1
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Yee C, Xiao Y, Chen H, Reddy AR, Xu B, Medwig-Kinney TN, Zhang W, Boyle AP, Herbst WA, Xiang YK, Matus DQ, Shen K. An activity-regulated transcriptional program directly drives synaptogenesis. Nat Neurosci 2024:10.1038/s41593-024-01728-x. [PMID: 39103556 DOI: 10.1038/s41593-024-01728-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 07/11/2024] [Indexed: 08/07/2024]
Abstract
Although the molecular composition and architecture of synapses have been widely explored, much less is known about what genetic programs directly activate synaptic gene expression and how they are modulated. Here, using Caenorhabditis elegans dopaminergic neurons, we reveal that EGL-43/MECOM and FOS-1/FOS control an activity-dependent synaptogenesis program. Loss of either factor severely reduces presynaptic protein expression. Both factors bind directly to promoters of synaptic genes and act together with CUT homeobox transcription factors to activate transcription. egl-43 and fos-1 mutually promote each other's expression, and increasing the binding affinity of FOS-1 to the egl-43 locus results in increased presynaptic protein expression and synaptic function. EGL-43 regulates the expression of multiple transcription factors, including activity-regulated factors and developmental factors that define multiple aspects of dopaminergic identity. Together, we describe a robust genetic program underlying activity-regulated synapse formation during development.
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Affiliation(s)
- Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Hongwen Chen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anay R Reddy
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - Bing Xu
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
- VA Northern California Healthcare System, Mather, CA, USA
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Wendy A Herbst
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - Yang Kevin Xiang
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
- VA Northern California Healthcare System, Mather, CA, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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2
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Sohn J, Kwon S, Lee GY, Kim SS, Lee Y, Lee J, Jung Y, Ham S, Park HEH, Park S, Ha SG, Lee D, Lee SJV. HLH-30/TFEB mediates sexual dimorphism in immunity in Caenorhabditis elegans. Autophagy 2024:1-15. [PMID: 38963038 DOI: 10.1080/15548627.2024.2375779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/29/2024] [Indexed: 07/05/2024] Open
Abstract
Sexual dimorphism affects various biological functions, including immune responses. However, the mechanisms by which sex alters immunity remain largely unknown. Using Caenorhabditis elegans as a model species, we showed that males exhibit enhanced immunity against various pathogenic bacteria through the upregulation of HLH-30 (Helix Loop Helix 30/TFEB (transcription factor EB)), a transcription factor crucial for macroautophagy/autophagy. Compared with hermaphroditic C. elegans, males displayed increased activity of HLH-30/TFEB, which contributed to enhanced antibacterial immunity. atg-2 (AuTophaGy (yeast Atg homolog) 2) upregulated by HLH-30/TFEB mediated increased immunity in male C. elegans. Thus, the males appear to be equipped with enhanced HLH-30/TFEB-mediated autophagy, which increases pathogen resistance, and this may functionally prolong mate-searching ability with reduced risk of infection.Abbreviations: atg-2: AuTophaGy (yeast Atg homolog) 2; FUDR: 5-fluoro-2'-deoxyuridine; GSEA: gene set enrichment analysis; HLH-30: Helix Loop Helix 30; LC3: microtubule associated protein 1 light chain 3; NGM: nematode growth media; RNA-seq: RNA sequencing; SEM: standard error of the mean; TFEB: transcription factor EB; WT: wild-type.
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Affiliation(s)
- Jooyeon Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sujeong Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Gee-Yoon Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sieun S Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yujin Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongsun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seokjin Ham
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Hae-Eun H Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Sangsoon Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seokjun G Ha
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Daehan Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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3
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Aguilar GR, Vidal B, Ji H, Evenblij J, Ji H, Valperga G, Liao CP, Fang-Yen C, Hobert O. Functional analysis of conserved C. elegans bHLH family members uncovers lifespan control by a peptidergic hub neuron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603289. [PMID: 39071424 PMCID: PMC11275782 DOI: 10.1101/2024.07.12.603289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Throughout the animal kingdom, several members of the basic helix-loop-helix (bHLH) family act as proneural genes during early steps of nervous system development. Roles of bHLH genes in specifying terminal differentiation of postmitotic neurons have been less extensively studied. We analyze here the function of five C. elegans bHLH genes, falling into three phylogenetically conserved subfamilies, which are continuously expressed in a very small number of postmitotic neurons in the central nervous system. We show (a) that two orthologs of the vertebrate bHLHb4/b5 genes, called hlh-17 and hlh-32, function redundantly to specify the identity of a single head interneuron (AUA), as well as an individual motor neuron (VB2), (b) that the PTF1a ortholog hlh-13 acts as a terminal selector to control terminal differentiation and function of the sole octopaminergic neuron class in C. elegans , RIC, and (c) that the NHLH1/2 ortholog hlh-15 controls terminal differentiation and function of the peptidergic AVK head interneuron class, a known neuropeptidergic signaling hub in the animal. Strikingly, through null mutant analysis and cell-specific rescue experiments, we find that loss of hlh-15/NHLH in the peptidergic AVK neurons and the resulting abrogation of neuropeptide secretion causes a substantially expanded lifespan of the animal, revealing an unanticipated impact of a central, peptidergic hub neuron in regulating lifespan, which we propose to be akin to hypothalamic control of lifespan in vertebrates. Taken together, our functional analysis reveals themes of bHLH gene function during terminal differentiation that are complementary to the earlier lineage specification roles of other bHLH family members. However, such late functions are much more sparsely employed by members of the bHLH transcription factor family, compared to the function of the much more broadly employed homeodomain transcription factor family.
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Cornwell AB, Zhang Y, Thondamal M, Johnson DW, Thakar J, Samuelson AV. The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction. GeroScience 2024:10.1007/s11357-024-01197-x. [PMID: 38878153 DOI: 10.1007/s11357-024-01197-x] [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: 02/16/2024] [Accepted: 05/08/2024] [Indexed: 06/25/2024] Open
Abstract
Dietary restriction (DR), the process of decreasing overall food consumption over an extended period of time, has been shown to increase longevity across evolutionarily diverse species and delay the onset of age-associated diseases in humans. In Caenorhabditis elegans, the Myc-family transcription factors (TFs) MXL-2 (Mlx) and MML-1 (MondoA/ChREBP), which function as obligate heterodimers, and PHA-4 (orthologous to FOXA) are both necessary for the full physiological benefits of DR. However, the adaptive transcriptional response to DR and the role of MML-1::MXL-2 and PHA-4 remains elusive. We identified the transcriptional signature of C. elegans DR, using the eat-2 genetic model, and demonstrate broad changes in metabolic gene expression in eat-2 DR animals, which requires both mxl-2 and pha-4. While the requirement for these factors in DR gene expression overlaps, we found many of the DR genes exhibit an opposing change in relative gene expression in eat-2;mxl-2 animals compared to wild-type, which was not observed in eat-2 animals with pha-4 loss. Surprisingly, we discovered more than 2000 genes synthetically dysregulated in eat-2;mxl-2, out of which the promoters of down-regulated genes were substantially enriched for PQM-1 and ELT-1/3 GATA TF binding motifs. We further show functional deficiencies of the mxl-2 loss in DR outside of lifespan, as eat-2;mxl-2 animals exhibit substantially smaller brood sizes and lay a proportion of dead eggs, indicating that MML-1::MXL-2 has a role in maintaining the balance between resource allocation to the soma and to reproduction under conditions of chronic food scarcity. While eat-2 animals do not show a significantly different metabolic rate compared to wild-type, we also find that loss of mxl-2 in DR does not affect the rate of oxygen consumption in young animals. The gene expression signature of eat-2 mutant animals is consistent with optimization of energy utilization and resource allocation, rather than induction of canonical gene expression changes associated with acute metabolic stress, such as induction of autophagy after TORC1 inhibition. Consistently, eat-2 animals are not substantially resistant to stress, providing further support to the idea that chronic DR may benefit healthspan and lifespan through efficient use of limited resources rather than broad upregulation of stress responses, and also indicates that MML-1::MXL-2 and PHA-4 may have distinct roles in promotion of benefits in response to different pro-longevity stimuli.
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Affiliation(s)
- Adam B Cornwell
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Yun Zhang
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Manjunatha Thondamal
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- MURTI Centre and Department of Biotechnology, School of Technology, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, Andhra Pradesh, 530045, India
| | - David W Johnson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- Department of Math and Science, Genesee Community College, One College Rd, Batavia, NY, 14020, USA
| | - Juilee Thakar
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Andrew V Samuelson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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5
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Metcalf MG, Monshietehadi S, Sahay A, Durieux J, Frakes AE, Velichkovska M, Mena C, Farinas A, Sanchez M, Dillin A. Cell non-autonomous control of autophagy and metabolism by glial cells. iScience 2024; 27:109354. [PMID: 38500817 PMCID: PMC10946330 DOI: 10.1016/j.isci.2024.109354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/01/2023] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Glia are the protectors of the nervous system, providing neurons with support and protection from cytotoxic insults. We previously discovered that four astrocyte-like glia can regulate organismal proteostasis and longevity in C. elegans. Expression of the UPRER transcription factor, XBP-1s, in these glia increases stress resistance, and longevity, and activates the UPRER in intestinal cells via neuropeptides. Autophagy, a key regulator of metabolism and aging, has been described as a cell autonomous process. Surprisingly, we find that glial XBP-1s enhances proteostasis and longevity by cell non-autonomously reprogramming organismal lipid metabolism and activating autophagy. Glial XBP-1s regulates the activation of another transcription factor, HLH-30/TFEB, in the intestine. HLH-30 activates intestinal autophagy, increases intestinal lipid catabolism, and upregulates a robust transcriptional program. Our study reveals a novel role for glia in regulating peripheral lipid metabolism, autophagy, and organellar health through peripheral activation of HLH-30 and autophagy.
