion of Sce or Scm resulted in internalized wings and thoracic clefts, and loss of Sce inhibited the EMT of the peripodial epithelium and basement membrane breakdown, ex vivo. Targeted DamID (TaDa) using Dam-Pol II showed that Sce knockdown caused a genomic transcriptional response consistent with a shift toward a more stable epithelial fate. Surprisingly only 17 genes were significantly upregulated in Sce-depleted cells, including Abd-B, abd-A, caudal, and nubbin. Each of these loci were enriched for Dam-Pc binding. Of the four genes, only Abd-B was robustly upregulated in cells lacking Sce expression. RNAi knockdown of all four genes could partly suppress the Sce RNAi eversion phenotype, though Abd-B had the strongest effect. Our results suggest that in the absence of continued PcG repression peripodial cells express genes such as Abd-B, which promote epithelial state and thereby disrupt eversion. Our results emphasize the important role that PcG suppression can play in maintaining cell states required for morphogenetic events throughout development and suggest that PcG repression of Hox genes may affect epithelial traits that could contribute to metastasis.
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Vaziri A, Khabiri M, Genaw BT, May CE, Freddolino PL, Dus M. Persistent epigenetic reprogramming of sweet taste by diet. SCIENCE ADVANCES 2020; 6:6/46/eabc8492. [PMID: 33177090 PMCID: PMC7673743 DOI: 10.1126/sciadv.abc8492] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/23/2020] [Indexed: 05/25/2023]
Abstract
Diets rich in sugar, salt, and fat alter taste perception and food preference, contributing to obesity and metabolic disorders, but the molecular mechanisms through which this occurs are unknown. Here, we show that in response to a high sugar diet, the epigenetic regulator Polycomb Repressive Complex 2.1 (PRC2.1) persistently reprograms the sensory neurons of Drosophila melanogaster flies to reduce sweet sensation and promote obesity. In animals fed high sugar, the binding of PRC2.1 to the chromatin of the sweet gustatory neurons is redistributed to repress a developmental transcriptional network that modulates the responsiveness of these cells to sweet stimuli, reducing sweet sensation. Half of these transcriptional changes persist despite returning the animals to a control diet, causing a permanent decrease in sweet taste. Our results uncover a new epigenetic mechanism that, in response to the dietary environment, regulates neural plasticity and feeding behavior to promote obesity.
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Affiliation(s)
- Anoumid Vaziri
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI 49109, USA
| | - Morteza Khabiri
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Brendan T Genaw
- Program in Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christina E May
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI 49109, USA
- The Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Monica Dus
- The Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA.
- Department of Molecular, Cellular and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI 49109, USA
- Program in Biology, College of Literature, Science, and the Arts, The University of Michigan, Ann Arbor, MI, 48109, USA
- The Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI 49109, USA
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Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 2020; 216:931-945. [PMID: 33037050 PMCID: PMC7768263 DOI: 10.1534/genetics.120.303774] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/09/2020] [Indexed: 11/23/2022] Open
Abstract
Differential gene expression across cell types underlies development and cell physiology in multicellular organisms. Caenorhabditis elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNA Polymerase DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, in sorted embryonic blastomeres and in different tissues from intact young adults by driving tissue-specific Dam fusion expression. We obtained meaningful transcriptional footprints in line with RNA-sequencing (RNA-seq) studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 3901 candidate genes with putatively active transcription in XXX cells, including the few previously known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX cells and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of RNA polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.
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46
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Estacio-Gómez A, Hassan A, Walmsley E, Le LW, Southall TD. Dynamic neurotransmitter specific transcription factor expression profiles during Drosophila development. Biol Open 2020; 9:9/5/bio052928. [PMID: 32493733 PMCID: PMC7286294 DOI: 10.1242/bio.052928] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The remarkable diversity of neurons in the nervous system is generated during development, when properties such as cell morphology, receptor profiles and neurotransmitter identities are specified. In order to gain a greater understanding of neurotransmitter specification we profiled the transcription state of cholinergic, GABAergic and glutamatergic neurons in vivo at three developmental time points. We identified 86 differentially expressed transcription factors that are uniquely enriched, or uniquely depleted, in a specific neurotransmitter type. Some transcription factors show a similar profile across development, others only show enrichment or depletion at specific developmental stages. Profiling of Acj6 (cholinergic enriched) and Ets65A (cholinergic depleted) binding sites in vivo reveals that they both directly bind the ChAT locus, in addition to a wide spectrum of other key neuronal differentiation genes. We also show that cholinergic enriched transcription factors are expressed in mostly non-overlapping populations in the adult brain, implying the absence of combinatorial regulation of neurotransmitter fate in this context. Furthermore, our data underlines that, similar to Caenorhabditis elegans, there are no simple transcription factor codes for neurotransmitter type specification. This article has an associated First Person interview with the first author of the paper. Summary: Transcriptome profiling of cholinergic, GABAergic and glutamatergic neurons in Drosophila identified multiple transcription factors as potential regulators of neurotransmitter fate.
