1
|
Hatch HAM, Belalcazar HM, Marshall OJ, Secombe J. A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. eLife 2021; 10:63886. [PMID: 33729157 PMCID: PMC7997662 DOI: 10.7554/elife.63886] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding their spatiotemporal requirements or neurodevelopmental contributions. Utilizing the mushroom body (MB), a major learning and memory center within the Drosophila brain, we demonstrate that KDM5 is required within ganglion mother cells and immature neurons for proper axogenesis. Moreover, the mechanism by which KDM5 functions in this context is independent of its canonical histone demethylase activity. Using in vivo transcriptional and binding analyses, we identify a network of genes directly regulated by KDM5 that are critical modulators of neurodevelopment. We find that KDM5 directly regulates the expression of prospero, a transcription factor that we demonstrate is essential for MB morphogenesis. Prospero functions downstream of KDM5 and binds to approximately half of KDM5-regulated genes. Together, our data provide evidence for a KDM5-Prospero transcriptional axis that is essential for proper MB development.
Collapse
Affiliation(s)
- Hayden AM Hatch
- Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine, Bronx, United States
| | - Helen M Belalcazar
- Department of Genetics Albert Einstein College of Medicine, Bronx, United States
| | - Owen J Marshall
- Menzies Institute for Medical Research University of Tasmania, Hobart, Australia
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine, Bronx, United States.,Department of Genetics Albert Einstein College of Medicine, Bronx, United States
| |
Collapse
|
2
|
Bravo González‐Blas C, Quan X, Duran‐Romaña R, Taskiran II, Koldere D, Davie K, Christiaens V, Makhzami S, Hulselmans G, de Waegeneer M, Mauduit D, Poovathingal S, Aibar S, Aerts S. Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics. Mol Syst Biol 2020; 16:e9438. [PMID: 32431014 PMCID: PMC7237818 DOI: 10.15252/msb.20209438] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 01/02/2023] Open
Abstract
Single-cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type-specific enhancers, we deconvolute cell type-specific effects of bulk-derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.
Collapse
Affiliation(s)
| | - Xiao‐Jiang Quan
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Duygu Koldere
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Valerie Christiaens
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Samira Makhzami
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Maxime de Waegeneer
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - David Mauduit
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | | | - Sara Aibar
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| | - Stein Aerts
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Department of Human GeneticsKU LeuvenLeuvenBelgium
| |
Collapse
|
3
|
Guo P, Lee CH, Lei H, Zheng Y, Pulgar Prieto KD, Pan D. Nerfin-1 represses transcriptional output of Hippo signaling in cell competition. eLife 2019; 8:38843. [PMID: 30901309 PMCID: PMC6430605 DOI: 10.7554/elife.38843] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 02/25/2019] [Indexed: 12/29/2022] Open
Abstract
The Hippo tumor suppressor pathway regulates tissue growth in Drosophila by restricting the activity of the transcriptional coactivator Yorkie (Yki), which normally complexes with the TEF/TEAD family DNA-binding transcription factor Scalloped (Sd) to drive the expression of growth-promoting genes. Given its pivotal role as a central hub in mediating the transcriptional output of Hippo signaling, there is great interest in understanding the molecular regulation of the Sd-Yki complex. In this study, we identify Nerfin-1 as a transcriptional repressor that antagonizes the activity of the Sd-Yki complex by binding to the TEA DNA-binding domain of Sd. Consistent with its biochemical function, ectopic expression of Nerfin-1 results in tissue undergrowth in an Sd-dependent manner. Conversely, loss of Nerfin-1 enhances the ability of winner cells to eliminate loser cells in multiple scenarios of cell competition. We further show that INSM1, the mammalian ortholog of Nerfin-1, plays a conserved role in repressing the activity of the TEAD-YAP complex. These findings reveal a novel regulatory mode converging on the transcriptional output of the Hippo pathway that may be exploited for modulating the YAP oncoprotein in cancer and regenerative medicine. Animals uses a range of mechanisms to stop their organs from growing once they have reached the right shape and size. One of these processes, a set of chemical messages called the Hippo pathway, controls the balance of cell death and cell division. In fruit flies, Hippo works by repressing a complex formed of two proteins, Yorkie and Scalloped, which normally switch genes on to encourage cells to grow. Yorkie is also involved in cell competition, a process in which cells in a tissue compare themselves to each other. Healthier ‘winner’ cells then kill neighboring ‘loser’ cells that are weaker or damaged. This ensures that the tissue keeps working properly. Despite Yorkie and Scalloped being key to control the growth and health of tissues, how the activity of these proteins is regulated was not well understood. To investigate, Guo et al. conducted a series experiments on fruit flies and found that a protein called Nerfin-1 can bind onto Scalloped to stop the Scalloped-Yorkie complex from switching on genes. As a result, flies with too much Nerfin-1 had stunted tissue growth. In addition, Guo et al. confirmed that the Nerfin-1 equivalent in mammals acts in the same way. Further work revealed that Nerfin-1 also plays a role in cell competition: without this protein, ‘winner’ cells became 'super winners', eliminating even more of the loser cells. Besides regulating the size of organs, the Hippo pathway is also involved in stopping cells from dividing uncontrollably and becoming cancerous. Further research may therefore focus on Nerfin-1 and its equivalent in mammals to understand how this protein could contribute to the emergence of cancer.
Collapse
Affiliation(s)
- Pengfei Guo
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chang-Hyun Lee
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Huiyan Lei
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yonggang Zheng
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Katiuska Daniela Pulgar Prieto
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| |
Collapse
|
4
|
Froldi F, Pachnis P, Szuperák M, Costas O, Fernando T, Gould AP, Cheng LY. Histidine is selectively required for the growth of Myc-dependent dedifferentiation tumours in the Drosophila CNS. EMBO J 2019; 38:embj.201899895. [PMID: 30804004 PMCID: PMC6443203 DOI: 10.15252/embj.201899895] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 01/09/2019] [Accepted: 01/16/2019] [Indexed: 12/31/2022] Open
Abstract
Rewired metabolism of glutamine in cancer has been well documented, but less is known about other amino acids such as histidine. Here, we use Drosophila cancer models to show that decreasing the concentration of histidine in the diet strongly inhibits the growth of mutant clones induced by loss of Nerfin‐1 or gain of Notch activity. In contrast, changes in dietary histidine have much less effect on the growth of wildtype neural stem cells and Prospero neural tumours. The reliance of tumours on dietary histidine and also on histidine decarboxylase (Hdc) depends upon their growth requirement for Myc. We demonstrate that Myc overexpression in nerfin‐1 tumours is sufficient to switch their mode of growth from histidine/Hdc sensitive to resistant. This study suggests that perturbations in histidine metabolism selectively target neural tumours that grow via a dedifferentiation process involving large cell size increases driven by Myc.
Collapse
Affiliation(s)
- Francesca Froldi
- Peter MacCallum Cancer Centre, Parkville, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | | | - Milán Szuperák
- Peter MacCallum Cancer Centre, Parkville, Vic., Australia.,Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Olivia Costas
- Peter MacCallum Cancer Centre, Parkville, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia
| | | | | | - Louise Y Cheng
- Peter MacCallum Cancer Centre, Parkville, Vic., Australia .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic., Australia.,The Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Vic., Australia
| |
Collapse
|
5
|
Stratmann J, Ekman H, Thor S. Branching gene regulatory network dictating different aspects of a neuronal cell identity. Development 2019; 146:dev.174300. [DOI: 10.1242/dev.174300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/22/2019] [Indexed: 12/30/2022]
Abstract
The nervous system displays a daunting cellular diversity. Neuronal sub-types differ from each other in several aspects, including their neurotransmitter expression and axon projection. These aspects can converge, but can also diverge, such that neurons expressing the same neurotransmitter may project axons to different targets. It is not well understood how regulatory programs converge/diverge to associate/dissociate different cell fate features. Studies of the Drosophila Tv1 neurons have identified a regulatory cascade; ladybird early -> collier -> apterous/eyes absent -> dimmed, which specifies Tv1 neurotransmitter expression. Here, we conduct genetic and transcriptome analysis to address how other aspects of Tv1 cell fate is governed. We find that an initiator terminal selector gene triggers a feedforward loop which branches into different subroutines, each of which establishes different features of this one unique neuronal cell fate.