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Affiliation(s)
- Melissa G. Metcalf
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Samira Monshietehadi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Arushi Sahay
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jenni Durieux
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ashley E. Frakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Martina Velichkovska
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cesar Mena
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amelia Farinas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Melissa Sanchez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew Dillin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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6
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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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7
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Sepulveda GP, Gushchanskaia ES, Mora-Martin A, Esse R, Nikorich I, Ceballos A, Kwan J, Blum BC, Dholiya P, Emili A, Perissi V, Cardamone MD, Grishok A. DOT1L stimulates MYC/Mondo transcription factor activity by promoting its degradation cycle on chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579191. [PMID: 38370658 PMCID: PMC10871221 DOI: 10.1101/2024.02.06.579191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The proto-oncogene c-MYC is a key representative of the MYC transcription factor network regulating growth and metabolism. MML-1 (Myc- and Mondo-like) is its homolog in C. elegans. The functional and molecular cooperation between c-MYC and H3 lysine 79 methyltransferase DOT1L was demonstrated in several human cancer types, and we have earlier discovered the connection between C. elegans MML-1 and DOT-1.1. Here, we demonstrate the critical role of DOT1L/DOT-1.1 in regulating c-MYC/MML-1 target genes genome-wide by ensuring the removal of "spent" transcription factors from chromatin by the nuclear proteasome. Moreover, we uncover a previously unrecognized proteolytic activity of DOT1L, which may facilitate c-MYC turnover. This new mechanism of c-MYC regulation by DOT1L may lead to the development of new approaches for cancer treatment.
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Affiliation(s)
- Gian P. Sepulveda
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ekaterina S. Gushchanskaia
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Tessera Therapeutics, Somerville, MA, 02143, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Ruben Esse
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Cell and Gene Therapy Catapult, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Iana Nikorich
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ainhoa Ceballos
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Present address: Research Unit, Diagnostica Longwood S.L. 50011 Zaragoza, Spain
| | - Julian Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Benjamin C. Blum
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Prakruti Dholiya
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrew Emili
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
- Division of Computational Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: OHSU Knight Cancer Institute, School of Medicine, Portland, OR, 97239, USA
| | - Valentina Perissi
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Maria D. Cardamone
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Korro Bio Inc., Cambridge, MA, 02139, USA
| | - Alla Grishok
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Genome Science Institute, Boston University, Boston, MA, 02118, USA
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8
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Cornwell A, Zhang Y, Thondamal M, Johnson DW, Thakar J, Samuelson AV. The C. elegans Myc-family of transcription factors coordinate a dynamic adaptive response to dietary restriction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568222. [PMID: 38045350 PMCID: PMC10690244 DOI: 10.1101/2023.11.22.568222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Dietary restriction (DR), the process of decreasing overall food consumption over an extended period of time, has been shown to increase longevity across evolutionarily diverse species and delay the onset of age-associated diseases in humans. In Caenorhabditis elegans, the Myc-family transcription factors (TFs) MXL-2 (Mlx) and MML-1 (MondoA/ChREBP), which function as obligate heterodimers, and PHA-4 (orthologous to forkhead box transcription factor A) are both necessary for the full physiological benefits of DR. However, the adaptive transcriptional response to DR and the role of MML-1::MXL-2 and PHA-4 remains elusive. We identified the transcriptional signature of C. elegans DR, using the eat-2 genetic model, and demonstrate broad changes in metabolic gene expression in eat-2 DR animals, which requires both mxl-2 and pha-4. While the requirement for these factors in DR gene expression overlaps, we found many of the DR genes exhibit an opposing change in relative gene expression in eat-2;mxl-2 animals compared to wild-type, which was not observed in eat-2 animals with pha-4 loss. We further show functional deficiencies of the mxl-2 loss in DR outside of lifespan, as eat-2;mxl-2 animals exhibit substantially smaller brood sizes and lay a proportion of dead eggs, indicating that MML-1::MXL-2 has a role in maintaining the balance between resource allocation to the soma and to reproduction under conditions of chronic food scarcity. While eat-2 animals do not show a significantly different metabolic rate compared to wild-type, we also find that loss of mxl-2 in DR does not affect the rate of oxygen consumption in young animals. The gene expression signature of eat-2 mutant animals is consistent with optimization of energy utilization and resource allocation, rather than induction of canonical gene expression changes associated with acute metabolic stress -such as induction of autophagy after TORC1 inhibition. Consistently, eat-2 animals are not substantially resistant to stress, providing further support to the idea that chronic DR may benefit healthspan and lifespan through efficient use of limited resources rather than broad upregulation of stress responses, and also indicates that MML-1::MXL-2 and PHA-4 may have different roles in promotion of benefits in response to different pro-longevity stimuli.
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Affiliation(s)
- Adam Cornwell
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Yun Zhang
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Manjunatha Thondamal
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Biological Sciences, GITAM University, Andhra Pradesh, India
| | - David W Johnson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Math and Science, Genesee Community College, One College Rd Batavia, NY 14020, USA
| | - Juilee Thakar
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Andrew V Samuelson
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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9
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Liska D, Wolfe Z, Norris A. VISTA: visualizing the spatial transcriptome of the C.elegans nervous system. BIOINFORMATICS ADVANCES 2023; 3:vbad127. [PMID: 37810458 PMCID: PMC10560093 DOI: 10.1093/bioadv/vbad127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/07/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023]
Abstract
Summary Profiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode worm Caenorhabditis elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm's invariant cell lineage and a series of recently generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a "spatial heatmap" in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated from in vivo reporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future. Availability and implementation VISTA is freely available at the following URL: https://public.tableau.com/app/profile/smu.oit.data.insights/viz/VISTA_16814210566130/VISTA.
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Affiliation(s)
- David Liska
- Office of Information Technology, Southern Methodist University, Dallas, TX 75205, United States
| | - Zachery Wolfe
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75205, United States
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75205, United States
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10
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Liska D, Wolfe Z, Norris A. VISTA: Visualizing the Spatial Transcriptome of the C. elegans Nervous System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538711. [PMID: 37163055 PMCID: PMC10168398 DOI: 10.1101/2023.04.28.538711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Profiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode worm C. elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm's invariant cell lineage and a series of recently-generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a "spatial heatmap" in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated from in vivo reporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation, and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future.
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Affiliation(s)
- David Liska
- Office of Information Technology, Southern Methodist University. Dallas, TX USA
| | - Zachery Wolfe
- Department of Biological Sciences, Southern Methodist University. Dallas, TX USA
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University. Dallas, TX USA
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11
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Klumpe HE, Garcia-Ojalvo J, Elowitz MB, Antebi YE. The computational capabilities of many-to-many protein interaction networks. Cell Syst 2023; 14:430-446. [PMID: 37348461 PMCID: PMC10318606 DOI: 10.1016/j.cels.2023.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Many biological circuits comprise sets of protein variants that interact with one another in a many-to-many, or promiscuous, fashion. These architectures can provide powerful computational capabilities that are especially critical in multicellular organisms. Understanding the principles of biochemical computations in these circuits could allow more precise control of cellular behaviors. However, these systems are inherently difficult to analyze, due to their large number of interacting molecular components, partial redundancies, and cell context dependence. Here, we discuss recent experimental and theoretical advances that are beginning to reveal how promiscuous circuits compute, what roles those computations play in natural biological contexts, and how promiscuous architectures can be applied for the design of synthetic multicellular behaviors.
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Affiliation(s)
- Heidi E Klumpe
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Yaron E Antebi
- Department of Molecular Genetics, Weizmann Institute of Science 76100, Rehovot, Israel.
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12
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Marri D, Filipovic D, Kana O, Tischkau S, Bhattacharya S. Prediction of mammalian tissue-specific CLOCK-BMAL1 binding to E-box DNA motifs. Sci Rep 2023; 13:7742. [PMID: 37173345 PMCID: PMC10182026 DOI: 10.1038/s41598-023-34115-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The Brain and Muscle ARNTL-Like 1 protein (BMAL1) forms a heterodimer with either Circadian Locomotor Output Cycles Kaput (CLOCK) or Neuronal PAS domain protein 2 (NPAS2) to act as a master regulator of the mammalian circadian clock gene network. The dimer binds to E-box gene regulatory elements on DNA, activating downstream transcription of clock genes. Identification of transcription factor binding sites and genomic features that correlate to DNA binding by BMAL1 is a challenging problem, given that CLOCK-BMAL1 or NPAS2-BMAL1 bind to several distinct binding motifs (CANNTG) on DNA. Using three different types of tissue-specific machine learning models with features based on (1) DNA sequence, (2) DNA sequence plus DNA shape, and (3) DNA sequence and shape plus histone modifications, we developed an interpretable predictive model of genome-wide BMAL1 binding to E-box motifs and dissected the mechanisms underlying BMAL1-DNA binding. Our results indicated that histone modifications, the local shape of the DNA, and the flanking sequence of the E-box motif are sufficient predictive features for BMAL1-DNA binding. Our models also provide mechanistic insights into tissue specificity of DNA binding by BMAL1.
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Affiliation(s)
- Daniel Marri
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - David Filipovic
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Omar Kana
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Shelley Tischkau
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Sudin Bhattacharya
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA.
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA.
