1
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Lupiáñez DG. Marsupial genomes reveal how a skin membrane for gliding evolved. Nature 2024; 629:43-44. [PMID: 38658712 DOI: 10.1038/d41586-024-01021-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
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2
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Patil G, van Zon JS. Timers, variability, and body-wide coordination: C. elegans as a model system for whole-animal developmental timing. Curr Opin Genet Dev 2024; 85:102172. [PMID: 38432125 DOI: 10.1016/j.gde.2024.102172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Successful development requires both precise timing of cellular processes, such as division and differentiation, and tight coordination of timing between tissues and organs. Yet, how time information is encoded with high precision and synchronized between tissues, despite inherent molecular noise, is unsolved. Here, we propose the nematode C. elegans as a unique model system for studying body-wide control of developmental timing. Recent studies combining genetics, quantitative analysis, and simulations have 1) mapped core timers controlling larval development, indicating temporal gradients as an underlying mechanism, and 2) elucidated general principles that make timing insensitive to inherent fluctuations and variation in environmental conditions. As the molecular regulators of C. elegans developmental timing are broadly conserved, these mechanisms likely apply also to higher organisms.
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3
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Bernard EIM, Towler BP, Rogoyski OM, Newbury SF. Characterisation of the in-vivo miRNA landscape in Drosophila ribonuclease mutants reveals Pacman-mediated regulation of the highly conserved let-7 cluster during apoptotic processes. Front Genet 2024; 15:1272689. [PMID: 38444757 PMCID: PMC10912645 DOI: 10.3389/fgene.2024.1272689] [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: 08/04/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
The control of gene expression is a fundamental process essential for correct development and to maintain homeostasis. Many post-transcriptional mechanisms exist to maintain the correct levels of each RNA transcript within the cell. Controlled and targeted cytoplasmic RNA degradation is one such mechanism with the 5'-3' exoribonuclease Pacman (XRN1) and the 3'-5' exoribonuclease Dis3L2 playing crucial roles. Loss of function mutations in either Pacman or Dis3L2 have been demonstrated to result in distinct phenotypes, and both have been implicated in human disease. One mechanism by which gene expression is controlled is through the function of miRNAs which have been shown to be crucial for the control of almost all cellular processes. Although the biogenesis and mechanisms of action of miRNAs have been comprehensively studied, the mechanisms regulating their own turnover are not well understood. Here we characterise the miRNA landscape in a natural developing tissue, the Drosophila melanogaster wing imaginal disc, and assess the importance of Pacman and Dis3L2 on the abundance of miRNAs. We reveal a complex landscape of miRNA expression and show that whilst a null mutation in dis3L2 has a minimal effect on the miRNA expression profile, loss of Pacman has a profound effect with a third of all detected miRNAs demonstrating Pacman sensitivity. We also reveal a role for Pacman in regulating the highly conserved let-7 cluster (containing miR-100, let-7 and miR-125) and present a genetic model outlining a positive feedback loop regulated by Pacman which enhances our understanding of the apoptotic phenotype observed in Pacman mutants.
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Affiliation(s)
- Elisa I. M. Bernard
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Benjamin P. Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Oliver M. Rogoyski
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Sarah F. Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
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4
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Emans SW, Yerevanian A, Ahsan FM, Rotti JF, Zhou Y, Cedillo L, Soukas AA. GRD-1/PTR-11, the C. elegans hedgehog/patched-like morphogen-receptor pair, modulates developmental rate. Development 2023; 150:dev201974. [PMID: 37982457 PMCID: PMC10753586 DOI: 10.1242/dev.201974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
Both hedgehog (Hh) and target of rapamycin complex 2 (TORC2) are central, evolutionarily conserved signaling pathways that regulate development and metabolism. In C. elegans, loss of the essential TORC2 component RICTOR (rict-1) causes delayed development, shortened lifespan, reduced brood, small size and increased fat. Here, we report that knockdown of both the hedgehog-related morphogen grd-1 and its patched-related receptor ptr-11 rescues delayed development in TORC2 loss-of-function mutants, and grd-1 and ptr-11 overexpression delays wild-type development to a similar level to that in TORC2 loss-of-function animals. These findings potentially indicate an unexpected role for grd-1 and ptr-11 in slowing developmental rate downstream of a nutrient-sensing pathway. Furthermore, we implicate the chronic stress transcription factor pqm-1 as a key transcriptional effector in this slowing of whole-organism growth by grd-1 and ptr-11. We propose that TORC2, grd-1 and ptr-11 may act linearly or converge on pqm-1 to delay organismal development.