Collapse
Affiliation(s)
- Johannes Stratmann
- Department of Clinical and Experimental Medicine, Linkoping University, SE-581 85 Linkoping, Sweden
| | - Helen Ekman
- Department of Clinical and Experimental Medicine, Linkoping University, SE-581 85 Linkoping, Sweden
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, SE-581 85 Linkoping, Sweden
- School of Biomedical Sciences, University of Queensland, St Lucia QLD 4072, Australia
| |
Collapse
|
6
|
The Scalloped and Nerfin-1 Transcription Factors Cooperate to Maintain Neuronal Cell Fate. Cell Rep 2018; 25:1561-1576.e7. [DOI: 10.1016/j.celrep.2018.10.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/14/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023] Open
|
7
|
Lin X, Wang F, Li Y, Zhai C, Wang G, Zhang X, Gao Y, Yi T, Sun D, Wu S. The SCF ubiquitin ligase Slimb controls Nerfin-1 turnover in Drosophila. Biochem Biophys Res Commun 2018; 495:629-633. [DOI: 10.1016/j.bbrc.2017.11.090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/13/2017] [Indexed: 12/14/2022]
|
8
|
Kavaler J, Duan H, Aradhya R, de Navas LF, Joseph B, Shklyar B, Lai EC. miRNA suppression of a Notch repressor directs non-neuronal fate in Drosophila mechanosensory organs. J Cell Biol 2017; 217:571-583. [PMID: 29196461 PMCID: PMC5800810 DOI: 10.1083/jcb.201706101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/12/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
Large-scale knockout studies suggest that most miRNAs are phenotypically dispensable. However, Kavaler et al. show here that developmental specification toward a non-neuronal fate in the Drosophila melanogaster peripheral sensory organ lineage depends critically on mir-279/996 repression of the Notch repressor Insensible. Although there is abundant evidence that individual microRNA (miRNA) loci repress large cohorts of targets, large-scale knockout studies suggest that most miRNAs are phenotypically dispensable. Here, we identify a rare case of developmental cell specification that is highly dependent on miRNA control of an individual target. We observe that binary cell fate choice in the Drosophila melanogaster peripheral sensory organ lineage is controlled by the non-neuronally expressed mir-279/996 cluster, with a majority of notum sensory organs exhibiting transformation of sheath cells into ectopic neurons. The mir-279/996 defect phenocopies Notch loss of function during the sheath–neuron cell fate decision, suggesting the miRNAs facilitate Notch signaling. Consistent with this, mir-279/996 knockouts are strongly enhanced by Notch heterozygosity, and activated nuclear Notch is impaired in the miRNA mutant. Although Hairless (H) is the canonical nuclear Notch pathway inhibitor, and H heterozygotes exhibit bristle cell fate phenotypes reflecting gain-of-Notch signaling, H/+ does not rescue mir-279/996 mutants. Instead, we identify Insensible (Insb), another neural nuclear Notch pathway inhibitor, as a critical direct miR-279/996 target. Insb is posttranscriptionally restricted to neurons by these miRNAs, and its heterozygosity strongly suppresses ectopic peripheral nervous system neurons in mir-279/996 mutants. Thus, proper assembly of multicellular mechanosensory organs requires a double-negative circuit involving miRNA-mediated suppression of a Notch repressor to assign non-neuronal cell fate.
Collapse
Affiliation(s)
| | - Hong Duan
- Department of Developmental Biology, Sloan-Kettering Institute, New York, NY
| | - Rajaguru Aradhya
- Department of Developmental Biology, Sloan-Kettering Institute, New York, NY
| | - Luis F de Navas
- Department of Developmental Biology, Sloan-Kettering Institute, New York, NY
| | - Brian Joseph
- Department of Developmental Biology, Sloan-Kettering Institute, New York, NY.,Gerstner Sloan-Kettering Graduate Program of Biomedical Sciences, New York, NY
| | - Boris Shklyar
- Department of Developmental Biology, Sloan-Kettering Institute, New York, NY
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, New York, NY .,Gerstner Sloan-Kettering Graduate Program of Biomedical Sciences, New York, NY
| |
Collapse
|
9
|
Cagirici HB, Biyiklioglu S, Budak H. Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly. FRONTIERS IN PLANT SCIENCE 2017; 8:1653. [PMID: 29038661 PMCID: PMC5630980 DOI: 10.3389/fpls.2017.01653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/08/2017] [Indexed: 05/23/2023]
Abstract
Wheat Stem Sawfly (WSS), Cephus Cinctus Norton (Hymenoptera: Cephidae), is one of the most important pests, causing yield and economic losses in wheat and barley. The lack of information about molecular mechanisms of WSS for defeating plant's resistance prevents application of effective pest control strategies therefore, it is essential to identify the genes and their regulators behind WSS infestations. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are recognized with their regulatory functions on gene expression, tuning protein production by controlling transcriptional and post-transcriptional activities. A transcriptome-guided approach was followed in order to identify miRNAs, lncRNAs, and mRNA of WSS, and their interaction networks. A total of 1,893 were presented here as differentially expressed between larva and adult WSS insects. There were 11 miRNA families detected in WSS transcriptome. Together with the annotation of 1,251 novel mRNAs, the amount of genetic information available for WSS was expanded. The network between WSS miRNAs, lncRNAs, and mRNAs suggested miRNA-mediated regulatory roles of lncRNAs as competing endogenous RNAs. In the light of the previous evidence that small RNA molecules of a pathogen could suppress the immune response of host plant, we analyzed the putative interactions between larvae and wheat at the miRNA level. Overall, this study provides a profile of larva and adult WSS life stages in terms of coding and non-coding elements. These findings also emphasize the potential roles of wheat and larval miRNAs in wheat resistance to infestation and in the suppression of resistance which is critical for the development of effective pest control strategies.
Collapse
Affiliation(s)
- Halise B. Cagirici
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Sezgi Biyiklioglu
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States
| |
Collapse
|
10
|
Xu J, Hao X, Yin MX, Lu Y, Jin Y, Xu J, Ge L, Wu W, Ho M, Yang Y, Zhao Y, Zhang L. Prevention of medulla neuron dedifferentiation by Nerfin-1 requires inhibition of Notch activity. Development 2017; 144:1510-1517. [PMID: 28242614 DOI: 10.1242/dev.141341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 02/17/2017] [Indexed: 11/20/2022]
Abstract
The Drosophila larval central nervous system comprises the central brain, ventral nerve cord and optic lobe. In these regions, neuroblasts (NBs) divide asymmetrically to self-renew and generate differentiated neurons or glia. To date, mechanisms of preventing neuron dedifferentiation are still unclear, especially in the optic lobe. Here, we show that the zinc-finger transcription factor Nerfin-1 is expressed in early-stage medulla neurons and is essential for maintaining their differentiation. Loss of Nerfin-1 activates Notch signaling, which promotes neuron-to-NB reversion. Repressing Notch signaling largely rescues dedifferentiation in nerfin-1 mutant clones. Thus, we conclude that Nerfin-1 represses Notch activity in medulla neurons and prevents them from dedifferentiation.