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
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13
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Ghaddar A, Mony VK, Mishra S, Berhanu S, Johnson JC, Enriquez-Hesles E, Harrison E, Patel A, Horak MK, Smith JS, O'Rourke EJ. Increased alcohol dehydrogenase 1 activity promotes longevity. Curr Biol 2023; 33:1036-1046.e6. [PMID: 36805847 PMCID: PMC10236445 DOI: 10.1016/j.cub.2023.01.059] [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: 08/05/2022] [Revised: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023]
Abstract
Several molecules can extend healthspan and lifespan across organisms. However, most are upstream signaling hubs or transcription factors orchestrating complex anti-aging programs. Therefore, these molecules point to but do not reveal the fundamental mechanisms driving longevity. Instead, downstream effectors that are necessary and sufficient to promote longevity across conditions or organisms may reveal the fundamental anti-aging drivers. Toward this goal, we searched for effectors acting downstream of the transcription factor EB (TFEB), known as HLH-30 in C. elegans, because TFEB/HLH-30 is necessary across anti-aging interventions and its overexpression is sufficient to extend C. elegans lifespan and reduce biomarkers of aging in mammals including humans. As a result, we present an alcohol-dehydrogenase-mediated anti-aging response (AMAR) that is essential for C. elegans longevity driven by HLH-30 overexpression, caloric restriction, mTOR inhibition, and insulin-signaling deficiency. The sole overexpression of ADH-1 is sufficient to activate AMAR, which extends healthspan and lifespan by reducing the levels of glycerol-an age-associated and aging-promoting alcohol. Adh1 overexpression is also sufficient to promote longevity in yeast, and adh-1 orthologs are induced in calorically restricted mice and humans, hinting at ADH-1 acting as an anti-aging effector across phyla.
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Affiliation(s)
- Abbas Ghaddar
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Vinod K Mony
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Swarup Mishra
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Samuel Berhanu
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - James C Johnson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Elisa Enriquez-Hesles
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Emma Harrison
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Aaroh Patel
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Mary Kate Horak
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA; Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Eyleen J O'Rourke
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA; Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA; Robert M. Berne Cardiovascular Research Center, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA.
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14
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Luan Y, Tang Z, He Y, Xie Z. Intra-Domain Residue Coevolution in Transcription Factors Contributes to DNA Binding Specificity. Microbiol Spectr 2023; 11:e0365122. [PMID: 36943132 PMCID: PMC10100741 DOI: 10.1128/spectrum.03651-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Understanding the basis of the DNA-binding specificity of transcription factors (TFs) has been of long-standing interest. Despite extensive efforts to map millions of putative TF binding sequences, identifying the critical determinants for DNA binding specificity remains a major challenge. The coevolution of residues in proteins occurs due to a shared evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically collected publicly available data sets from multiple large-scale high-throughput TF-DNA interaction screening experiments for the major TF families with large numbers of TF members. These families included the Homeobox, HLH, bZIP_1, Ets, HMG_box, ZF-C4, and Zn_clus TFs. We detected TF subclass-determining sites (TSDSs) and showed that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs, particularly for the Homeobox, HLH, Ets, bZIP_1, and HMG_box TF families. By in silico modeling, we showed that mutation of the highly coevolving residues could significantly reduce the stability of the TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity. Overall, our study gave evidence that coevolved residues relate to transcriptional regulation and provided insights into the potential application of engineered DNA-binding domains and proteins. IMPORTANCE While unraveling DNA-binding specificity of TFs is the key to understanding the basis and molecular mechanism of gene expression regulation, identifying the critical determinants that contribute to DNA binding specificity remains a major challenge. In this study, we provided evidence showing that coevolving residues in TF domains contributed to DNA binding specificity. We demonstrated that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs. Mutation of the coevolving residue pairs (CRPs) could significantly reduce the stability of THE TF-DNA complex, and even the distant residues from the DNA interface contribute to TF-DNA binding activity. Collectively, our study expands our knowledge of the interactions among coevolved residues in TFs, tertiary contacting, and functional importance in refined transcriptional regulation. Understanding the impact of coevolving residues in TFs will help understand the details of transcription of gene regulation and advance the application of engineered DNA-binding domains and protein.
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Affiliation(s)
- Yizhao Luan
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zehua Tang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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15
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Ge Y, Chen X, Nan N, Bard J, Wu F, Yergeau D, Liu T, Wang J, Mu X. Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res 2023; 51:2151-2176. [PMID: 36715342 PMCID: PMC10018358 DOI: 10.1093/nar/gkad026] [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: 04/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
How the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. In this study, we dissect the changes in the epigenetic landscape during early retinal cell differentiation by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages. Using CUT&Tag, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2 and Isl1, including those dependent on Atoh7, and uncover the sequential and combinatorial interactions of these factors with the epigenetic landscape to control gene expression along individual retinal cell lineages such as retinal ganglion cells (RGCs). Our results reveal a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from multipotent retinal progenitor cells (RPCs).
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xushen Chen
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Nan Nan
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jie Wang
- Correspondence may also be addressed to Jie Wang.
| | - Xiuqian Mu
- To whom correspondence should be addressed. Tel: +1 716 881 7463; Fax: +1 716 887 2991;
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16
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Goswamy D, Gonzalez X, Labed SA, Irazoqui JE. C. elegans orphan nuclear receptor NHR-42 represses innate immunity and promotes lipid loss downstream of HLH-30/TFEB. Front Immunol 2023; 14:1094145. [PMID: 36860863 PMCID: PMC9968933 DOI: 10.3389/fimmu.2023.1094145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
In recent years, transcription factors of the Microphthalmia-TFE (MiT) family, including TFEB and TFE3 in mammals and HLH-30 in Caenorhabditis elegans, have emerged as important regulators of innate immunity and inflammation in invertebrates and vertebrates. Despite great strides in knowledge, the mechanisms that mediate downstream actions of MiT transcription factors in the context of innate host defense remain poorly understood. Here, we report that HLH-30, which promotes lipid droplet mobilization and host defense, induces the expression of orphan nuclear receptor NHR-42 during infection with Staphylococcus aureus. Remarkably, NHR-42 loss of function promoted host infection resistance, genetically defining NHR-42 as an HLH-30-controlled negative regulator of innate immunity. During infection, NHR-42 was required for lipid droplet loss, suggesting that it is an important effector of HLH-30 in lipid immunometabolism. Moreover, transcriptional profiling of nhr-42 mutants revealed wholesale activation of an antimicrobial signature, of which abf-2, cnc-2, and lec-11 were important for the enhanced survival of infection of nhr-42 mutants. These results advance our knowledge of the mechanisms by which MiT transcription factors promote host defense, and by analogy suggest that TFEB and TFE3 may similarly promote host defense via NHR-42-homologous nuclear receptors in mammals.
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Affiliation(s)
| | | | | | - Javier E. Irazoqui
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, United States
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17
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Masoudi N, Schnabel R, Yemini E, Leyva-Díaz E, Hobert O. Cell-specific effects of the sole C. elegans Daughterless/E protein homolog, HLH-2, on nervous system development. Development 2023; 150:286219. [PMID: 36595352 PMCID: PMC10108603 DOI: 10.1242/dev.201366] [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: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 01/04/2023]
Abstract
Are there common mechanisms of neurogenesis used throughout an entire nervous system? We explored to what extent canonical proneural class I/II bHLH complexes are responsible for neurogenesis throughout the entire Caenorhabditis elegans nervous system. Distinct, lineage-specific proneural class II bHLH factors are generally thought to operate via interaction with a common, class I bHLH subunit, encoded by Daughterless in flies, the E proteins in vertebrates and HLH-2 in C. elegans. To eliminate function of all proneuronal class I/II bHLH complexes, we therefore genetically removed maternal and zygotic hlh-2 gene activity. We observed broad effects on neurogenesis, but still detected normal neurogenesis in many distinct neuron-producing lineages of the central and peripheral nervous system. Moreover, we found that hlh-2 selectively affects some aspects of neuron differentiation while leaving others unaffected. Although our studies confirm the function of proneuronal class I/II bHLH complexes in many different lineages throughout a nervous system, we conclude that their function is not universal, but rather restricted by lineage, cell type and components of differentiation programs affected.
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Affiliation(s)
- Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA.,University of Massachusetts, Department of Neurobiology, Worcester, MA 1605-2324, USA
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
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18
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Konrad KD, Song JL. NeuroD1 localizes to the presumptive ganglia and gut of the sea urchin larvae. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000682. [PMID: 36468156 PMCID: PMC9709636 DOI: 10.17912/micropub.biology.000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 01/25/2023]
Abstract
NeuroD is a transcription factor (TF) that plays a dual role in vertebrate neurogenesis and glucose homeostasis in the pancreas. We identified a NeuroD antibody developed against human that cross-reacts with the sea urchin NeuroD1. NeuroD1 protein localizes to the presumptive ganglia and neurofilament structures in the ciliary band of the sea urchin larvae. In addition, we also observed NeuroD1 in the perinuclear region in the sea urchin gut which is analogous to the mammalian pancreas. These results suggest that NeuroD1 may play an evolutionarily conserved role in the invertebrate sea urchin.