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Affiliation(s)
- Sinclair W. Emans
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Biological and Biomedical Sciences, Division of Medical Science, Harvard Medical School, Boston, MA 02115, USA
| | - Armen Yerevanian
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Fasih M. Ahsan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Biological and Biomedical Sciences, Division of Medical Science, Harvard Medical School, Boston, MA 02115, USA
| | - Jen F. Rotti
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yifei Zhou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lucydalila Cedillo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Biological and Biomedical Sciences, Division of Medical Science, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander A. Soukas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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5
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Doi A, Suarez GD, Droste R, Horvitz HR. A DEAD-box helicase drives the partitioning of a pro-differentiation NAB protein into nuclear foci. Nat Commun 2023; 14:6593. [PMID: 37852948 PMCID: PMC10584935 DOI: 10.1038/s41467-023-42345-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
How cells regulate gene expression in a precise spatiotemporal manner during organismal development is a fundamental question in biology. Although the role of transcriptional condensates in gene regulation has been established, little is known about the function and regulation of these molecular assemblies in the context of animal development and physiology. Here we show that the evolutionarily conserved DEAD-box helicase DDX-23 controls cell fate in Caenorhabditis elegans by binding to and facilitating the condensation of MAB-10, the C. elegans homolog of mammalian NGFI-A-binding (NAB) protein. MAB-10 is a transcriptional cofactor that functions with the early growth response (EGR) protein LIN-29 to regulate the transcription of genes required for exiting the cell cycle, terminal differentiation, and the larval-to-adult transition. We suggest that DEAD-box helicase proteins function more generally during animal development to control the condensation of NAB proteins important in cell identity and that this mechanism is evolutionarily conserved. In mammals, such a mechanism might underlie terminal cell differentiation and when dysregulated might promote cancerous growth.
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Affiliation(s)
- Akiko Doi
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Gianmarco D Suarez
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Rita Droste
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - H Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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6
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Fung W, Tan TM, Kolotuev I, Heiman MG. A sex-specific switch in a single glial cell patterns the apical extracellular matrix. Curr Biol 2023; 33:4174-4186.e7. [PMID: 37708887 PMCID: PMC10578079 DOI: 10.1016/j.cub.2023.08.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/17/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
Apical extracellular matrix (aECM) constitutes the interface between every tissue and the outside world. It is patterned into diverse tissue-specific structures through unknown mechanisms. Here, we show that a male-specific genetic switch in a single C. elegans glial cell patterns the overlying aECM from a solid sheet to an ∼200 nm pore, thus allowing a male sensory neuron to access the environment. Using cell-specific genetic sex reversal, we find that this switch reflects an inherent sex difference in the glial cell that is independent of the sex identity of the surrounding neurons. Through candidate and unbiased genetic screens, we find that this glial sex difference is controlled by factors shared with neurons (mab-3, lep-2, and lep-5) as well as previously unidentified regulators whose effects may be glia specific (nfya-1, bed-3, and jmjd-3.1). The switch results in male-specific glial expression of a secreted Hedgehog-related protein, GRL-18, that we discover localizes to transient nanoscale rings at sites where aECM pores will form. Using electron microscopy, we find that blocking male-specific gene expression in glia prevents pore formation, whereas forcing male-specific glial gene expression induces an ectopic pore. Thus, a switch in gene expression in a single cell is necessary and sufficient to pattern aECM into a specific structure. Our results highlight that aECM is not a simple homogeneous meshwork, but instead is composed of discrete local features that reflect the identity of the underlying cells.
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Affiliation(s)
- Wendy Fung
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Taralyn M Tan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, 1015 Lausanne, Switzerland
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA.
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7
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Temporal control of neuronal wiring. Semin Cell Dev Biol 2023; 142:81-90. [PMID: 35644877 DOI: 10.1016/j.semcdb.2022.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/22/2022]
Abstract
Wiring an animal brain is a complex process involving a staggering number of cell-types born at different times and locations in the developing brain. Incorporation of these cells into precise circuits with high fidelity is critical for animal survival and behavior. Assembly of neuronal circuits is heavily dependent upon proper timing of wiring programs, requiring neurons to express specific sets of genes (sometimes transiently) at the right time in development. While cell-type specificity of genetic programs regulating wiring has been studied in detail, mechanisms regulating proper timing and coordination of these programs across cell-types are only just beginning to emerge. In this review, we discuss some temporal regulators of wiring programs and how their activity is controlled over time and space. A common feature emerges from these temporal regulators - they are induced by cell-extrinsic cues and control transcription factors capable of regulating a highly cell-type specific set of target genes. Target specificity in these contexts comes from cell-type specific transcription factors. We propose that the spatiotemporal specificity of wiring programs is controlled by the combinatorial activity of temporal programs and cell-type specific transcription factors. Going forward, a better understanding of temporal regulators will be key to understanding the mechanisms underlying brain wiring, and will be critical for the development of in vitro models like brain organoids.