Collapse
Affiliation(s)
- Jiajun Xu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Xue Hao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Meng-Xin Yin
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Yi Lu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Yunyun Jin
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Jinjin Xu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Ling Ge
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Wenqing Wu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China
| | - Margaret Ho
- Department of Anatomy and Neurobiology, Tongji University, School of Medicine, Shanghai 200092, People's Republic of China
| | - Yingzi Yang
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Yun Zhao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, People's Republic of China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People's Republic of China .,School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, People's Republic of China
| |
Collapse
|
11
|
de Taffin M, Carrier Y, Dubois L, Bataillé L, Painset A, Le Gras S, Jost B, Crozatier M, Vincent A. Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks. PLoS One 2015. [PMID: 26204530 PMCID: PMC4512700 DOI: 10.1371/journal.pone.0133387] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles.
Collapse
Affiliation(s)
- Mathilde de Taffin
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Yannick Carrier
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Laurence Dubois
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Laetitia Bataillé
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Anaïs Painset
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
- Plate-forme bio-informatique Genotoul/MIA-T, INRA, Borde Rouge, 31326, Castanet-Tolosan, France
| | - Stéphanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, 67404, Illkirch, France
| | - Bernard Jost
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, 67404, Illkirch, France
| | - Michèle Crozatier
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Alain Vincent
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
- * E-mail:
| |
Collapse
|
12
|
Froldi F, Szuperak M, Weng CF, Shi W, Papenfuss AT, Cheng LY. The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells. Genes Dev 2015; 29:129-43. [PMID: 25593306 PMCID: PMC4298133 DOI: 10.1101/gad.250282.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Froldi et al. show that the Drosophila zinc finger transcription factor Nervous fingers 1 (Nerfin-1) locks neurons into differentiation, preventing their reversion into neuroblasts. The loss of Nerfin-1 causes reversion to multipotency and results in tumors in several neural lineages. RNA-seq and ChIP analysis show that Nerfin-1 administers its function by repression of self-renewing genes and activation of differentiation-specific genes. Cellular dedifferentiation is the regression of a cell from a specialized state to a more multipotent state and is implicated in cancer. However, the transcriptional network that prevents differentiated cells from reacquiring stem cell fate is so far unclear. Neuroblasts (NBs), the Drosophila neural stem cells, are a model for the regulation of stem cell self-renewal and differentiation. Here we show that the Drosophila zinc finger transcription factor Nervous fingers 1 (Nerfin-1) locks neurons into differentiation, preventing their reversion into NBs. Following Prospero-dependent neuronal specification in the ganglion mother cell (GMC), a Nerfin-1-specific transcriptional program maintains differentiation in the post-mitotic neurons. The loss of Nerfin-1 causes reversion to multipotency and results in tumors in several neural lineages. Both the onset and rate of neuronal dedifferentiation in nerfin-1 mutant lineages are dependent on Myc- and target of rapamycin (Tor)-mediated cellular growth. In addition, Nerfin-1 is required for NB differentiation at the end of neurogenesis. RNA sequencing (RNA-seq) and chromatin immunoprecipitation (ChIP) analysis show that Nerfin-1 administers its function by repression of self-renewing-specific and activation of differentiation-specific genes. Our findings support the model of bidirectional interconvertibility between neural stem cells and their post-mitotic progeny and highlight the importance of the Nerfin-1-regulated transcriptional program in neuronal maintenance.
Collapse
Affiliation(s)
- Francesca Froldi
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Milan Szuperak
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Chen-Fang Weng
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Anthony T Papenfuss
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Louise Y Cheng
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia;
| |
Collapse
|
13
|
Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S. Transcription factor networks in Drosophila melanogaster. Cell Rep 2014; 8:2031-2043. [PMID: 25242320 DOI: 10.1016/j.celrep.2014.08.038] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/09/2014] [Accepted: 08/16/2014] [Indexed: 11/15/2022] Open
Abstract
Specific cellular fates and functions depend on differential gene expression, which occurs primarily at the transcriptional level and is controlled by complex regulatory networks of transcription factors (TFs). TFs act through combinatorial interactions with other TFs, cofactors, and chromatin-remodeling proteins. Here, we define protein-protein interactions using a coaffinity purification/mass spectrometry method and study 459 Drosophila melanogaster transcription-related factors, representing approximately half of the established catalog of TFs. We probe this network in vivo, demonstrating functional interactions for many interacting proteins, and test the predictive value of our data set. Building on these analyses, we combine regulatory network inference models with physical interactions to define an integrated network that connects combinatorial TF protein interactions to the transcriptional regulatory network of the cell. We use this integrated network as a tool to connect the functional network of genetic modifiers related to mastermind, a transcriptional cofactor of the Notch pathway.
Collapse
Affiliation(s)
- David Y Rhee
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dong-Yeon Cho
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Bo Zhai
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Slattery
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christina Y Wong
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Teresa M Przytycka
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Obar
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Spyros Artavanis-Tsakonas
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Biogen Idec, Inc., Cambridge, MA 02142, USA.
| |
Collapse
|
14
|
Ferrero E, Fischer B, Russell S. SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete. Genome Biol 2014; 15:R74. [PMID: 24886562 PMCID: PMC4072944 DOI: 10.1186/gb-2014-15-5-r74] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 05/30/2014] [Indexed: 12/31/2022] Open
Abstract
Background Sox proteins encompass an evolutionarily conserved family of transcription factors with critical roles in animal development and stem cell biology. In common with vertebrates, the Drosophila group B proteins SoxNeuro and Dichaete are involved in central nervous system development, where they play both similar and unique roles in gene regulation. Sox genes show extensive functional redundancy across metazoans, but the molecular basis underpinning functional compensation mechanisms at the genomic level are currently unknown. Results Using a combination of genome-wide binding analysis and gene expression profiling, we show that SoxNeuro directs embryonic neural development from the early specification of neuroblasts through to the terminal differentiation of neurons and glia. To address the issue of functional redundancy and compensation at a genomic level, we compare SoxNeuro and Dichaete binding, identifying common and independent binding events in wild-type conditions, as well as instances of compensation and loss of binding in mutant backgrounds. Conclusions We find that early aspects of group B Sox functions in the central nervous system, such as stem cell maintenance and dorsoventral patterning, are highly conserved. However, in contrast to vertebrates, we find that Drosophila group B1 proteins also play prominent roles during later aspects of neural morphogenesis. Our analysis of the functional relationship between SoxNeuro and Dichaete uncovers evidence for redundant and independent functions for each protein, along with unexpected examples of compensation and interdependency, thus providing new insights into the general issue of transcription factor functional redundancy.