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Affiliation(s)
| | - Jia L. Song
- University of Delaware
,
Correspondence to: Jia L. Song (
)
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19
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Mor E, Pernisová M, Minne M, Cerutti G, Ripper D, Nolf J, Andres J, Ragni L, Zurbriggen MD, De Rybel B, Vernoux T. bHLH heterodimer complex variations regulate cell proliferation activity in the meristems of Arabidopsis thaliana. iScience 2022; 25:105364. [PMID: 36339262 PMCID: PMC9626673 DOI: 10.1016/j.isci.2022.105364] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 08/08/2022] [Accepted: 10/12/2022] [Indexed: 11/12/2022] Open
Abstract
Root, shoot, and lateral meristems are the main regions of cell proliferation in plants. It has been proposed that meristems might have evolved dedicated transcriptional networks to balance cell proliferation. Here, we show that basic helix-loop-helix (bHLH) transcription factor heterodimers formed by members of the TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) subclades are general regulators of cell proliferation in all meristems. Yet, genetics and expression analyses suggest specific functions of these transcription factors in distinct meristems, possibly due to their expression domains determining heterodimer complex variations within meristems, and to a certain extent to the absence of some of them in a given meristem. Target gene specificity analysis for heterodimer complexes focusing on the LONELY GUY gene targets further suggests differences in transcriptional responses through heterodimer diversification that could allow a common bHLH heterodimer complex module to contribute to cell proliferation control in multiple meristems. Expression of TMO5 and LHW bHLH clade members varies in distinct meristems Single mutant analyses reveal functional specificity in meristems Variations in TMO5/LHW heterodimer complexes affect target gene regulation TMO5/LHW complexes are regulators of cell proliferation in all plant meristems
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20
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Rashid A, Tevlin M, Lu Y, Shaham S. A developmental pathway for epithelial-to-motoneuron transformation in C. elegans. Cell Rep 2022; 40:111414. [PMID: 36170838 PMCID: PMC9579992 DOI: 10.1016/j.celrep.2022.111414] [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: 12/21/2021] [Revised: 07/18/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Motoneurons and motoneuron-like pancreatic β cells arise from radial glia and ductal cells, respectively, both tube-lining progenitors that share molecular regulators. To uncover programs underlying motoneuron formation, we studied a similar, cell-division-independent transformation of the C. elegans tube-lining Y cell into the PDA motoneuron. We find that lin-12/Notch acts through ngn-1/Ngn and its regulator hlh-16/Olig to control transformation timing. lin-12 loss blocks transformation, while lin-12(gf) promotes precocious PDA formation. Early basal expression of ngn-1/Ngn and hlh-16/Olig depends on sem-4/Sall and egl-5/Hox. Later, coincident with Y cell morphological changes, ngn-1/Ngn expression is upregulated in a sem-4/Sall and egl-5/Hox-dependent but hlh-16/Olig-independent manner. Subsequently, Y cell retrograde extension forms an anchored process priming PDA axon extension. Extension requires ngn-1-dependent expression of the cytoskeleton organizers UNC-119, UNC-44/ANK, and UNC-33/CRMP, which also activate PDA terminal-gene expression. Our findings uncover cell-division-independent regulatory events leading to motoneuron generation, suggesting a conserved pathway for epithelial-to-motoneuron/motoneuron-like cell differentiation. Rashid et al. report on a conserved epithelial-to-motoneuron transformation pathway in C. elegans requiring ngn-1/Ngn and hlh-16/Olig. lin-12/Notch regulates transformation timing through these genes, while ngn-1/Ngn and hlh-16/Olig expression levels are regulated by sem-4/Sall and egl-5/Hox. Unexpectedly, the cytoskeleton organizers UNC-119, UNC-44, and UNC-33, which are ngn-1/Ngn targets, promote motoneuron terminal identity.
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Affiliation(s)
- Alina Rashid
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Maya Tevlin
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yun Lu
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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21
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Bhattacharya S, Horowitz BB, Zhang J, Li X, Zhang H, Giese GE, Holdorf AD, Walhout AJ. A metabolic regulatory network for the Caenorhabditis elegans intestine. iScience 2022; 25:104688. [PMID: 35847555 PMCID: PMC9283940 DOI: 10.1016/j.isci.2022.104688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/12/2022] [Accepted: 06/24/2022] [Indexed: 11/12/2022] Open
Abstract
Metabolic perturbations can affect gene expression, for instance to rewire metabolism. While numerous efforts have measured gene expression in response to individual metabolic perturbations, methods that determine all metabolic perturbations that affect the expression for a given gene or set of genes have not been available. Here, we use a gene-centered approach to derive a first-pass metabolic regulatory network for Caenorhabditis elegans by performing RNAi of more than 1,400 metabolic genes with a set of 19 promoter reporter strains that express a fluorescent protein in the animal's intestine. We find that metabolic perturbations generally increase promoter activity, which contrasts with transcription factor (TF) RNAi, which tends to repress promoter activity. We identify several TFs that modulate promoter activity in response to perturbations of the electron transport chain and explore complex genetic interactions among metabolic pathways. This work provides a blueprint for a systems-level understanding of how metabolism affects gene expression.
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Affiliation(s)
- Sushila Bhattacharya
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Brent B. Horowitz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jingyan Zhang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xuhang Li
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hefei Zhang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gabrielle E. Giese
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy D. Holdorf
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Albertha J.M. Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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22
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Matty MA, Lau HE, Haley JA, Singh A, Chakraborty A, Kono K, Reddy KC, Hansen M, Chalasani SH. Intestine-to-neuronal signaling alters risk-taking behaviors in food-deprived Caenorhabditis elegans. PLoS Genet 2022; 18:e1010178. [PMID: 35511794 PMCID: PMC9070953 DOI: 10.1371/journal.pgen.1010178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/30/2022] [Indexed: 11/19/2022] Open
Abstract
Animals integrate changes in external and internal environments to generate behavior. While neural circuits detecting external cues have been mapped, less is known about how internal states like hunger are integrated into behavioral outputs. Here, we use the nematode C. elegans to examine how changes in internal nutritional status affect chemosensory behaviors. We show that acute food deprivation leads to a reversible decline in repellent, but not attractant, sensitivity. This behavioral change requires two conserved transcription factors MML-1 (MondoA) and HLH-30 (TFEB), both of which translocate from the intestinal nuclei to the cytoplasm during food deprivation. Next, we identify the insulin-like peptide INS-31 as a candidate ligand relaying food-status signals from the intestine to other tissues. Further, we show that neurons likely use the DAF-2 insulin receptor and AGE-1/PI-3 Kinase, but not DAF-16/FOXO to integrate these intestine-released peptides. Altogether, our study shows how internal food status signals are integrated by transcription factors and intestine-neuron signaling to generate flexible behaviors via the gut-brain axis.
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Affiliation(s)
- Molly A. Matty
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Hiu E. Lau
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jessica A. Haley
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, California, United States of America
| | - Anupama Singh
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Ahana Chakraborty
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Karina Kono
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Kirthi C. Reddy
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Malene Hansen
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Sreekanth H. Chalasani
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
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23
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Reuter AS, Stern D, Bernard A, Goossens C, Lavergne A, Flasse L, Von Berg V, Manfroid I, Peers B, Voz ML. Identification of an evolutionarily conserved domain in Neurod1 favouring enteroendocrine versus goblet cell fate. PLoS Genet 2022; 18:e1010109. [PMID: 35286299 PMCID: PMC8959185 DOI: 10.1371/journal.pgen.1010109] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 03/28/2022] [Accepted: 02/17/2022] [Indexed: 12/16/2022] Open
Abstract
ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues, coordinating the acquisition of generic cell fates and of specific subtype identities. How these factors, recognizing highly similar DNA motifs, display specific activities, is not yet fully understood. To address this issue, we overexpressed different ARP/ASCL factors in zebrafish ascl1a-/- mutant embryos to determine which ones are able to rescue the intestinal secretory lineage. We found that Ascl1a/b, Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors. Indeed, Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells. Gain-of-function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19-aa ultra-conserved element (UCE), present in all Neurod members but absent in the other ARP/ASCL proteins. Importantly, inserting the UCE into the Ascl1a protein reverses the rescuing capacity of this Ascl1a chimeric protein that cannot rescue the goblet cells anymore but can efficiently rescue the enteroendocrine cells. This novel domain acts indeed as a goblet cell fate repressor that inhibits gfi1aa expression, known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of the enteroendocrine cells, phenotype also observed in the neurod1 null mutant. This highlights the crucial function of the UCE domain for NeuroD1 activity in the intestine. As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed, we can envision a similar role of the UCE in other tissues, allowing Neurod1 to repress Gfi1 to influence the balance between cell fates. It is not yet clear how highly related factors like the ARP/Ascl factors display specific activities even though they recognize the same consensus DNA motif. This specificity could be provided by their cellular environment or by intrinsic properties of the factors themselves. To distinguish between these two possibilities, we have expressed several ARP/Ascl factors in the ascl1a-/- mutant to determine which ones are able to rescue the intestinal secretory defects. We found that Ascl1a/b and Atoh1a/b are able to rescue the goblet cells while Neurod1 rescues the enteroendocrine lineage. Furthermore, we show that the specific Neurod1 activity is conferred by the presence of a 19-aa ultra-conserved element (UCE), present in all vertebrate Neurod members but absent in all the other ARP/ASCL proteins. This UCE domain, so far uncharacterized, acts as a goblet cell fate repressor and inhibits gfi1aa expression, known to be important for goblet cell differentiation. Inserting the UCE into Ascl1a protein reverses the rescuing capacity of this chimeric protein that cannot rescue the goblet cells anymore but can efficiently rescue the enteroendocrine cells. This study therefore highlights an unique intrinsic property of Neurod1 allowing it to repress Gfi1 to influence the balance between cell fates. As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed, we can envision a similar role of the UCE in other tissues, allowing Neurod1 to repress Gfi1 to influence the balance between cell fates.
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Affiliation(s)
- Anne Sophie Reuter
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - David Stern
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Alice Bernard
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Chiara Goossens
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Arnaud Lavergne
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Lydie Flasse
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Virginie Von Berg
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Isabelle Manfroid
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
| | - Marianne L. Voz
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Liège, Belgium
- * E-mail:
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24
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Sang Y, Ren J, Aballay A. The transcription factor HLH-26 controls probiotic-mediated protection against intestinal infection through up-regulation of the Wnt/BAR-1 pathway. PLoS Biol 2022; 20:e3001581. [PMID: 35263319 PMCID: PMC8936500 DOI: 10.1371/journal.pbio.3001581] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/21/2022] [Accepted: 02/23/2022] [Indexed: 12/31/2022] Open
Abstract
Probiotics play a critical role in the control of host intestinal microbial balance, protecting the host from gastrointestinal pathogens, modulating the host immune response, and decreasing host susceptibility to infection. To understand the mechanism underlying the protective effect of probiotics against infections through immune regulation, we examined protection against Salmonella enterica infection following exposure to nonpathogenic Enterococcus faecium in the nematode Caenorhabditis elegans. We found that the transcription factor HLH-26, a REF-1 family member of basic helix-loop-helix transcription factors, was required in the intestine for E. faecium-mediated protection of C. elegans against a lethal S. enterica infection. In addition, we uncovered that defense response genes controlled by the canonical Wnt/BAR-1 pathway were activated upon exposure to E. faecium in an HLH-26-dependent manner. Our findings highlight a role for REF-1/HLH-26 in the control of the Wnt/BAR-1 pathway in probiotic-mediated protection against gut infection.