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8
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Dash PK, Gupta P, Sreevathsa R, Pradhan SK, Sanjay TD, Mohanty MR, Roul PK, Singh NK, Rai R. Phylogenomic Analysis of micro-RNA Involved in Juvenile to Flowering-Stage Transition in Photophilic Rice and Its Sister Species. Cells 2023; 12:1370. [PMID: 37408207 DOI: 10.3390/cells12101370] [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: 03/13/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 07/07/2023] Open
Abstract
Vegetative to reproductive phase transition in phototropic plants is an important developmental process and is sequentially mediated by the expression of micro-RNA MIR172. To obtain insight into the evolution, adaptation, and function of MIR172 in photophilic rice and its wild relatives, we analyzed the genescape of a 100 kb segment harboring MIR172 homologs from 11 genomes. The expression analysis of MIR172 revealed its incremental accumulation from the 2-leaf to 10-leaf stage, with maximum expression coinciding with the flag-leaf stage in rice. Nonetheless, the microsynteny analysis of MIR172s revealed collinearity within the genus Oryza, but a loss of synteny was observed in (i) MIR172A in O. barthii (AA) and O. glaberima (AA); (ii) MIR172B in O. brachyantha (FF); and (iii) MIR172C in O. punctata (BB). Phylogenetic analysis of precursor sequences/region of MIR172 revealed a distinct tri-modal clade of evolution. The genomic information generated in this investigation through comparative analysis of MIRNA, suggests mature MIR172s to have evolved in a disruptive and conservative mode amongst all Oryza species with a common origin of descent. Further, the phylogenomic delineation provided an insight into the adaptation and molecular evolution of MIR172 to changing environmental conditions (biotic and abiotic) of phototropic rice through natural selection and the opportunity to harness untapped genomic regions from rice wild relatives (RWR).
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Affiliation(s)
- Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Payal Gupta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | | | | | - Mihir Ranjan Mohanty
- Department of Genetics & Plant Breeding (RRTTS, Jeypore), Odisha University of Agriculture and Technology, Bhubaneswar 751003, India
| | - Pravat K Roul
- Department of Genetics & Plant Breeding (RRTTS, Jeypore), Odisha University of Agriculture and Technology, Bhubaneswar 751003, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rhitu Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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9
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Fung W, Tan TM, Kolotuev I, Heiman MG. A sex-specific switch in a single glial cell patterns the apical extracellular matrix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533199. [PMID: 36993293 PMCID: PMC10055199 DOI: 10.1101/2023.03.17.533199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Apical extracellular matrix (aECM) constitutes the interface between every tissue and the outside world. It is patterned into diverse tissue-specific structures through unknown mechanisms. Here, we show that a male-specific genetic switch in a single C. elegans glial cell patterns the aECM into a ∼200 nm pore, allowing a male sensory neuron to access the environment. We find that this glial sex difference is controlled by factors shared with neurons ( mab-3, lep-2, lep-5 ) as well as previously unidentified regulators whose effects may be glia-specific ( nfya-1, bed-3, jmjd-3.1 ). The switch results in male-specific expression of a Hedgehog-related protein, GRL-18, that we discover localizes to transient nanoscale rings at sites of aECM pore formation. Blocking male-specific gene expression in glia prevents pore formation, whereas forcing male-specific expression induces an ectopic pore. Thus, a switch in gene expression in a single cell is necessary and sufficient to pattern aECM into a specific structure.
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Affiliation(s)
- Wendy Fung
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
| | - Taralyn M. Tan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, 1015 Lausanne, Switzerland
| | - Maxwell G. Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115, USA
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10
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Xu Y, Zhang T, Zhou Q, Hu M, Qi Y, Xue Y, Nie Y, Wang L, Bao Z, Shi W. A single-cell transcriptome atlas profiles early organogenesis in human embryos. Nat Cell Biol 2023; 25:604-615. [PMID: 36928764 DOI: 10.1038/s41556-023-01108-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4-6 week human embryos when essentially all organs are just laid out. On the basis of over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 clusters in 18 developmental systems, which were annotated with a collection of ontology and markers from 157 publications. Together with spatial transcriptome on embryonic sections, we characterized the molecule and spatial architecture of previously unappreciated cell types. Combined with data from other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation. Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.