Collapse
|
15
|
Welcker JE, Hernandez-Miranda LR, Paul FE, Jia S, Ivanov A, Selbach M, Birchmeier C. Insm1 controls development of pituitary endocrine cells and requires a SNAG domain for function and for recruitment of histone-modifying factors. Development 2013; 140:4947-58. [DOI: 10.1242/dev.097642] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The Insm1 gene encodes a zinc finger factor expressed in many endocrine organs. We show here that Insm1 is required for differentiation of all endocrine cells in the pituitary. Thus, in Insm1 mutant mice, hormones characteristic of the different pituitary cell types (thyroid-stimulating hormone, follicle-stimulating hormone, melanocyte-stimulating hormone, adrenocorticotrope hormone, growth hormone and prolactin) are absent or produced at markedly reduced levels. This differentiation deficit is accompanied by upregulated expression of components of the Notch signaling pathway, and by prolonged expression of progenitor markers, such as Sox2. Furthermore, skeletal muscle-specific genes are ectopically expressed in endocrine cells, indicating that Insm1 participates in the repression of an inappropriate gene expression program. Because Insm1 is also essential for differentiation of endocrine cells in the pancreas, intestine and adrenal gland, it is emerging as a transcription factor that acts in a pan-endocrine manner. The Insm1 factor contains a SNAG domain at its N-terminus, and we show here that the SNAG domain recruits histone-modifying factors (Kdm1a, Hdac1/2 and Rcor1-3) and other proteins implicated in transcriptional regulation (Hmg20a/b and Gse1). Deletion of sequences encoding the SNAG domain in mice disrupted differentiation of pituitary endocrine cells, and resulted in an upregulated expression of components of the Notch signaling pathway and ectopic expression of skeletal muscle-specific genes. Our work demonstrates that Insm1 acts in the epigenetic and transcriptional network that controls differentiation of endocrine cells in the anterior pituitary gland, and that it requires the SNAG domain to exert this function in vivo.
Collapse
Affiliation(s)
- Jochen E. Welcker
- Developmental Biology/Signal Transduction Group, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Luis R. Hernandez-Miranda
- Developmental Biology/Signal Transduction Group, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Florian E. Paul
- Cell Signaling and Mass Spectrometry Group, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Shiqi Jia
- Developmental Biology/Signal Transduction Group, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Andranik Ivanov
- Systems Biology of Gene Regulatory Elements Group, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Matthias Selbach
- Cell Signaling and Mass Spectrometry Group, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction Group, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| |
Collapse
|
16
|
Feng G, Yi P, Yang Y, Chai Y, Tian D, Zhu Z, Liu J, Zhou F, Cheng Z, Wang X, Li W, Ou G. Developmental stage-dependent transcriptional regulatory pathways control neuroblast lineage progression. Development 2013; 140:3838-47. [DOI: 10.1242/dev.098723] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Neuroblasts generate neurons with different functions by asymmetric cell division, cell cycle exit and differentiation. The underlying transcriptional regulatory pathways remain elusive. Here, we performed genetic screens in C. elegans and identified three evolutionarily conserved transcription factors (TFs) essential for Q neuroblast lineage progression. Through live cell imaging and genetic analysis, we showed that the storkhead TF HAM-1 regulates spindle positioning and myosin polarization during asymmetric cell division and that the PAR-1-like kinase PIG-1 is a transcriptional regulatory target of HAM-1. The TEAD TF EGL-44, in a physical association with the zinc-finger TF EGL-46, instructs cell cycle exit after the terminal division. Finally, the Sox domain TF EGL-13 is necessary and sufficient to establish the correct neuronal fate. Genetic analysis further demonstrated that HAM-1, EGL-44/EGL-46 and EGL-13 form three transcriptional regulatory pathways. We have thus identified TFs that function at distinct developmental stages to ensure appropriate neuroblast lineage progression and suggest that their vertebrate homologs might similarly regulate neural development.
Collapse
Affiliation(s)
- Guoxin Feng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Peishan Yi
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Yihong Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Yongping Chai
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Dong Tian
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Zhiwen Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Jianhong Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Fanli Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Ze Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Xiangming Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Wei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Guangshuo Ou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| |
Collapse
|
17
|
Abstract
CO(2) sensation represents an interesting example of nervous system and behavioral evolutionary divergence. The underlying molecular mechanisms, however, are not understood. Loss of microRNA-279 in Drosophila melanogaster leads to the formation of a CO(2) sensory system partly similar to the one of mosquitoes. Here, we show that a novel allele of the pleiotropic transcription factor Prospero resembles the miR-279 phenotype. We use a combination of genetics and in vitro and in vivo analysis to demonstrate that Pros participates in the regulation of miR-279 expression, and that reexpression of miR-279 rescues the pros CO(2) neuron phenotype. We identify common target molecules of miR-279 and Pros in bioinformatics analysis, and show that overexpression of the transcription factors Nerfin-1 and Escargot (Esg) is sufficient to induce formation of CO(2) neurons on maxillary palps. Our results suggest that Prospero restricts CO(2) neuron formation indirectly via miR-279 and directly by repressing the shared target molecules, Nerfin-1 and Esg, during olfactory system development. Given the important role of Pros in differentiation of the nervous system, we anticipate that miR-mediated signal tuning represents a powerful method for olfactory sensory system diversification during evolution.
Collapse
|
18
|
Kuzin A, Kundu M, Brody T, Odenwald WF. Functional analysis of conserved sequences within a temporally restricted neural precursor cell enhancer. Mech Dev 2011; 128:165-77. [PMID: 21315151 PMCID: PMC3095431 DOI: 10.1016/j.mod.2011.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/28/2011] [Accepted: 02/02/2011] [Indexed: 11/18/2022]
Abstract
Many of the key regulators of Drosophila CNS neural identity are expressed in defined temporal orders during neuroblast (NB) lineage development. To begin to understand the structural and functional complexity of enhancers that regulate ordered NB gene expression programs, we have undertaken the mutational analysis of the temporally restricted nerfin-1 NB enhancer. Our previous studies have localized the enhancer to a region just proximal to the nerfin-1 transcription start site. Analysis of this enhancer, using the phylogenetic footprint program EvoPrinter, reveals the presence of multiple sequence blocks that are conserved among drosophilids. cis-Decoder alignments of these conserved sequence blocks (CSBs) has identified shorter elements that are conserved in other Drosophila NB enhancers. Mutagenesis of the enhancer reveals that although each CSB is required for wild-type expression, neither position nor orientation of the CSBs within the enhancer is crucial for enhancer function; removal of less-conserved or non-conserved sequences flanking CSB clusters also does not significantly alter enhancer activity. While all three conserved E-box transcription factor (TF) binding sites (CAGCTG) are required for full function, adding an additional site at different locations within non-conserved sequences interferes with enhancer activity. Of particular note, none of the mutations resulted in ectopic reporter expression outside of the early NB expression window, suggesting that the temporally restricted pattern is defined by transcriptional activators and not by direct DNA binding repressors. Our work also points to an unexpectedly large number of TFs required for optimal enhancer function - mutant TF analysis has identified at least four that are required for full enhancer regulation.
Collapse
Affiliation(s)
- Alexander Kuzin
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| | - Mukta Kundu
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| | - Thomas Brody
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| | - Ward F. Odenwald
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| |
Collapse
|
19
|
Neural development features: spatio-temporal development of the Caenorhabditis elegans neuronal network. PLoS Comput Biol 2011; 7:e1001044. [PMID: 21253561 PMCID: PMC3017107 DOI: 10.1371/journal.pcbi.1001044] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 12/01/2010] [Indexed: 11/19/2022] Open
Abstract
The nematode Caenorhabditis elegans, with information on neural connectivity, three-dimensional position and cell linage, provides a unique system for understanding the development of neural networks. Although C. elegans has been widely studied in the past, we present the first statistical study from a developmental perspective, with findings that raise interesting suggestions on the establishment of long-distance connections and network hubs. Here, we analyze the neuro-development for temporal and spatial features, using birth times of neurons and their three-dimensional positions. Comparisons of growth in C. elegans with random spatial network growth highlight two findings relevant to neural network development. First, most neurons which are linked by long-distance connections are born around the same time and early on, suggesting the possibility of early contact or interaction between connected neurons during development. Second, early-born neurons are more highly connected (tendency to form hubs) than later-born neurons. This indicates that the longer time frame available to them might underlie high connectivity. Both outcomes are not observed for random connection formation. The study finds that around one-third of electrically coupled long-range connections are late forming, raising the question of what mechanisms are involved in ensuring their accuracy, particularly in light of the extremely invariant connectivity observed in C. elegans. In conclusion, the sequence of neural network development highlights the possibility of early contact or interaction in securing long-distance and high-degree connectivity.