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Affiliation(s)
- Yu Sang
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jie Ren
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Alejandro Aballay
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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25
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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: 6] [Impact Index Per Article: 3.0] [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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26
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Carey-Fung O, O’Brien M, Beasley JT, Johnson AAT. A Model to Incorporate the bHLH Transcription Factor OsIRO3 within the Rice Iron Homeostasis Regulatory Network. Int J Mol Sci 2022; 23:ijms23031635. [PMID: 35163555 PMCID: PMC8835859 DOI: 10.3390/ijms23031635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Iron (Fe) homeostasis in plants is governed by a complex network of regulatory elements and transcription factors (TFs), as both Fe toxicity and deficiency negatively impact plant growth and physiology. The Fe homeostasis network is well characterized in Arabidopsis thaliana and remains poorly understood in monocotyledon species such as rice (Oryza sativa L.). Recent investigation of the rice Fe homeostasis network revealed OsIRO3, a basic Helix–Loop–Helix (bHLH) TF as a putative negative regulator of genes involved in Fe uptake, transport, and storage. We employed CRISPR-Cas9 gene editing to target the OsIRO3 coding sequence and generate two independent T-DNA-free, loss-of-function iro3 mutants in rice cv. Nipponbare. The iro3 mutant plants had similar phenotype under nutrient-sufficient conditions and had stunted growth under Fe-deficient conditions, relative to a T-DNA free, wild-type control (WT). Under Fe deficiency, iro3 mutant shoots had reduced expression of Fe chelator biosynthetic genes (OsNAS1, OsNAS2, and OsNAAT1) and upregulated expression of an Fe transporter gene (OsYSL15), relative to WT shoots. We place our results in the context of the existing literature and generate a model describing the role of OsIRO3 in rice Fe homeostasis and reinforce the essential function of OsIRO3 in the rice Fe deficiency response.
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Affiliation(s)
- Oscar Carey-Fung
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; (O.C.-F.); (J.T.B.)
| | - Martin O’Brien
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC 3086, Australia;
| | - Jesse T. Beasley
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; (O.C.-F.); (J.T.B.)
| | - Alexander A. T. Johnson
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; (O.C.-F.); (J.T.B.)
- Correspondence: ; Tel.: +61-3-8344-3969
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27
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Lu CJ, Meng Y, Wang YL, Zhang T, Yang GF, Mo MH, Ji KF, Liang LM, Zou CG, Zhang KQ. Survival and infectivity of second-stage root-knot nematode Meloidogyne incognita juveniles depend on lysosome-mediated lipolysis. J Biol Chem 2022; 298:101637. [PMID: 35085555 PMCID: PMC8861644 DOI: 10.1016/j.jbc.2022.101637] [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: 11/02/2021] [Revised: 01/03/2022] [Accepted: 01/18/2022] [Indexed: 11/25/2022] Open
Abstract
Adaptation to nutrient deprivation depends on the activation of metabolic programs to use reserves of energy. When outside a host plant, second-stage juveniles (J2) of the root-knot nematode (Meloidogyne spp.), an important group of pests responsible for severe losses in the production of crops (e.g., rice, wheat, and tomato), are unable to acquire food. Although lipid hydrolysis has been observed in J2 nematodes, its role in fitness and the underlying mechanisms remain unknown. Using RNA-seq analysis, here, we demonstrated that in the absence of host plants, the pathway for the biosynthesis of polyunsaturated fatty acids was upregulated, thereby increasing the production of arachidonic acid in middle-stage J2 Meloidogyne incognita worms. We also found that arachidonic acid upregulated the expression of the transcription factor hlh-30b, which in turn induced lysosomal biogenesis. Lysosomes promoted lipid hydrolysis via a lysosomal lipase, LIPL-1. Furthermore, our data demonstrated that blockage of lysosomal lipolysis reduced both lifespan and locomotion of J2 worms. Strikingly, disturbance of lysosomal lipolysis resulted in a decline in infectivity of these juveniles on tomato roots. Our findings not only reveal the molecular mechanism of lipolysis in J2 worms but also suggest potential novel strategies for the management of root-knot nematode pests.
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Affiliation(s)
- Chao-Jun Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yang Meng
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yan-Li Wang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Tao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Gui-Fang Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Kai-Fang Ji
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Lian-Ming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Cheng-Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China.
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Yunnan University, Kunming, Yunnan, China.
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28
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Filippopoulou K, Couillault C, Bertrand V. Multiple neural bHLHs ensure the precision of a neuronal specification event in Caenorhabditis elegans. Biol Open 2021; 10:273578. [PMID: 34854469 PMCID: PMC8713986 DOI: 10.1242/bio.058976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Neural bHLH transcription factors play a key role in the early steps of neuronal specification in many animals. We have previously observed that the Achaete-Scute HLH-3, the Olig HLH-16 and their binding partner the E-protein HLH-2 activate the terminal differentiation program of a specific class of cholinergic neurons, AIY, in Caenorhabditis elegans. Here we identify a role for a fourth bHLH, the Neurogenin NGN-1, in this process, raising the question of why so many neural bHLHs are required for a single neuronal specification event. Using quantitative imaging we show that the combined action of different bHLHs is needed to activate the correct level of expression of the terminal selector transcription factors TTX-3 and CEH-10 that subsequently initiate and maintain the expression of a large battery of terminal differentiation genes. Surprisingly, the different bHLHs have an antagonistic effect on another target, the proapoptotic BH3-only factor EGL-1, normally not expressed in AIY and otherwise detrimental for its specification. We propose that the use of multiple neural bHLHs allows robust neuronal specification while, at the same time, preventing spurious activation of deleterious genes. Summary: During neuronal specification, the combined action of several neural bHLHs ensures the robust activation of terminal selector transcription factor expression and prevents the activation of deleterious genes.
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Affiliation(s)
| | - Carole Couillault
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille 13009, France
| | - Vincent Bertrand
- Aix Marseille Univ, CNRS, IBDM, Turing Center for Living Systems, Marseille 13009, France
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29
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Ceballos A, Esse R, Grishok A. The proline-rich domain of MML-1 is biologically important but not required for localization to target promoters. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 34778725 PMCID: PMC8579147 DOI: 10.17912/micropub.biology.000498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 11/22/2022]
Abstract
The only representative of the MYC superfamily transcription factors in C. elegans, MML-1 (Myc and Mondo-like 1), was shown to promote extended lifespan in a variety of models and to regulate some aspects of C. elegans development. This previous research did not involve molecular characterization of MML-1. Here we use available mml-1 mutant alleles and other reagents to demonstrate that MML-1 is modified by O-GlcNAc, binds to promoters of some genes directly regulated by the DOT-1.1 histone methyltransferase complex, and has a role in promoting neuronal migration. Surprisingly, we found that the deletion allele mml-1(ok849), which was considered a null, produces an internally truncated protein resulting from an in-frame deletion. Localization of this truncated product to MML-1 target promoters was not impaired. The deleted region of MML-1 is proline-rich, and its function is poorly understood in mammalian homologs of MML-1. Based on our work and previously published data we conclude that the internal proline-rich region of MML-1 is dispensable for DNA binding but is biologically important.
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Affiliation(s)
- Ainhoa Ceballos
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.,Present affiliation: Oncology Genomics Department, Diagnostica Longwood S.L. 50011 Zaragoza, Spain
| | - Ruben Esse
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.,Present affiliation: Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Alla Grishok
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.,Present affiliation: Boston University School of Medicine, Department of Biochemistry, Genome Science Institute, Boston, MA 02118, USA
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30
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Littleford HE, Kiontke K, Fitch DHA, Greenwald I. hlh-12, a gene that is necessary and sufficient to promote migration of gonadal regulatory cells in Caenorhabditis elegans, evolved within the Caenorhabditis clade. Genetics 2021; 219:iyab127. [PMID: 34740245 PMCID: PMC8570790 DOI: 10.1093/genetics/iyab127] [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: 05/24/2021] [Accepted: 07/30/2021] [Indexed: 11/12/2022] Open
Abstract
Specialized cells of the somatic gonad primordium of nematodes play important roles in the final form and function of the mature gonad. Caenorhabditis elegans hermaphrodites are somatic females that have a two-armed, U-shaped gonad that connects to the vulva at the midbody. The outgrowth of each gonad arm from the somatic gonad primordium is led by two female distal tip cells (fDTCs), while the anchor cell (AC) remains stationary and central to coordinate uterine and vulval development. The bHLH protein HLH-2 and its dimerization partners LIN-32 and HLH-12 had previously been shown to be required for fDTC specification. Here, we show that ectopic expression of both HLH-12 and LIN-32 in cells with AC potential transiently transforms them into fDTC-like cells. Furthermore, hlh-12 was known to be required for the fDTCs to sustain gonad arm outgrowth. Here, we show that ectopic expression of HLH-12 in the normally stationary AC causes displacement from its normal position and that displacement likely results from activation of the leader program of fDTCs because it requires genes necessary for gonad arm outgrowth. Thus, HLH-12 is both necessary and sufficient to promote gonadal regulatory cell migration. As differences in female gonadal morphology of different nematode species reflect differences in the fate or migratory properties of the fDTCs or of the AC, we hypothesized that evolutionary changes in the expression of hlh-12 may underlie the evolution of such morphological diversity. However, we were unable to identify an hlh-12 ortholog outside of Caenorhabditis. Instead, by performing a comprehensive phylogenetic analysis of all Class II bHLH proteins in multiple nematode species, we found that hlh-12 evolved within the Caenorhabditis clade, possibly by duplicative transposition of hlh-10. Our analysis suggests that control of gene regulatory hierarchies for gonadogenesis can be remarkably plastic during evolution without adverse phenotypic consequence.