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Affiliation(s)
- Yichi Xu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Tengjiao Zhang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qin Zhou
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Mengzhu Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Qi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yifang Xue
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Yuxiao Nie
- School of Pharmacy, Fudan University, Shanghai, China
| | - Lihui Wang
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
| | - Weiyang Shi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
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11
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Zhou J, Lin L, Cai H, Liu L, Wang H, Zhang J, Xia G, Wang J, Wang F, Wang C. SP1 impacts the primordial to primary follicle transition by regulating cholesterol metabolism in granulosa cells. FASEB J 2023; 37:e22767. [PMID: 36624701 DOI: 10.1096/fj.202201274rr] [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: 08/06/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
The primordial to primary follicle transition (PPT) in the ovary is critical to maintain sustainable reproductive resources in female mammals. However, it is unclear how granulosa cells (GCs) of the primary follicle participate in regulating PPT. This study focused on exploring the role of transcription factor Sp1 (SP1) in regulating PPT based on the fact that SP1 is pivotal for pregranulosa cell proliferation before primordial follicle formation. The results showed that mice fertility was prolonged when Sp1 was specifically depleted from GCs (GC- Sp1 -/- ). Besides, the PPT in GC- Sp1 -/- mice was reduced, resulting in more primordial follicles being preserved. Single-cell RNA-seq also indicated that the level of cholesterol metabolism was downregulated in GC- Sp1 -/- mice. Additionally, the PPT was promoted by either overexpression of ferredoxin-1 (FDX1), one of the key genes in mediating cholesterol metabolism or supplementing cholesterol for cultured fetal ovaries. Collectively, SP1 in GCs participates in the metabolism of cholesterol partially by regulating the transcription of Fdx1 during the PPT.
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Affiliation(s)
- Jiaqi Zhou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lin Lin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Han Cai
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Longping Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Huarong Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jingwen Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guoliang Xia
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.,Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, School of Life Sciences, Ningxia University, Yinchuan, China
| | - Jianbin Wang
- School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Fengchao Wang
- Transgenic Animal Center, National Institute of Biological Sciences, Beijing, China
| | - Chao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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12
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Rowton M, Perez-Cervantes C, Hur S, Jacobs-Li J, Lu E, Deng N, Guzzetta A, Hoffmann AD, Stocker M, Steimle JD, Lazarevic S, Oubaha S, Yang XH, Kim C, Yu S, Eckart H, Koska M, Hanson E, Chan SSK, Garry DJ, Kyba M, Basu A, Ikegami K, Pott S, Moskowitz IP. Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. Dev Cell 2022; 57:2181-2203.e9. [PMID: 36108627 PMCID: PMC10506397 DOI: 10.1016/j.devcel.2022.08.009] [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: 01/14/2022] [Revised: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022]
Abstract
Many developmental signaling pathways have been implicated in lineage-specific differentiation; however, mechanisms that explicitly control differentiation timing remain poorly defined in mammals. We report that murine Hedgehog signaling is a heterochronic pathway that determines the timing of progenitor differentiation. Hedgehog activity was necessary to prevent premature differentiation of second heart field (SHF) cardiac progenitors in mouse embryos, and the Hedgehog transcription factor GLI1 was sufficient to delay differentiation of cardiac progenitors in vitro. GLI1 directly activated a de novo progenitor-specific network in vitro, akin to that of SHF progenitors in vivo, which prevented the onset of the cardiac differentiation program. A Hedgehog signaling-dependent active-to-repressive GLI transition functioned as a differentiation timer, restricting the progenitor network to the SHF. GLI1 expression was associated with progenitor status across germ layers, and it delayed the differentiation of neural progenitors in vitro, suggesting a broad role for Hedgehog signaling as a heterochronic pathway.
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Affiliation(s)
- Megan Rowton
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Suzy Hur
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Jessica Jacobs-Li
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Emery Lu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Nikita Deng
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Alexander Guzzetta
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Andrew D Hoffmann
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Matthew Stocker
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sonja Lazarevic
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sophie Oubaha
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Xinan H Yang
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Chul Kim
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Shuhan Yu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Heather Eckart
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Mervenaz Koska
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Erika Hanson
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sunny S K Chan
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anindita Basu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Kohta Ikegami
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA.
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13
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Abstract
An enduring mystery of development is how its timing is controlled, particularly for development after birth, where timing is highly flexible and depends on environmental conditions, such as food availability and diet. We followed timing of cell- and organism-level events in individual Caenorhabditis elegans larvae developing from hatching to adulthood, uncovering widespread variations in event timing, both between isogenic individuals in the same environment and when changing conditions and genotypes. However, in almost all cases, we found that events occurred at the same time, when time was rescaled by the duration of development measured in each individual. This observation of “temporal scaling” poses strong constraints on models to explain timing of larval development. It is essential that correct temporal order of cellular events is maintained during animal development. During postembryonic development, the rate of development depends on external conditions, such as food availability, diet, and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism level is not known. We used a unique time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions, and cuticle shedding in individual Caenorhabditis elegans larvae, as they developed from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed “temporal scaling,” meaning that events occurred at the same time when measured relative to the total duration of development in each individual. We also observed pervasive changes in timing when temperature, diet, or genotype were varied, but with larval development divided in “epochs” that differed in how event timing was impacted. Yet, these variations in timing were still explained by temporal scaling when time was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lacking lin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing. However, shifting conditions middevelopment perturbed temporal scaling and changed event order in a highly condition-specific manner, indicating that a complex machinery is responsible for temporal scaling under constant conditions.