Collapse
|
20
|
Seetharam A, Bai Y, Stuart GW. A survey of well conserved families of C2H2 zinc-finger genes in Daphnia. BMC Genomics 2010; 11:276. [PMID: 20433734 PMCID: PMC2889900 DOI: 10.1186/1471-2164-11-276] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 04/30/2010] [Indexed: 12/15/2022] Open
Abstract
Background A recent comparative genomic analysis tentatively identified roughly 40 orthologous groups of C2H2 Zinc-finger proteins that are well conserved in "bilaterians" (i.e. worms, flies, and humans). Here we extend that analysis to include a second arthropod genome from the crustacean, Daphnia pulex. Results Most of the 40 orthologous groups of C2H2 zinc-finger proteins are represented by just one or two proteins within each of the previously surveyed species. Likewise, Daphnia were found to possess a similar number of orthologs for all of these small orthology groups. In contrast, the number of Sp/KLF homologs tends to be greater and to vary between species. Like the corresponding mammalian Sp/KLF proteins, most of the Drosophila and Daphnia homologs can be placed into one of three sub-groups: Class I-III. Daphnia were found to have three Class I proteins that roughly correspond to their Drosophila counterparts, dSP1, btd, CG5669, and three Class II proteins that roughly correspond to Luna, CG12029, CG9895. However, Daphnia have four additional KLF-Class II proteins that are most similar to the vertebrate KLF1/2/4 proteins, a subset not found in Drosophila. Two of these four proteins are encoded by genes linked in tandem. Daphnia also have three KLF-Class III members, one more than Drosophila. One of these is a likely Bteb2 homolog, while the other two correspond to Cabot and KLF13, a vertebrate homolog of Cabot. Conclusion Consistent with their likely roles as fundamental determinants of bilaterian form and function, most of the 40 groups of C2H2 zinc-finger proteins are conserved in kind and number in Daphnia. However, the KLF family includes several additional genes that are most similar to genes present in vertebrates but missing in Drosophila.
Collapse
Affiliation(s)
- Arun Seetharam
- Department of Biology, Indiana State University, Terre Haute, IN 47809, USA
| | | | | |
Collapse
|
21
|
Lan MS, Breslin MB. Structure, expression, and biological function of INSM1 transcription factor in neuroendocrine differentiation. FASEB J 2009; 23:2024-33. [PMID: 19246490 DOI: 10.1096/fj.08-125971] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Zinc-finger transcription factors are DNA-binding proteins that are implicated in many diverse biological functions. INSM1 (formerly IA-1) contains five zinc-finger motifs and functions as a transcription factor. INSM1 protein structure is highly conserved in homologues of different species. It is predominantly expressed in developing neuroendocrine tissues and the nervous system in mammals. INSM1 represents an important player in early embryonic neurogenesis. In pancreatic endocrine cell differentiation, Ngn3 first activates INSM1 and subsequently NeuroD/beta2. Conversely, INSM1 exerts a feedback mechanism to suppress NeuroD/beta2 and its own gene expression. INSM1 gene ablation in the mouse results in the impairment of pancreatic endocrine cell maturation. Further, deletion of INSM1 severely impairs catecholamine biosynthesis and secretion from the adrenal gland that results in early embryonic lethality. Genetically, INSM1 acts as a downstream factor of Mash 1 and Phox2b in the differentiation of the sympatho-adrenal lineage. In the developing neocortex, mouse embryos lacking INSM1 expression contain half the number of basal progenitors and show a reduction in cortical plate radial thickness. Cell signaling studies reveal that INSM1 contributes to the induction of cell cycle arrest/exit necessary to facilitate cellular differentiation. INSM1 is highly expressed in tumors of neuroendocrine origin. Hence, its promoter could serve as a tumor-specific promoter that drives a specific targeted cancer gene therapy for the treatment of neuroendocrine tumors. Taken together, all of these features of INSM1 strongly support its role as an important regulator during neuroendocrine differentiation.
Collapse
Affiliation(s)
- Michael S Lan
- Research Institute for Children, Children's Hospital, 200 Henry Clay Ave., Research and Education Bldg., Rm. 2211, New Orleans, LA 70118, USA.
| | | |
Collapse
|
22
|
Kuzin A, Kundu M, Ekatomatis A, Brody T, Odenwald WF. Conserved sequence block clustering and flanking inter-cluster flexibility delineate enhancers that regulate nerfin-1 expression during Drosophila CNS development. Gene Expr Patterns 2009; 9:65-72. [PMID: 19056518 PMCID: PMC5586073 DOI: 10.1016/j.gep.2008.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2008] [Revised: 10/21/2008] [Accepted: 10/23/2008] [Indexed: 10/21/2022]
Abstract
We have identified clusters of conserved sequences constituting discrete modular enhancers within the Drosophilanerfin-1 locus. nerfin-1 encodes a Zn-finger transcription factor that directs pioneer interneuron axon guidance. nerfin-1 mRNA is detected in many early delaminating neuroblasts, ganglion mother cells and transiently in nascent neurons. The comparative genomics analysis program EvoPrinter revealed conserved sequence blocks both upstream and downstream of the transcribed region. By using the aligning regions of different drosophilids as the reference DNA, EvoPrinter detects sequence length flexibility between clusters of conserved sequences and thus facilitates differentiation between closely associated modular enhancers. Expression analysis of enhancer-reporter transgenes identified enhancers that drive expression in different regions of the developing embryonic and adult nervous system, including subsets of embryonic CNS neuroblasts, GMCs, neurons and PNS neurons. In summary, EvoPrinter facilitates the discovery and analysis of enhancers that control crucial aspects of nerfin-1 expression.
Collapse
Affiliation(s)
- Alexander Kuzin
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
| | - Mukta Kundu
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
| | | | - Thomas Brody
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
| | - Ward F. Odenwald
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, USA
| |
Collapse
|
23
|
Leal SM, Qian L, Lacin H, Bodmer R, Skeath JB. Neuromancer1 and Neuromancer2 regulate cell fate specification in the developing embryonic CNS of Drosophila melanogaster. Dev Biol 2009; 325:138-50. [PMID: 19013145 PMCID: PMC2648533 DOI: 10.1016/j.ydbio.2008.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2008] [Revised: 10/01/2008] [Accepted: 10/02/2008] [Indexed: 12/14/2022]
Abstract
T-box genes encode a large family of transcription factors that regulate many developmental processes in vertebrates and invertebrates. In addition to their roles in regulating embryonic heart and epidermal development in Drosophila, we provide evidence that the T-box transcription factors neuromancer1 (nmr1) and neuromancer2 (nmr2) play key roles in embryonic CNS development. We verify that nmr1 and nmr2 function in a partially redundant manner to regulate neuronal cell fate by inhibiting even-skipped (eve) expression in specific cells in the CNS. Consistent with their redundant function, nmr1 and nmr2 exhibit overlapping yet distinct protein expression profiles within the CNS. Of note, nmr2 transcript and protein are expressed in identical patterns of segment polarity stripes, defined sets of neuroblasts, many ganglion mother cells and discrete populations of neurons. However, while we observe nmr1 transcripts in segment polarity stripes and specific neural precursors in early stages of CNS development, we first detect Nmr1 protein in later stages of CNS development where it is restricted to discrete subsets of Nmr2-positive neurons. Expression studies identify nearly all Nmr1/2 co-expressing neurons as interneurons, while a single Eve-positive U/CQ motor neuron weakly co-expresses Nmr2. Lineage studies map a subset of Nmr1/2-positive neurons to neuroblast lineages 2-2, 6-1, and 6-2 while genetic studies reveal that nmr2 collaborates with nkx6 to regulate eve expression in the CNS. Thus, nmr1 and nmr2 appear to act together as members of the combinatorial code of transcription factors that govern neuronal subtype identity in the CNS.