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Affiliation(s)
- Hana E Littleford
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Karin Kiontke
- Department of Biology, Center for Developmental Genetics, New York University, New York, NY 10003, USA
| | - David H A Fitch
- Department of Biology, Center for Developmental Genetics, New York University, New York, NY 10003, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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31
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Cook SJ, Vidal B, Hobert O. The bHLH-PAS gene hlh-34 is expressed in the AVH, not AVJ interneurons. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000467. [PMID: 34604715 PMCID: PMC8479555 DOI: 10.17912/micropub.biology.000467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022]
Abstract
Single neuron-specific drivers are important tools for visualizing neuron anatomy, manipulating neuron activity and gene rescue experiments. We report here that genomic regions upstream of the C. elegans bHLH-PAS gene hlh-34 can be used to drive gene expression exclusively in the AVH interneuron pair and not, as previously reported, the AVJ interneuron pair.
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Affiliation(s)
- Steven J. Cook
- Columbia University, Department of Biological Sciences, HHMI, New York, NY
| | - Berta Vidal
- Columbia University, Department of Biological Sciences, HHMI, New York, NY
| | - Oliver Hobert
- Columbia University, Department of Biological Sciences, HHMI, New York, NY,
Correspondence to: Oliver Hobert ()
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32
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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33
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Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM. Molecular topography of an entire nervous system. Cell 2021; 184:4329-4347.e23. [PMID: 34237253 DOI: 10.1016/j.cell.2021.06.023] [Citation(s) in RCA: 274] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/09/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses distinct codes of ∼23 neuropeptide genes and ∼36 neuropeptide receptors, delineating a complex and expansive "wireless" signaling network. To demonstrate the utility of this comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression and (2) reveal adhesion proteins with potential roles in process placement and synaptic specificity. Our expression data are available at https://cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity, and function throughout the C. elegans nervous system.
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Affiliation(s)
- Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Alexis Weinreb
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Alec Barrett
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Chuan Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Erdem Varol
- Department of Statistics, Columbia University, New York, NY, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Lori Glenwinkel
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Abigail Poff
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Manasa Basavaraju
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Steven J Cook
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Alexander Abrams
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Berta Vidal
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Cyril Cros
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Marc Hammarlund
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA.
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34
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Dall KB, Havelund JF, Harvald EB, Witting M, Færgeman NJ. HLH-30-dependent rewiring of metabolism during starvation in C. elegans. Aging Cell 2021; 20:e13342. [PMID: 33724708 PMCID: PMC8045935 DOI: 10.1111/acel.13342] [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: 01/06/2020] [Revised: 02/08/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
One of the most fundamental challenges for all living organisms is to sense and respond to alternating nutritional conditions in order to adapt their metabolism and physiology to promote survival and achieve balanced growth. Here, we applied metabolomics and lipidomics to examine temporal regulation of metabolism during starvation in wild‐type Caenorhabditis elegans and in animals lacking the transcription factor HLH‐30. Our findings show for the first time that starvation alters the abundance of hundreds of metabolites and lipid species in a temporal‐ and HLH‐30‐dependent manner. We demonstrate that premature death of hlh‐30 animals under starvation can be prevented by supplementation of exogenous fatty acids, and that HLH‐30 is required for complete oxidation of long‐chain fatty acids. We further show that RNAi‐mediated knockdown of the gene encoding carnitine palmitoyl transferase I (cpt‐1) only impairs survival of wild‐type animals and not of hlh‐30 animals. Strikingly, we also find that compromised generation of peroxisomes by prx‐5 knockdown renders hlh‐30 animals hypersensitive to starvation, which cannot be rescued by supplementation of exogenous fatty acids. Collectively, our observations show that mitochondrial functions are compromised in hlh‐30 animals and that hlh‐30 animals rewire their metabolism to largely depend on functional peroxisomes during starvation, underlining the importance of metabolic plasticity to maintain survival.
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Affiliation(s)
- Kathrine B. Dall
- Department of Biochemistry and Molecular Biology Villum Center for Bioanalytical Sciences University of Southern Denmark Odense M Denmark
| | - Jesper F. Havelund
- Department of Biochemistry and Molecular Biology Villum Center for Bioanalytical Sciences University of Southern Denmark Odense M Denmark
| | - Eva B. Harvald
- Department of Biochemistry and Molecular Biology Villum Center for Bioanalytical Sciences University of Southern Denmark Odense M Denmark
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry Helmholtz Zentrum München Neuherberg Germany
- Metabolomics and Proteomics Core Helmholtz Zentrum München Neuherberg Germany
- Chair of Analytical Food Chemistry Technische Universität München Freising Germany
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology Villum Center for Bioanalytical Sciences University of Southern Denmark Odense M Denmark
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35
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Haeussler S, Yeroslaviz A, Rolland SG, Luehr S, Lambie EJ, Conradt B. Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. G3-GENES GENOMES GENETICS 2021; 11:6204483. [PMID: 33784383 PMCID: PMC8495942 DOI: 10.1093/g3journal/jkab095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/18/2021] [Indexed: 01/22/2023]
Abstract
Mitochondrial dynamics plays an important role in mitochondrial quality control and the adaptation of metabolic activity in response to environmental changes. The disruption of mitochondrial dynamics has detrimental consequences for mitochondrial and cellular homeostasis and leads to the activation of the mitochondrial unfolded protein response (UPRmt), a quality control mechanism that adjusts cellular metabolism and restores homeostasis. To identify genes involved in the induction of UPRmt in response to a block in mitochondrial fusion, we performed a genome-wide RNAi screen in Caenorhabditis elegans mutants lacking the gene fzo-1, which encodes the ortholog of mammalian Mitofusin, and identified 299 suppressors and 86 enhancers. Approximately 90% of these 385 genes are conserved in humans, and one third of the conserved genes have been implicated in human disease. Furthermore, many have roles in developmental processes, which suggests that mitochondrial function and the response to stress are defined during development and maintained throughout life. Our dataset primarily contains mitochondrial enhancers and non-mitochondrial suppressors of UPRmt, indicating that the maintenance of mitochondrial homeostasis has evolved as a critical cellular function, which, when disrupted, can be compensated for by many different cellular processes. Analysis of the subsets 'non-mitochondrial enhancers' and 'mitochondrial suppressors' suggests that organellar contact sites, especially between the ER and mitochondria, are of importance for mitochondrial homeostasis. In addition, we identified several genes involved in IP3 signaling that modulate UPRmt in fzo-1 mutants and found a potential link between pre-mRNA splicing and UPRmt activation.
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Affiliation(s)
- Simon Haeussler
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Assa Yeroslaviz
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Planegg-Martinsried, Germany
| | - Stéphane G Rolland
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, South Korea
| | - Sebastian Luehr
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Eric J Lambie
- Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Barbara Conradt
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Center for Integrated Protein Science, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Research Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6AP, United Kingdom
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36
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Li Y, Ding W, Li CY, Liu Y. HLH-11 modulates lipid metabolism in response to nutrient availability. Nat Commun 2020; 11:5959. [PMID: 33235199 PMCID: PMC7686365 DOI: 10.1038/s41467-020-19754-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
The ability of organisms to sense nutrient availability and tailor their metabolic states to withstand nutrient deficiency is critical for survival. To identify previously unknown regulators that couple nutrient deficiency to body fat utilization, we performed a cherry-picked RNAi screen in C. elegans and found that the transcription factor HLH-11 regulates lipid metabolism in response to food availability. In well-fed worms, HLH-11 suppresses transcription of lipid catabolism genes. Upon fasting, the HLH-11 protein level is reduced through lysosome- and proteasome-mediated degradation, thus alleviating the inhibitory effect of HLH-11, activating the transcription of lipid catabolism genes, and utilizing fat. Additionally, lipid profiling revealed that reduction in the HLH-11 protein level remodels the lipid landscape in C. elegans. Moreover, TFAP4, the mammalian homolog of HLH-11, plays an evolutionarily conserved role in regulating lipid metabolism in response to starvation. Thus, TFAP4 may represent a potential therapeutic target for lipid storage disorders. Organismal metabolism fluctuates depending on nutritional conditions. Here, the authors show that, in C. elegans, HLH-11 negatively regulates lipid metabolism genes in the presence of nutrients and that its abundance decreased in response to starvation, thereby promoting fat utilization.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, 100871, Beijing, China
| | - Ying Liu
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, 100871, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China. .,Beijing Advanced Innovation Center for Genomics, Peking University, 100871, Beijing, China.
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37
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The Conserved ASCL1/MASH-1 Ortholog HLH-3 Specifies Sex-Specific Ventral Cord Motor Neuron Fate in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:4201-4213. [PMID: 32973001 PMCID: PMC7642948 DOI: 10.1534/g3.120.401458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neural specification is regulated by one or many transcription factors that control expression of effector genes that mediate function and determine neuronal type. Here we identify a novel role for one conserved proneural factor, the bHLH protein HLH-3, implicated in the specification of sex-specific ventral cord motor neurons in C. elegans. Proneural genes act in early stages of neurogenesis in early progenitors, but here, we demonstrate a later role for hlh-3. First, we document that differentiation of the ventral cord type C motor neuron class (VC) within their neuron class, is dynamic in time and space. Expression of VC class-specific and subclass-specific identity genes is distinct through development and is dependent on the VC position along the A-P axis and their proximity to the vulva. Our characterization of the expression of VC class and VC subclass-specific differentiation markers in the absence of hlh-3 function reveals that VC fate specification, differentiation, and morphology requires hlh-3 function. Finally, we conclude that hlh-3 cell-autonomously specifies VC cell fate.