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14
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Gao J, Zhang K, Cheng YJ, Yu S, Shang GD, Wang FX, Wu LY, Xu ZG, Mai YX, Zhao XY, Zhai D, Lian H, Wang JW. A robust mechanism for resetting juvenility during each generation in Arabidopsis. NATURE PLANTS 2022; 8:257-268. [PMID: 35318444 DOI: 10.1038/s41477-022-01110-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 02/10/2022] [Indexed: 05/02/2023]
Abstract
Multicellular organisms undergo several developmental transitions during their life cycles. In contrast to animals, the plant germline is derived from adult somatic cells. As such, the juvenility of a plant must be reset in each generation. Previous studies have demonstrated that the decline in the levels of miR156/7 with age drives plant maturation. Here we show that the resetting of plant juvenility during each generation is mediated by de novo activation of MIR156/7 in Arabidopsis. Blocking this process leads to a shortened juvenile phase and premature flowering in the offspring. In particular, an Arabidopsis plant devoid of miR156/7 flowers even without formation of rosette leaves in long days. Mechanistically, we find that different MIR156/7 genes are reset at different developmental stages through distinct reprogramming routes. Among these genes, MIR156A, B and C are activated de novo during sexual reproduction and embryogenesis, while MIR157A and C are reset upon seed germination. This redundancy generates a robust reset mechanism that ensures accurate restoration of the juvenile phase in each plant generation.
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Affiliation(s)
- Jian Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Ke Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying-Juan Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Sha Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Fu-Xiang Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Lian-Yu Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Yan-Xia Mai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xin-Yan Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, China
| | - Dong Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Heng Lian
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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15
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Network Approaches to Study Endogenous RNA Competition and Its Impact on Tissue-Specific microRNA Functions. Biomolecules 2022; 12:biom12020332. [PMID: 35204832 PMCID: PMC8868585 DOI: 10.3390/biom12020332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
microRNAs are small non-coding RNAs that play a key role in regulating gene expression. These molecules exert their function through sequence complementarity with microRNA responsive elements and are typically located in the 3′ untranslated region of mRNAs, negatively regulating expression. Even though the relevant role of miRNA-dependent regulation is broadly recognized, the principles governing their ability to lead to specific functional outcomes in distinct cell types are still not well understood. In recent years, an intriguing hypothesis proposed that miRNA-responsive elements act as communication links between different RNA species, making the investigation of microRNA function even more complex than previously thought. The competing endogenous RNA hypothesis suggests the presence of a new level of regulation, whereby a specific RNA transcript can indirectly influence the abundance of other transcripts by limiting the availability of a common miRNA, acting as a “molecular sponge”. Since this idea has been proposed, several studies have tried to pinpoint the interaction networks that have been established between different RNA species and whether they contribute to normal cell function and disease. The focus of this review is to highlight recent developments and achievements made towards the process of characterizing competing endogenous RNA networks and their role in cellular function.
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16
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Abstract
Biological development is often described as a dynamic, emergent process. This is evident across a variety of phenomena, from the temporal organization of cell types in the embryo to compounding trends that affect large-scale differentiation. To better understand this, we propose combining quantitative investigations of biological development with theory-building techniques. This provides an alternative to the gene-centric view of development: namely, the view that developmental genes and their expression determine the complexity of the developmental phenotype. Using the model system Caenorhabditis elegans, we examine time-dependent properties of the embryonic phenotype and utilize the unique life-history properties to demonstrate how these emergent properties can be linked together by data analysis and theory-building. We also focus on embryogenetic differentiation processes, and how terminally-differentiated cells contribute to structure and function of the adult phenotype. Examining embryogenetic dynamics from 200 to 400 min post-fertilization provides basic quantitative information on developmental tempo and process. To summarize, theory construction techniques are summarized and proposed as a way to rigorously interpret our data. Our proposed approach to a formal data representation that can provide critical links across life-history, anatomy and function.