Collapse
Affiliation(s)
- S M Leal
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | | | | | | | | |
Collapse
|
24
|
Parlier D, Ariza A, Christulia F, Genco F, Vanhomwegen J, Kricha S, Souopgui J, Bellefroid EJ. Xenopus zinc finger transcription factor IA1 (Insm1) expression marks anteroventral noradrenergic neuron progenitors in Xenopus embryos. Dev Dyn 2008; 237:2147-57. [PMID: 18627098 DOI: 10.1002/dvdy.21621] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The evolutionarily conserved IA1 (Insm1) gene is strongly expressed in the developing nervous system. Here, we show that IA1 is expressed during Xenopus laevis embryogenesis in neural plate primary neurons as well as in a population of uncharacterized anteroventral cells that form in front of the cement gland and that we identified as noradrenergic neurons. We also show that the formation of those anteroventral cells is dependent on BMPs and inhibited by Notch and that it is regulated by the transcription factors Xash1, Phox2, and Hand2. Finally, we provide functional evidence suggesting that IA1 may also play a role in their formation. Together, our results reveal that IA1 constitutes a novel player downstream of Xash1 in the formation of a previously unidentified population of Xenopus noradrenergic primary neurons.
Collapse
Affiliation(s)
- Damien Parlier
- Laboratoire d'Embryologie Moléculaire, Université Libre de Bruxelles, Institut de Biologie et de Médecine Moléculaires (IBMM), Gosselies, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Farkas LM, Haffner C, Giger T, Khaitovich P, Nowick K, Birchmeier C, Pääbo S, Huttner WB. Insulinoma-Associated 1 Has a Panneurogenic Role and Promotes the Generation and Expansion of Basal Progenitors in the Developing Mouse Neocortex. Neuron 2008; 60:40-55. [DOI: 10.1016/j.neuron.2008.09.020] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 07/07/2008] [Accepted: 09/05/2008] [Indexed: 02/04/2023]
|
26
|
Abstract
In a recent paper, Cayirlioglu et al. report that the disruption of a specific miRNA, miR-279, which normally acts to inhibit the transcription factor Nerfin-1, uncovers a population of hybrid CO2 neurons in the Drosophila maxillary palp.1 Normally, fruit fly CO2 neurons are found only in the antennae, while mosquito CO2 neurons are found only in the maxillary palps. The hybrid neurons in this miRNA mutant may, thus, recapitulate an evolutionary intermediate unseen since the divergence of these two dipteran lineages over 250 million years ago.
Collapse
Affiliation(s)
- Walton D Jones
- Biological Sciences, KAIST, 335 Gwanghangno, Yuseong-gu, Daejeon, 305-701, Republic of Korea.
| |
Collapse
|
27
|
Colomb S, Joly W, Bonneaud N, Maschat F. A concerted action of Engrailed and Gooseberry-Neuro in neuroblast 6-4 is triggering the formation of embryonic posterior commissure bundles. PLoS One 2008; 3:e2197. [PMID: 18493305 PMCID: PMC2373891 DOI: 10.1371/journal.pone.0002197] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 04/03/2008] [Indexed: 11/19/2022] Open
Abstract
One challenging question in neurogenesis concerns the identification of cues that trigger axonal growth and pathfinding to form stereotypic neuronal networks during the construction of a nervous system. Here, we show that in Drosophila, Engrailed (EN) and Gooseberry-Neuro (GsbN) act together as cofactors to build the posterior commissures (PCs), which shapes the ventral nerve cord. Indeed, we show that these two proteins are acting together in axon growth and midline crossing, and that this concerted action occurs at early development, in neuroblasts. More precisely, we identified that their expressions in NB 6-4 are necessary and sufficient to trigger the formation of the PCs, demonstrating that segmentation genes such as EN and GsbN play a crucial role in the determination of NB 6-4 in a way that will later influence growth and guidance of all the axons that form the PCs. We also demonstrate a more specific function of GsbN in differentiated neurons, leading to fasciculations between axons, which might be required to obtain PC mature axon bundles.
Collapse
Affiliation(s)
| | - Willy Joly
- Human Genetics Institute, Montpellier, France
| | | | | |
Collapse
|
28
|
Duggan A, Madathany T, de Castro SCP, Gerrelli D, Guddati K, García-Añoveros J. Transient expression of the conserved zinc finger gene INSM1 in progenitors and nascent neurons throughout embryonic and adult neurogenesis. J Comp Neurol 2008; 507:1497-520. [PMID: 18205207 DOI: 10.1002/cne.21629] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INSM1 is a zinc-finger protein expressed in the developing nervous system and pancreas as well as in medulloblastomas and neuroendocrine tumors. With in situ hybridization combined with immunohistochemistry, we detected INSM1 mRNA in all embryonic to adult neuroproliferative areas examined: embryonic neocortex, ganglionic eminence, midbrain, retina, hindbrain, and spinal cord; autonomic, dorsal root, trigeminal and spiral ganglia; olfactory and vomeronasal organ epithelia; postnatal cerebellum; and juvenile to adult subgranular zone of dentate gyrus, subventricular zone, and rostral migratory stream leading to olfactory bulb. In most of these neurogenic areas, subsets of neuronal progenitors and nascent, but not mature, neurons express INSM1. For example, in developing cerebellum, INSM1 is present in proliferating progenitors of the outer external granule layer (EGL) and in postmitotic cells of the inner EGL, but not in mature granule cell neurons. Also, lining the neural tube from spinal cord to neocortex in mouse as well as human embryos, cells undergoing mitosis apically do not express INSM1. By contrast, nonsurface progenitors located in the basal ventricular and/or subventricular zones express INSM1. Whereas apical progenitors are proliferative and generate one or two additional progenitors, basal progenitors are thought to divide terminally and symmetrically to produce two neurons. The nematode ortholog of INSM1, EGL-46, is expressed during terminal symmetric neurogenic divisions and regulates the termination of proliferation. We propose that, in mice and humans, INSM1 is likewise expressed transiently during terminal neurogenic divisions, from late progenitors to nascent neurons, and particularly during symmetric neuronogenic divisions.
Collapse
Affiliation(s)
- Anne Duggan
- Department of Anesthesiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | | | | |
Collapse
|
29
|
Miguel-Aliaga I, Thor S, Gould AP. Postmitotic specification of Drosophila insulinergic neurons from pioneer neurons. PLoS Biol 2008; 6:e58. [PMID: 18336071 PMCID: PMC2265769 DOI: 10.1371/journal.pbio.0060058] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 01/23/2008] [Indexed: 11/25/2022] Open
Abstract
Insulin and related peptides play important and conserved functions in growth and metabolism. Although Drosophila has proved useful for the genetic analysis of insulin functions, little is known about the transcription factors and cell lineages involved in insulin production. Within the embryonic central nervous system, the MP2 neuroblast divides once to generate a dMP2 neuron that initially functions as a pioneer, guiding the axons of other later-born embryonic neurons. Later during development, dMP2 neurons in anterior segments undergo apoptosis but their posterior counterparts persist. We show here that surviving posterior dMP2 neurons no longer function in axonal scaffolding but differentiate into neuroendocrine cells that express insulin-like peptide 7 (Ilp7) and innervate the hindgut. We find that the postmitotic transition from pioneer to insulin-producing neuron is a multistep process requiring retrograde bone morphogenetic protein (BMP) signalling and four transcription factors: Abdominal-B, Hb9, Fork Head, and Dimmed. These five inputs contribute in a partially overlapping manner to combinatorial codes for dMP2 apoptosis, survival, and insulinergic differentiation. Ectopic reconstitution of this code is sufficient to activate Ilp7 expression in other postmitotic neurons. These studies reveal striking similarities between the transcription factors regulating insulin expression in insect neurons and mammalian pancreatic beta-cells.