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38
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Littlejohn NK, Seban N, Liu CC, Srinivasan S. A feedback loop governs the relationship between lipid metabolism and longevity. eLife 2020; 9:58815. [PMID: 33078707 PMCID: PMC7575325 DOI: 10.7554/elife.58815] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022] Open
Abstract
The relationship between lipid metabolism and longevity remains unclear. Although fat oxidation is essential for weight loss, whether it remains beneficial when sustained for long periods, and the extent to which it may attenuate or augment lifespan remain important unanswered questions. Here, we develop an experimental handle in the Caenorhabditis elegans model system, in which we uncover the mechanisms that connect long-term fat oxidation with longevity. We find that sustained β-oxidation via activation of the conserved triglyceride lipase ATGL-1, triggers a feedback transcriptional loop that involves the mito-nuclear transcription factor ATFS-1, and a previously unknown and highly conserved repressor of ATGL-1 called HLH-11/AP4. This feedback loop orchestrates the dual control of fat oxidation and lifespan, and shields the organism from life-shortening mitochondrial stress in the face of continuous fat oxidation. Thus, we uncover one mechanism by which fat oxidation can be sustained for long periods without deleterious effects on longevity.
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Affiliation(s)
- Nicole K Littlejohn
- Department of Neuroscience and The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States
| | - Nicolas Seban
- Department of Neuroscience and The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States
| | - Chung-Chih Liu
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, United States
| | - Supriya Srinivasan
- Department of Neuroscience and The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States
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39
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Abstract
Sexual interactions negatively impact health and longevity in many species across the animal kingdom. C. elegans has been established as a good model to study how mating and intense sexual interactions influence longevity of the individuals. In this chapter, we review the most recent discoveries in this field. We first describe the phenotypes caused by intense mating, including shrinking, fat loss, and glycogen loss. We then describe three major mechanisms underlying mating-induced killing: germline activation, seminal fluid transfer, and male pheromone-mediated toxicity. Next, we summarize the current knowledge of genetic pathways involved in regulating mating-induced death, including DAF-9/DAF-12 steroid signaling, Insulin/IGF-1 signaling (IIS), and TOR signaling. Finally, we discuss the possible fitness benefits of mating-induced death. Throughout this review, we compare and contrast mating-induced death between the sexes and among different species in an effort to discuss this phenomenon and underlying mechanisms from the evolutionary perspective. Further investigation using mated C. elegans will improve our understanding of sexual antagonism, as well as the coordination between reproduction and somatic longevity in response to various external signals. Due to the evolutionary conservation in many aspects of mating-induced death, what we learn from a short-lived mated worm could provide new strategies to improve our own fitness and longevity.
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Affiliation(s)
- Cheng Shi
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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40
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Majidi SP, Reddy NC, Moore MJ, Chen H, Yamada T, Andzelm MM, Cherry TJ, Hu LS, Greenberg ME, Bonni A. Chromatin Environment and Cellular Context Specify Compensatory Activity of Paralogous MEF2 Transcription Factors. Cell Rep 2020; 29:2001-2015.e5. [PMID: 31722213 PMCID: PMC6874310 DOI: 10.1016/j.celrep.2019.10.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/04/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Compensation among paralogous transcription factors (TFs) confers genetic robustness of cellular processes, but how TFs dynamically respond to paralog depletion on a genome-wide scale in vivo remains incompletely understood. Using single and double conditional knockout of myocyte enhancer factor 2 (MEF2) family TFs in granule neurons of the mouse cerebellum, we find that MEF2A and MEF2D play functionally redundant roles in cerebellar-dependent motor learning. Although both TFs are highly expressed in granule neurons, transcriptomic analyses show MEF2D is the predominant genomic regulator of gene expression in vivo. Strikingly, genome-wide occupancy analyses reveal upon depletion of MEF2D, MEF2A occupancy robustly increases at a subset of sites normally bound to MEF2D. Importantly, sites experiencing compensatory MEF2A occupancy are concentrated within open chromatin and undergo functional compensation for genomic activation and gene expression. Finally, motor activity induces a switch from non-compensatory to compensatory MEF2-dependent gene regulation. These studies uncover genome-wide functional interdependency between paralogous TFs in the brain. Majidi et al. study how transcription factors respond to paralog depletion by conditionally depleting MEF2A and MEF2D in mouse cerebellum. Depletion of MEF2D induces functionally compensatory genomic occupancy by MEF2A. Compensation occurs within accessible chromatin in a context-dependent manner. This study explores the interdependency between paralogous transcription factors.
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Affiliation(s)
- Shahriyar P Majidi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; MD-PhD Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Naveen C Reddy
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hao Chen
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Milena M Andzelm
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy J Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9(th) Ave., Seattle, WA 98101, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda S Hu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA.
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41
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cnd-1/NeuroD1 Functions with the Homeobox Gene ceh-5/Vax2 and Hox Gene ceh-13/labial To Specify Aspects of RME and DD Neuron Fate in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:3071-3085. [PMID: 32601060 PMCID: PMC7466980 DOI: 10.1534/g3.120.401515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Identifying the mechanisms behind neuronal fate specification are key to understanding normal neural development in addition to neurodevelopmental disorders such as autism and schizophrenia. In vivo cell fate specification is difficult to study in vertebrates. However, the nematode Caenorhabditis elegans, with its invariant cell lineage and simple nervous system of 302 neurons, is an ideal organism to explore the earliest stages of neural development. We used a comparative transcriptome approach to examine the role of cnd-1/NeuroD1 in C. elegans nervous system development and function. This basic helix-loop-helix transcription factor is deeply conserved across phyla and plays a crucial role in cell fate specification in both the vertebrate nervous system and pancreas. We find that cnd-1 controls expression of ceh-5, a Vax2-like homeobox class transcription factor, in the RME head motorneurons and PVQ tail interneurons. We also show that cnd-1 functions redundantly with the Hox gene ceh-13/labial in defining the fate of DD1 and DD2 embryonic ventral nerve cord motorneurons. These data highlight the utility of comparative transcriptomes for identifying transcription factor targets and understanding gene regulatory networks.
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42
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Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML. A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell Rep 2020; 27:955-970.e7. [PMID: 30995488 PMCID: PMC6485956 DOI: 10.1016/j.celrep.2019.03.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/04/2019] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation. Combinatorial regulation by transcription factors (TFs) is one mechanism for achieving condition and tissue-specific gene regulation. Shokri et al. mapped TF-TF interactions between most Drosophila TFs, reporting a comprehensive TF-TF network integrated with previously known interactions. They used this network to discern distinct TF-DNA binding modes.
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Affiliation(s)
- Leila Shokri
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sachi Inukai
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Antonina Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Kathryn Weinand
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA
| | - Korneel Hens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anastasia Vedenko
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen S Gisselbrecht
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Johannes Bischof
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Edy Furger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Jean-Daniel Feuz
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martha L Bulyk
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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43
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Christensen EL, Beasley A, Radchuk J, Mielko ZE, Preston E, Stuckett S, Murray JI, Hudson ML. ngn-1/neurogenin Activates Transcription of Multiple Terminal Selector Transcription Factors in the Caenorhabditis elegans Nervous System. G3 (BETHESDA, MD.) 2020; 10:1949-1962. [PMID: 32273286 PMCID: PMC7263688 DOI: 10.1534/g3.120.401126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/30/2020] [Indexed: 11/18/2022]
Abstract
Proper nervous system development is required for an organism's survival and function. Defects in neurogenesis have been linked to neurodevelopmental disorders such as schizophrenia and autism. Understanding the gene regulatory networks that orchestrate neural development, specifically cascades of proneural transcription factors, can better elucidate which genes are most important during early neurogenesis. Neurogenins are a family of deeply conserved factors shown to be both necessary and sufficient for the development of neural subtypes. However, the immediate downstream targets of neurogenin are not well characterized. The objective of this study was to further elucidate the role of ngn-1/neurogenin in nervous system development and to identify its downstream transcriptional targets, using the nematode Caenorhabditis elegans as a model for this work. We found that ngn-1 is required for axon outgrowth, nerve ring architecture, and neuronal cell fate specification. We also showed that ngn-1 may have roles in neuroblast migration and epithelial integrity during embryonic development. Using RNA sequencing and comparative transcriptome analysis, we identified eight transcription factors (hlh-34/NPAS1, unc-42/PROP1, ceh-17/PHOX2A, lim-4/LHX6, fax-1/NR2E3, lin-11/LHX1, tlp-1/ZNF503, and nhr-23/RORB) whose transcription is activated, either directly or indirectly, by ngn-1 Our results show that ngn-1 has a role in transcribing known terminal regulators that establish and maintain cell fate of differentiated neural subtypes and confirms that ngn-1 functions as a proneural transcription factor in C. elegans neurogenesis.
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Affiliation(s)
- Elyse L Christensen
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144
| | - Alexandra Beasley
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144
| | - Jessica Radchuk
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144
| | - Zachery E Mielko
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144
| | - Elicia Preston
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Sidney Stuckett
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144
| | - John I Murray
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Martin L Hudson
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144
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44
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Foster JM, Grote A, Mattick J, Tracey A, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A, Holroyd N, Korlach J, Li Y, Libro S, Lustigman S, Michalski ML, Paulini M, Rogers MB, Teigen L, Twaddle A, Welch L, Berriman M, Dunning Hotopp JC, Ghedin E. Sex chromosome evolution in parasitic nematodes of humans. Nat Commun 2020; 11:1964. [PMID: 32327641 PMCID: PMC7181701 DOI: 10.1038/s41467-020-15654-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/20/2020] [Indexed: 11/09/2022] Open
Abstract
Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.