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17
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Dobreva MP, Camacho J, Abzhanov A. Time to synchronize our clocks: Connecting developmental mechanisms and evolutionary consequences of heterochrony. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:87-106. [PMID: 34826199 DOI: 10.1002/jez.b.23103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Heterochrony, defined as a change in the timing of developmental events altering the course of evolution, was first recognized by Ernst Haeckel in 1866. Haeckel's original definition was meant to explain the observed parallels between ontogeny and phylogeny, but the interpretation of his work became a source of controversy over time. Heterochrony took its modern meaning following the now classical work in the 1970-80s by Steven J. Gould, Pere Alberch, and co-workers. Predicted and described heterochronic scenarios emphasize the many ways in which developmental changes can influence evolution. However, while important examples of heterochrony detected with comparative morphological methods have multiplied, the more mechanistic understanding of this phenomenon lagged conspicuously behind. Considering the rapid progress in imaging and molecular tools available now for developmental biologists, this review aims to stress the need to take heterochrony research to the next level. It is time to synchronize the different levels of heterochrony research into a single analysis flow: from studies on organismal-level morphology to cells to molecules and genes, using complementary techniques. To illustrate how to achieve a more comprehensive understanding of phyletic morphological diversification associated with heterochrony, we discuss several recent case studies at various phylogenetic scales that combine morphological, cellular, and molecular analyses. Such a synergistic approach offers to more fully integrate phylogenetic and ontogenetic dimensions of the fascinating evolutionary phenomenon of heterochrony.
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Affiliation(s)
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Arkhat Abzhanov
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
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18
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Cell division in the shoot apical meristem is a trigger for miR156 decline and vegetative phase transition in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2115667118. [PMID: 34750273 DOI: 10.1073/pnas.2115667118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
What determines the rate at which a multicellular organism matures is a fundamental question in biology. In plants, the decline of miR156 with age serves as an intrinsic, evolutionarily conserved timer for the juvenile-to-adult phase transition. However, the way in which age regulates miR156 abundance is poorly understood. Here, we show that the rate of decline in miR156 is correlated with developmental age rather than chronological age. Mechanistically, we found that cell division in the apical meristem is a trigger for miR156 decline. The transcriptional activity of MIR156 genes is gradually attenuated by the deposition of the repressive histone mark H3K27me3 along with cell division. Our findings thus provide a plausible explanation of why the maturation program of a multicellular organism is unidirectional and irreversible under normal growth conditions and suggest that cell quiescence is the fountain of youth in plants.
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19
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Liu J, Sauer MA, Hussein SG, Yang J, Tenen DG, Chai L. SALL4 and microRNA: The Role of Let-7. Genes (Basel) 2021; 12:1301. [PMID: 34573282 PMCID: PMC8467721 DOI: 10.3390/genes12091301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
SALL4 is a zinc finger transcription factor that belongs to the spalt-like (SALL) gene family. It plays important roles in the maintenance of self-renewal and pluripotency of embryonic stem cells, and its expression is repressed in most adult organs. SALL4 re-expression has been observed in different types of human cancers, and dysregulation of SALL4 contributes to the pathogenesis, metastasis, and even drug resistance of multiple cancer types. Surprisingly, little is known regarding how SALL4 expression is controlled, but recently microRNAs (miRNAs) have emerged as important regulators of SALL4. Due to the ability of regulating targets differentially in specific tissues, and recent advances in systemic and organ specific miRNA delivery mechanisms, miRNAs have emerged as promising therapeutic targets for cancer treatment. In this review, we summarize current knowledge of the interaction between SALL4 and miRNAs in mammalian development and cancer, paying particular attention to the emerging roles of the Let-7/Lin28 axis. In addition, we discuss the therapeutic prospects of targeting SALL4 using miRNA-based strategies, with a focus on the Let-7/LIN28 axis.
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Affiliation(s)
- Jun Liu
- Department of Pathology, Brigham & Women’s Hospital, Boston, MA 02115, USA; (J.L.); (M.A.S.); (J.Y.)
| | - Madeline A. Sauer
- Department of Pathology, Brigham & Women’s Hospital, Boston, MA 02115, USA; (J.L.); (M.A.S.); (J.Y.)
| | | | - Junyu Yang
- Department of Pathology, Brigham & Women’s Hospital, Boston, MA 02115, USA; (J.L.); (M.A.S.); (J.Y.)
| | - Daniel G. Tenen
- Cancer Science Institute, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Li Chai
- Department of Pathology, Brigham & Women’s Hospital, Boston, MA 02115, USA; (J.L.); (M.A.S.); (J.Y.)