Collapse
Affiliation(s)
- Irene Miguel-Aliaga
- Division of Developmental Neurobiology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University Medical School, Linkoping, Sweden
| | - Alex P Gould
- Division of Developmental Neurobiology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| |
Collapse
|
30
|
Cayirlioglu P, Kadow IG, Zhan X, Okamura K, Suh GSB, Gunning D, Lai EC, Zipursky SL. Hybrid neurons in a microRNA mutant are putative evolutionary intermediates in insect CO2 sensory systems. Science 2008; 319:1256-60. [PMID: 18309086 PMCID: PMC2714168 DOI: 10.1126/science.1149483] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Carbon dioxide (CO2) elicits different olfactory behaviors across species. In Drosophila, neurons that detect CO2 are located in the antenna, form connections in a ventral glomerulus in the antennal lobe, and mediate avoidance. By contrast, in the mosquito these neurons are in the maxillary palps (MPs), connect to medial sites, and promote attraction. We found in Drosophila that loss of a microRNA, miR-279, leads to formation of CO2 neurons in the MPs. miR-279 acts through down-regulation of the transcription factor Nerfin-1. The ectopic neurons are hybrid cells. They express CO2 receptors and form connections characteristic of CO2 neurons, while exhibiting wiring and receptor characteristics of MP olfactory receptor neurons (ORNs). We propose that this hybrid ORN reveals a cellular intermediate in the evolution of species-specific behaviors elicited by CO2.
Collapse
Affiliation(s)
- Pelin Cayirlioglu
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ilona Grunwald Kadow
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Xiaoli Zhan
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Katsutomo Okamura
- Sloan-Kettering Institute, 521 Rockefeller Research Labs, 1275 York Avenue, Box 252, New York, NY 10021, USA
| | - Greg S. B. Suh
- Division of Biology 216-76, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dorian Gunning
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Eric C. Lai
- Sloan-Kettering Institute, 521 Rockefeller Research Labs, 1275 York Avenue, Box 252, New York, NY 10021, USA
| | - S. Lawrence Zipursky
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
31
|
Kuzin A, Kundu M, Brody T, Odenwald WF. The Drosophila nerfin-1 mRNA requires multiple microRNAs to regulate its spatial and temporal translation dynamics in the developing nervous system. Dev Biol 2007; 310:35-43. [PMID: 17714701 PMCID: PMC2064069 DOI: 10.1016/j.ydbio.2007.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 06/06/2007] [Accepted: 07/14/2007] [Indexed: 11/24/2022]
Abstract
The mRNA encoding the Drosophila Zn-finger transcription factor Nerfin-1, required for CNS axon pathfinding events, is subject to post-transcriptional silencing. Although nerfin-1 mRNA is expressed in many neural precursor cells including all early delaminating CNS neuroblasts, the encoded Nerfin-1 protein is detected only in the nuclei of neural precursors that divide just once to generate neurons and then only transiently in nascent neurons. Using a nerfin-1 promoter-controlled reporter transgene, replacement of the nerfin-1 3' UTR with the viral SV-40 3' UTR releases the neuroblast translational block and prolongs reporter protein expression in neurons. Comparative genomics analysis reveals that the nerfin-1 mRNA 3' UTR contains multiple highly conserved sequence blocks that either harbor and/or overlap 21 predicted binding sites for 18 different microRNAs. To determine the functional significance of these microRNA-binding sites and less conserved microRNA target sites, we have studied their ability to block or limit the expression of reporter protein in nerfin-1-expressing cells during embryonic development. Our results indicate that no single microRNA is sufficient to fully inhibit protein expression but rather multiple microRNAs that target different binding sites are required to block ectopic protein expression in neural precursor cells and temporally restrict expression in neurons. Taken together, these results suggest that multiple microRNAs play a cooperative role in the post-transcriptional regulation of nerfin-1 mRNA, and the high degree of microRNA-binding site evolutionary conservation indicates that all members of the Drosophila genus employ a similar strategy to regulate the onset and extinction dynamics of Nerfin-1 expression.
Collapse
Affiliation(s)
- Alexander Kuzin
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| | - Mukta Kundu
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| | - Thomas Brody
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| | - Ward F. Odenwald
- Neural Cell-Fate Determinants Section, NINDS, NIH Bethesda, Maryland, USA
| |
Collapse
|
32
|
Brody T, Rasband W, Baler K, Kuzin A, Kundu M, Odenwald WF. cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers. Genome Biol 2007; 8:R75. [PMID: 17490485 PMCID: PMC1929141 DOI: 10.1186/gb-2007-8-5-r75] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 12/18/2006] [Accepted: 05/09/2007] [Indexed: 12/01/2022] Open
Abstract
: The use of cis-Decoder, a new tool for discovery of conserved sequence elements that are shared between similarly regulating enhancers, suggests that enhancers use overlapping repertoires of highly conserved core elements. A systematic approach is described for analysis of evolutionarily conserved cis-regulatory DNA using cis-Decoder, a tool for discovery of conserved sequence elements that are shared between similarly regulated enhancers. Analysis of 2,086 conserved sequence blocks (CSBs), identified from 135 characterized enhancers, reveals most CSBs consist of shorter overlapping/adjacent elements that are either enhancer type-specific or common to enhancers with divergent regulatory behaviors. Our findings suggest that enhancers employ overlapping repertoires of highly conserved core elements.
Collapse
Affiliation(s)
- Thomas Brody
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, 20892, USA
| | - Wayne Rasband
- Office of Scientific Director, IRP, NIMH, NIH, Bethesda, MD, 20892, USA
| | - Kevin Baler
- Office of Scientific Director, IRP, NIMH, NIH, Bethesda, MD, 20892, USA
| | - Alexander Kuzin
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, 20892, USA
| | - Mukta Kundu
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, 20892, USA
| | - Ward F Odenwald
- Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, 20892, USA
| |
Collapse
|
33
|
Spletter ML, Liu J, Liu J, Su H, Giniger E, Komiyama T, Quake S, Luo L. Lola regulates Drosophila olfactory projection neuron identity and targeting specificity. Neural Dev 2007; 2:14. [PMID: 17634136 PMCID: PMC1947980 DOI: 10.1186/1749-8104-2-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 07/16/2007] [Indexed: 11/25/2022] Open
Abstract
Background Precise connections of neural circuits can be specified by genetic programming. In the Drosophila olfactory system, projection neurons (PNs) send dendrites to single glomeruli in the antenna lobe (AL) based upon lineage and birth order and send axons with stereotyped terminations to higher olfactory centers. These decisions are likely specified by a PN-intrinsic transcriptional code that regulates the expression of cell-surface molecules to instruct wiring specificity. Results We find that the loss of longitudinals lacking (lola), which encodes a BTB-Zn-finger transcription factor with 20 predicted splice isoforms, results in wiring defects in both axons and dendrites of all lineages of PNs. RNA in situ hybridization and quantitative RT-PCR suggest that most if not all lola isoforms are expressed in all PNs, but different isoforms are expressed at widely varying levels. Overexpression of individual lola isoforms fails to rescue the lola null phenotypes and causes additional phenotypes. Loss of lola also results in ectopic expression of Gal4 drivers in multiple cell types and in the loss of transcription factor gene lim1 expression in ventral PNs. Conclusion Our results indicate that lola is required for wiring of axons and dendrites of most PN classes, and suggest a need for its molecular diversity. Expression pattern changes of Gal4 drivers in lola-/- clones imply that lola normally represses the expression of these regulatory elements in a subset of the cells surrounding the AL. We propose that Lola functions as a general transcription factor that regulates the expression of multiple genes ultimately controlling PN identity and wiring specificity.