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Affiliation(s)
- Alicia Estacio-Gómez
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Amira Hassan
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Emma Walmsley
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Lily Wong Le
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Tony D Southall
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
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Hassan A, Araguas Rodriguez P, Heidmann SK, Walmsley EL, Aughey GN, Southall TD. Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neurons. eLife 2020; 9:e55159. [PMID: 32255428 PMCID: PMC7170655 DOI: 10.7554/elife.55159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
Condensin complexes are essential for mitotic chromosome assembly and segregation during cell divisions, however, little is known about their functions in post-mitotic cells. Here we report a role for the condensin I subunit Cap-G in Drosophila neurons. We show that, despite not requiring condensin for mitotic chromosome compaction, post-mitotic neurons express Cap-G. Knockdown of Cap-G specifically in neurons (from their birth onwards) results in developmental arrest, behavioural defects, and dramatic gene expression changes, including reduced expression of a subset of neuronal genes and aberrant expression of genes that are not normally expressed in the developing brain. Knockdown of Cap-G in mature neurons results in similar phenotypes but to a lesser degree. Furthermore, we see dynamic binding of Cap-G at distinct loci in progenitor cells and differentiated neurons. Therefore, Cap-G is essential for proper gene expression in neurons and plays an important role during the early stages of neuronal development.
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Affiliation(s)
- Amira Hassan
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | | | | | - Emma L Walmsley
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Gabriel N Aughey
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Tony D Southall
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
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Hakes AE, Brand AH. Tailless/TLX reverts intermediate neural progenitors to stem cells driving tumourigenesis via repression of asense/ASCL1. eLife 2020; 9:e53377. [PMID: 32073402 PMCID: PMC7058384 DOI: 10.7554/elife.53377] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/19/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the sequence of events leading to cancer relies in large part upon identifying the tumour cell of origin. Glioblastoma is the most malignant brain cancer but the early stages of disease progression remain elusive. Neural lineages have been implicated as cells of origin, as have glia. Interestingly, high levels of the neural stem cell regulator TLX correlate with poor patient prognosis. Here we show that high levels of the Drosophila TLX homologue, Tailless, initiate tumourigenesis by reverting intermediate neural progenitors to a stem cell state. Strikingly, we could block tumour formation completely by re-expressing Asense (homologue of human ASCL1), which we show is a direct target of Tailless. Our results predict that expression of TLX and ASCL1 should be mutually exclusive in glioblastoma, which was verified in single-cell RNA-seq of human glioblastoma samples. Counteracting high TLX is a potential therapeutic strategy for suppressing tumours originating from intermediate progenitor cells.
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Affiliation(s)
- Anna E Hakes
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Andrea H Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
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Khaminets A, Ronnen-Oron T, Baldauf M, Meier E, Jasper H. Cohesin controls intestinal stem cell identity by maintaining association of Escargot with target promoters. eLife 2020; 9:e48160. [PMID: 32022682 PMCID: PMC7002041 DOI: 10.7554/elife.48160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 01/18/2020] [Indexed: 12/27/2022] Open
Abstract
Intestinal stem cells (ISCs) maintain regenerative capacity of the intestinal epithelium. Their function and activity are regulated by transcriptional changes, yet how such changes are coordinated at the genomic level remains unclear. The Cohesin complex regulates transcription globally by generating topologically-associated DNA domains (TADs) that link promotor regions with distant enhancers. We show here that the Cohesin complex prevents premature differentiation of Drosophila ISCs into enterocytes (ECs). Depletion of the Cohesin subunit Rad21 and the loading factor Nipped-B triggers an ISC to EC differentiation program that is independent of Notch signaling, but can be rescued by over-expression of the ISC-specific escargot (esg) transcription factor. Using damID and transcriptomic analysis, we find that Cohesin regulates Esg binding to promoters of differentiation genes, including a group of Notch target genes involved in ISC differentiation. We propose that Cohesin ensures efficient Esg-dependent gene repression to maintain stemness and intestinal homeostasis.
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Affiliation(s)
| | | | - Maik Baldauf
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Elke Meier
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Heinrich Jasper
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
- Buck Institute for Research on AgingNovatoUnited States
- Immunology DiscoveryGenentech, IncSouth San FranciscoUnited States
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50
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Liu X, Shen J, Xie L, Wei Z, Wong C, Li Y, Zheng X, Li P, Song Y. Mitotic Implantation of the Transcription Factor Prospero via Phase Separation Drives Terminal Neuronal Differentiation. Dev Cell 2020; 52:277-293.e8. [DOI: 10.1016/j.devcel.2019.11.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 10/09/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
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