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20
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Heredia F, Volonté Y, Pereirinha J, Fernandez-Acosta M, Casimiro AP, Belém CG, Viegas F, Tanaka K, Menezes J, Arana M, Cardoso GA, Macedo A, Kotowicz M, Prado Spalm FH, Dibo MJ, Monfardini RD, Torres TT, Mendes CS, Garelli A, Gontijo AM. The steroid-hormone ecdysone coordinates parallel pupariation neuromotor and morphogenetic subprograms via epidermis-to-neuron Dilp8-Lgr3 signal induction. Nat Commun 2021; 12:3328. [PMID: 34099654 PMCID: PMC8184853 DOI: 10.1038/s41467-021-23218-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
Innate behaviors consist of a succession of genetically-hardwired motor and physiological subprograms that can be coupled to drastic morphogenetic changes. How these integrative responses are orchestrated is not completely understood. Here, we provide insight into these mechanisms by studying pupariation, a multi-step innate behavior of Drosophila larvae that is critical for survival during metamorphosis. We find that the steroid-hormone ecdysone triggers parallel pupariation neuromotor and morphogenetic subprograms, which include the induction of the relaxin-peptide hormone, Dilp8, in the epidermis. Dilp8 acts on six Lgr3-positive thoracic interneurons to couple both subprograms in time and to instruct neuromotor subprogram switching during behavior. Our work reveals that interorgan feedback gates progression between subunits of an innate behavior and points to an ancestral neuromodulatory function of relaxin signaling.
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Affiliation(s)
- Fabiana Heredia
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Yanel Volonté
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- INIBIBB, Instituto de Investigaciones Bioquímicas de Bahia Blanca, Universidad Nacional del Sur - CONICET, Bahía Blanca, Argentina
| | - Joana Pereirinha
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Institute of Molecular Biology, Mainz, Germany
| | - Magdalena Fernandez-Acosta
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Andreia P Casimiro
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Cláudia G Belém
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- The Francis Crick Institute, London, UK
| | - Filipe Viegas
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Kohtaro Tanaka
- Instituto Gulbenkian de Ciências, Oeiras, Portugal
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Juliane Menezes
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Maite Arana
- INIBIBB, Instituto de Investigaciones Bioquímicas de Bahia Blanca, Universidad Nacional del Sur - CONICET, Bahía Blanca, Argentina
| | - Gisele A Cardoso
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Laboratório de Genômica e Evolução de Artrópodes, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
- CBMEG, Universidade Estadual de Campinas, Campinas, Brazil
| | - André Macedo
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Malwina Kotowicz
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- DZNE, Helmholtz Association, Bonn, Germany
| | - Facundo H Prado Spalm
- INIBIBB, Instituto de Investigaciones Bioquímicas de Bahia Blanca, Universidad Nacional del Sur - CONICET, Bahía Blanca, Argentina
| | - Marcos J Dibo
- INIBIBB, Instituto de Investigaciones Bioquímicas de Bahia Blanca, Universidad Nacional del Sur - CONICET, Bahía Blanca, Argentina
| | - Raquel D Monfardini
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Laboratório de Genômica e Evolução de Artrópodes, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - Tatiana T Torres
- Laboratório de Genômica e Evolução de Artrópodes, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - César S Mendes
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Andres Garelli
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal.
- INIBIBB, Instituto de Investigaciones Bioquímicas de Bahia Blanca, Universidad Nacional del Sur - CONICET, Bahía Blanca, Argentina.
| | - Alisson M Gontijo
- CEDOC, Chronic Diseases Research Center, NOVA Medical School | Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal.
- The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Rua do Instituto Bacteriológico 5, 1150-190, Lisbon, Portugal.
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21
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Xu Y, Zhang L, Liu Y, Topalidou I, Hassinan C, Ailion M, Zhao Z, Wang T, Chen Z, Bai J. Dopamine receptor DOP-1 engages a sleep pathway to modulate swimming in C. elegans. iScience 2021; 24:102247. [PMID: 33796839 PMCID: PMC7995527 DOI: 10.1016/j.isci.2021.102247] [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: 10/12/2020] [Revised: 02/06/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
Animals require robust yet flexible programs to support locomotion. Here we report a pathway that connects the D1-like dopamine receptor DOP-1 with a sleep mechanism to modulate swimming in C. elegans. We show that DOP-1 plays a negative role in sustaining swimming behavior. By contrast, a pathway through the D2-like dopamine receptor DOP-3 negatively regulates the initiation of swimming, but its impact fades quickly over a few minutes. We find that DOP-1 and the GPCR kinase (G-protein-coupled receptor kinase-2) function in the sleep interneuron RIS, where DOP-1 modulates the secretion of a sleep neuropeptide FLP-11. We further show that DOP-1 and FLP-11 act in the same pathway to modulate swimming. Together, these results delineate a functional connection between a dopamine receptor and a sleep program to regulate swimming in C. elegans. The temporal transition between DOP-3 and DOP-1 pathways highlights the dynamic nature of neuromodulation for rhythmic movements that persist over time.