Collapse
Affiliation(s)
- Maria Lynn Spletter
- Howard Hughes Medical Institute, Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
| | - Jian Liu
- Howard Hughes Medical Institute, Department of Bioengineering, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Engineering, Emory University, Atlanta, Georgia 30322, USA
| | - Justin Liu
- Howard Hughes Medical Institute, Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
| | - Helen Su
- Howard Hughes Medical Institute, Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Takaki Komiyama
- Howard Hughes Medical Institute, Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Stephen Quake
- Howard Hughes Medical Institute, Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
34
|
Sánchez-Soriano N, Tear G, Whitington P, Prokop A. Drosophila as a genetic and cellular model for studies on axonal growth. Neural Dev 2007; 2:9. [PMID: 17475018 PMCID: PMC1876224 DOI: 10.1186/1749-8104-2-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Accepted: 05/02/2007] [Indexed: 11/10/2022] Open
Abstract
One of the most fascinating processes during nervous system development is the establishment of stereotypic neuronal networks. An essential step in this process is the outgrowth and precise navigation (pathfinding) of axons and dendrites towards their synaptic partner cells. This phenomenon was first described more than a century ago and, over the past decades, increasing insights have been gained into the cellular and molecular mechanisms regulating neuronal growth and navigation. Progress in this area has been greatly assisted by the use of simple and genetically tractable invertebrate model systems, such as the fruit fly Drosophila melanogaster. This review is dedicated to Drosophila as a genetic and cellular model to study axonal growth and demonstrates how it can and has been used for this research. We describe the various cellular systems of Drosophila used for such studies, insights into axonal growth cones and their cytoskeletal dynamics, and summarise identified molecular signalling pathways required for growth cone navigation, with particular focus on pathfinding decisions in the ventral nerve cord of Drosophila embryos. These Drosophila-specific aspects are viewed in the general context of our current knowledge about neuronal growth.
Collapse
Affiliation(s)
- Natalia Sánchez-Soriano
- The Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK
| | - Guy Tear
- MRC Centre for Developmental Neurobiology, Guy's Campus, King's College, London, UK
| | - Paul Whitington
- Department of Anatomy and Cell Biology, University of Melbourne, Victoria, Australia
| | - Andreas Prokop
- The Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK
| |
Collapse
|
35
|
Joly W, Mugat B, Maschat F. Engrailed controls the organization of the ventral nerve cord through frazzled regulation. Dev Biol 2006; 301:542-54. [PMID: 17126316 DOI: 10.1016/j.ydbio.2006.10.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 09/20/2006] [Accepted: 10/14/2006] [Indexed: 11/19/2022]
Abstract
In Drosophila, the ventral nerve cord (VNC) architecture is built from neuroblasts that are specified during embryonic development, mainly by transcription factors. Here we show that Engrailed, a homeodomain transcription factor known to be involved in the establishment of neuroblast identity, is also directly implicated in the regulation of axonal guidance cues. Posterior commissures (PC) are missing in engrailed mutant embryos, and axonal pathfinding defects are observed when Engrailed is ectopically expressed at early stages, prior to neuronal specification. We also show that frazzled, enabled, and trio, all of which are potential direct targets of Engrailed and are involved in axonal navigation, interact genetically with engrailed to form posterior commissures in the developing VNC. The regulation of frazzled expression in engrailed-expressing neuroblasts contributes significantly to the formation of the posterior commissures by acting on axon growth. Finally, we identified a small genomic fragment within intron 1 of frazzled that can mediate activation by Engrailed in vivo when fused to a GFP reporter. These results indicate that Engrailed's function during the segregation of the neuroblasts is crucial for regulating different actors that are later involved in axon guidance.
Collapse
Affiliation(s)
- Willy Joly
- Institute of Human Genetics, IGH, UPR 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | | | | |
Collapse
|
36
|
Gierl MS, Karoulias N, Wende H, Strehle M, Birchmeier C. The zinc-finger factor Insm1 (IA-1) is essential for the development of pancreatic beta cells and intestinal endocrine cells. Genes Dev 2006; 20:2465-78. [PMID: 16951258 PMCID: PMC1560419 DOI: 10.1101/gad.381806] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The pancreatic and intestinal primordia contain epithelial progenitor cells that generate many cell types. During development, specific programs of gene expression restrict the developmental potential of such progenitors and promote their differentiation. The Insm1 (insulinoma-associated 1, IA-1) gene encodes a Zinc-finger factor that was discovered in an insulinoma cDNA library. We show that pancreatic and intestinal endocrine cells express Insm1 and require Insm1 for their development. In the pancreas of Insm1 mutant mice, endocrine precursors are formed, but only few insulin-positive beta cells are generated. Instead, endocrine precursor cells accumulate that express none of the pancreatic hormones. A similar change is observed in the development of intestine, where endocrine precursor cells are formed but do not differentiate correctly. A hallmark of endocrine cell differentiation is the accumulation of proteins that participate in secretion and vesicle transport, and we find many of the corresponding genes to be down-regulated in Insm1 mutant mice. Insm1 thus controls a gene expression program that comprises hormones and proteins of the secretory machinery. Our genetic analysis has revealed a key role of Insm1 in differentiation of pancreatic and intestinal endocrine cells.
Collapse
Affiliation(s)
- Mathias S Gierl
- Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | | | | | | | | |
Collapse
|
37
|
Lukowski CM, Ritzel RG, Waskiewicz AJ. Expression of two insm1-like genes in the developing zebrafish nervous system. Gene Expr Patterns 2006; 6:711-8. [PMID: 16487754 DOI: 10.1016/j.modgep.2005.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Revised: 12/22/2005] [Accepted: 12/23/2005] [Indexed: 11/17/2022]
Abstract
Insulinoma associated-1 (INSM1, formerly IA-1) is a Cys(2)-His(2) zinc finger transcription factor sharing conserved regions with Caenorhabditis elegans EGL-46 and Drosophila Nerfin-1. INSM, EGL-46, and Nerfin proteins comprise the EIN family of zinc finger transcription factors. egl-46 and nerfin-1 have been implicated in various aspects of neuronal differentiation including cell fate specification, axon guidance decisions and cell migration. Murine Insm1 has a restricted expression pattern in the developing CNS. We have characterized two zebrafish (Danio rerio) Insm1-like genes, insm1a and insm1b, and analyzed their expression patterns during embryonic development. Zebrafish insm1a and insm1b share an embryonic expression pattern comparable to the proneural deltaA as well as overlapping the neuronal marker elavl3. The expression pattern observed for zebrafish insm1a and insm1b is similar to other EIN homologues. Both zebrafish insm1-like transcripts are also present in a region of the embryo where pancreatic progenitors originate. The expression data along with functional characterization of invertebrate homologues suggest a conserved pathway involving the EIN transcription factors in early neurogenesis.
Collapse
Affiliation(s)
- Chris M Lukowski
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, Alta., Canada
| | | | | |
Collapse
|