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Affiliation(s)
- Jeremy M Foster
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Alexandra Grote
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - John Mattick
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Matthew Chung
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Adam Geber
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Yichao Li
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Silvia Libro
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Michelle L Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Matthew B Rogers
- Department of Surgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, 15224, USA
| | - Laura Teigen
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Alan Twaddle
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julie C Dunning Hotopp
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
- Department of Epidemiology, School of Global Public Health, New York University, New York, NY, 10003, USA.
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45
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Rozanov L, Ravichandran M, Grigolon G, Zanellati MC, Mansfeld J, Zarse K, Barzilai N, Atzmon G, Fischer F, Ristow M. Redox-mediated regulation of aging and healthspan by an evolutionarily conserved transcription factor HLH-2/Tcf3/E2A. Redox Biol 2020; 32:101448. [PMID: 32203922 PMCID: PMC7096751 DOI: 10.1016/j.redox.2020.101448] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/02/2020] [Indexed: 02/08/2023] Open
Abstract
Physiological aging is a complex process, influenced by a plethora of genetic and environmental factors. While being far from fully understood, a number of common aging hallmarks have been elucidated in recent years. Among these, transcriptomic alterations are hypothesized to represent a crucial early manifestation of aging. Accordingly, several transcription factors (TFs) have previously been identified as important modulators of lifespan in evolutionarily distant model organisms. Based on a set of TFs conserved between nematodes, zebrafish, mice, and humans, we here perform a RNA interference (RNAi) screen in C. elegans to discover evolutionarily conserved TFs impacting aging. We identify a basic helix-loop-helix TF, named HLH-2 in nematodes (Tcf3/E2A in mammals), to exert a pronounced lifespan-extending effect in C. elegans upon impairment. We further show that its impairment impacts cellular energy metabolism, increases parameters of healthy aging, and extends nematodal lifespan in a ROS-dependent manner. We then identify arginine kinases, orthologues of mammalian creatine kinases, as a target of HLH-2 transcriptional regulation, serving to mediate the healthspan-promoting effects observed upon impairment of hlh-2 expression. Consistently, HLH-2 is shown to epistatically interact with core components of known lifespan-regulating pathways, i.e. AAK-2/AMPK and LET-363/mTOR, as well as the aging-related TFs SKN-1/Nrf2 and HSF-1. Lastly, single-nucelotide polymorphisms (SNPs) in Tcf3/E2A are associated with exceptional longevity in humans. Together, these findings demonstrate that HLH-2 regulates energy metabolism via arginine kinases and thereby affects the aging phenotype dependent on ROS-signaling and established canonical effectors. A C. elegans RNAi screen identifies conserved aging-related transcription factors. Impairment of transcription factor hlh-2 has the most pronounced effect on lifespan. C. elegans HLH-2 affects cellular energy homeostasis and redox signaling. HLH-2 modulates arginine kinase to interact with downstream longevity pathways. Polymorphisms (SNPs) in the hlh-2 orthologue Tcf3/E2A are linked to human longevity.
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Affiliation(s)
- Leonid Rozanov
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Meenakshi Ravichandran
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Maria Clara Zanellati
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Johannes Mansfeld
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Kim Zarse
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Nir Barzilai
- Albert Einstein College of Medicine, Departments of Genetics and of Medicine, Bronx, NY, 10461, USA
| | - Gil Atzmon
- Albert Einstein College of Medicine, Departments of Genetics and of Medicine, Bronx, NY, 10461, USA; University of Haifa, Faculty of Natural Sciences, Haifa, 3498838, Israel
| | - Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.
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46
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Franco-Juárez B, Mejía-Martínez F, Moreno-Arriola E, Hernández-Vázquez A, Gómez-Manzo S, Marcial-Quino J, Arreguín-Espinosa R, Velázquez-Arellano A, Ortega-Cuellar D. A high glucose diet induces autophagy in a HLH-30/TFEB-dependent manner and impairs the normal lifespan of C. elegans. Aging (Albany NY) 2019; 10:2657-2667. [PMID: 30299269 PMCID: PMC6224263 DOI: 10.18632/aging.101577] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/24/2018] [Indexed: 12/27/2022]
Abstract
A high-glucose diet (HGD) is associated with the development of metabolic diseases that decrease life expectancy, including obesity and type-2 diabetes (T2D); however, the mechanism through which a HGD does so is still unclear. Autophagy, an evolutionarily conserved mechanism, has been shown to promote both cell and organismal survival. The goal of this study was to determine whether exposure of Caenorhabditis elegans to a HGD affects autophagy and thus contributes to the observed lifespan reduction under a HGD. Unexpectedly, nematodes exposed to a HGD showed increased autophagic flux via an HLH-30/TFEB-dependent mechanism because animals with loss of HLH-30/TFEB, even those with high glucose exposure, had an extended lifespan, suggesting that HLH-30/TFEB might have detrimental effects on longevity through autophagy under this stress condition. Interestingly, pharmacological treatment with okadaic acid, an inhibitor of the PP2A and PP1 protein phosphatases, blocked HLH-30 nuclear translocation, but not TAX-6/calcineurin suppression by RNAi, during glucose exposure. Together, our data support the suggested dual role of HLH-30/TFEB and autophagy, which, depending on the cellular context, may promote either organismal survival or death.
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Affiliation(s)
- Berenice Franco-Juárez
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas UNAM - Instituto Nacional de Pediatría, Mexico City 04530, Mexico
| | - Fanny Mejía-Martínez
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
| | - Elizabeth Moreno-Arriola
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas UNAM - Instituto Nacional de Pediatría, Mexico City 04530, Mexico
| | - Alain Hernández-Vázquez
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas UNAM - Instituto Nacional de Pediatría, Mexico City 04530, Mexico
| | - Saul Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
| | - Jaime Marcial-Quino
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
| | - Roberto Arreguín-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico
| | - Antonio Velázquez-Arellano
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas UNAM - Instituto Nacional de Pediatría, Mexico City 04530, Mexico
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico
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47
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Dall KB, Færgeman NJ. Metabolic regulation of lifespan from a C. elegans perspective. GENES & NUTRITION 2019; 14:25. [PMID: 31428207 PMCID: PMC6694653 DOI: 10.1186/s12263-019-0650-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Decline of cellular functions especially cognitive is a major deficit that arises with age in humans. Harnessing the strengths of small and genetic tractable model systems has revealed key conserved regulatory biochemical and signaling pathways that control aging. Here, we review some of the key signaling and biochemical pathways that coordinate aging processes with special emphasis on Caenorhabditis elegans as a model system and discuss how nutrients and metabolites can regulate lifespan by coordinating signaling and epigenetic programs. We focus on central nutrient-sensing pathways such as mTOR and insulin/insulin-like growth factor signaling and key transcription factors including the conserved basic helix-loop-helix transcription factor HLH-30/TFEB.
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Affiliation(s)
- Kathrine B. Dall
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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48
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Yang W, Petersen C, Pees B, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C, Schulenburg H. The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. Front Microbiol 2019; 10:1793. [PMID: 31440221 PMCID: PMC6693516 DOI: 10.3389/fmicb.2019.01793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
The biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiota affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode Caenorhabditis elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiota. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiota and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiota members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes, the affected functions, and ELT-2 target genes. Our analysis further identified a core set of 86 genes that consistently responded to the microbiota members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiota isolates on C. elegans life history and thereby provide a framework for further analysis of microbiota-mediated host functions.
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Affiliation(s)
- Wentao Yang
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Barbara Pees
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Silvio Waschina
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philipp Dirksen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Research Group Proteomics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Matthias Leippe
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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49
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Lee J, Taylor CA, Barnes KM, Shen A, Stewart EV, Chen A, Xiang YK, Bao Z, Shen K. A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes. eLife 2019; 8:e46703. [PMID: 31386623 PMCID: PMC6684318 DOI: 10.7554/elife.46703] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
Cellular differentiation requires both activation of target cell transcriptional programs and repression of non-target cell programs. The Myt1 family of zinc finger transcription factors contributes to fibroblast to neuron reprogramming in vitro. Here, we show that ztf-11 (Zinc-finger Transcription Factor-11), the sole Caenorhabditis elegans Myt1 homolog, is required for neurogenesis in multiple neuronal lineages from previously differentiated epithelial cells, including a neuron generated by a developmental epithelial-to-neuronal transdifferentiation event. ztf-11 is exclusively expressed in all neuronal precursors with remarkable specificity at single-cell resolution. Loss of ztf-11 leads to upregulation of non-neuronal genes and reduced neurogenesis. Ectopic expression of ztf-11 in epidermal lineages is sufficient to produce additional neurons. ZTF-11 functions together with the MuvB corepressor complex to suppress the activation of non-neuronal genes in neurons. These results dovetail with the ability of Myt1l (Myt1-like) to drive neuronal transdifferentiation in vitro in vertebrate systems. Together, we identified an evolutionarily conserved mechanism to specify neuronal cell fate by repressing non-neuronal genes.
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Affiliation(s)
- Joo Lee
- Department of BiochemistryStanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Caitlin A Taylor
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
| | | | - Ao Shen
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | | | - Allison Chen
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Yang K Xiang
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | - Zhirong Bao
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
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50
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Defoort J, Van de Peer Y, Vermeirssen V. Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. Nucleic Acids Res 2019; 46:6480-6503. [PMID: 29873777 PMCID: PMC6061849 DOI: 10.1093/nar/gky468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/14/2018] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein–protein, genetic and homologous interactions, and directed protein–DNA, regulatory and miRNA–mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similar modules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.
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Affiliation(s)
- Jonas Defoort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Vanessa Vermeirssen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
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