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Affiliation(s)
- Ye Xu
- Department of Clinical Medicine, Nanjing Medical University, Nanjing 211166, P. R. China.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA.,Department of Neurology, First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan 570102, P. R. China
| | - Lin Zhang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - Yan Liu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, WA 98195
| | - Cera Hassinan
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98019
| | - Michael Ailion
- Department of Biochemistry, University of Washington, WA 98195
| | - Zhenqiang Zhao
- Department of Neurology, First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan 570102, P. R. China
| | - Tan Wang
- Department of Neurology, First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan 570102, P. R. China
| | - Zhibin Chen
- Department of Clinical Medicine, Nanjing Medical University, Nanjing 211166, P. R. China.,Department of Neurology, First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan 570102, P. R. China
| | - Jihong Bai
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98019.,Department of Biochemistry, University of Washington, WA 98195
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22
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Cui Y, Cheng J, Ruan S, Qi P, Liu W, Bian H, Ye L, Zhang Y, Hu J, Dong G, Guo L, Zhang Y, Qian Q, Hu X. The heterochronic gene Oryza sativa LIKE HETEROCHROMATIN PROTEIN 1 modulates miR156b/c/i/e levels. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1839-1852. [PMID: 32644250 DOI: 10.1111/jipb.12991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
The juvenile-to-adult transition in plants involves changes in vegetative growth and plant architecture; the timing of this transition has important implications for agriculture. The microRNA miR156 regulates this transition and shoot maturation in plants. In Arabidopsis thaliana, deposition of histone H3 trimethylation on lysine 27 (H3K27me3, a repressive mark) at the MIR156A/C loci is regulated by Polycomb Repressive Complex 1 (PRC1) or PRC2, depending on the developmental stage. The levels of miR156 progressively decline during shoot maturation. The amount of H3K27me3 at MIR156A/C loci affects miR156 levels; however, whether this epigenetic regulation is conserved remains unclear. Here, we found that in rice (Oryza sativa), the putative PRC1 subunit LIKE HETEROCHROMATIN PROTEIN 1 (OsLHP1), with the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module, affects developmental phase transitions. Loss of OsLHP1 function results in ectopic expression of MIR156B/C/I/E, phenocopy of miR156 overexpression, and reduced H3k27me3 levels at MIR156B/C/I/E. This indicates that OsLHP1 has functionally diverged from Arabidopsis LHP1. Genetic and transcriptome analyses of wild-type, miR156b/c-overexpression, and Oslhp1-2 mutant plants suggest that OsLHP1 acts upstream of miR156 and SPL during the juvenile-to-adult transition. Therefore, modifying the OsLHP1-miR156-SPL pathway may enable alteration of the vegetative period and plant architecture.
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Affiliation(s)
- Yongtao Cui
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shuang Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peipei Qi
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuping Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xingming Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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Sun Y, Yu Q, Li L, Mei Z, Zhou B, Liu S, Pan T, Wu L, Lei Y, Liu L, Drmanac R, Ma K, Liu S. Single-cell RNA profiling links ncRNAs to spatiotemporal gene expression during C. elegans embryogenesis. Sci Rep 2020; 10:18863. [PMID: 33139759 PMCID: PMC7606524 DOI: 10.1038/s41598-020-75801-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/06/2020] [Indexed: 01/04/2023] Open
Abstract
Recent studies show that non-coding RNAs (ncRNAs) can regulate the expression of protein-coding genes and play important roles in mammalian development. Previous studies have revealed that during C. elegans (Caenorhabditis elegans) embryo development, numerous genes in each cell are spatiotemporally regulated, causing the cell to differentiate into distinct cell types and tissues. We ask whether ncRNAs participate in the spatiotemporal regulation of genes in different types of cells and tissues during the embryogenesis of C. elegans. Here, by using marker-free full-length high-depth single-cell RNA sequencing (scRNA-seq) technique, we sequence the whole transcriptomes from 1031 embryonic cells of C. elegans and detect 20,431 protein-coding genes, including 22 cell-type-specific protein-coding markers, and 9843 ncRNAs including 11 cell-type-specific ncRNA markers. We induce a ncRNAs-based clustering strategy as a complementary strategy to the protein-coding gene-based clustering strategy for single-cell classification. We identify 94 ncRNAs that have never been reported to regulate gene expressions, are co-expressed with 1208 protein-coding genes in cell type specific and/or embryo time specific manners. Our findings suggest that these ncRNAs could potentially influence the spatiotemporal expression of the corresponding genes during the embryogenesis of C. elegans.
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Affiliation(s)
- Yan Sun
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Qichao Yu
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Lei Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Biaofeng Zhou
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Shang Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Taotao Pan
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Liang Wu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Ying Lei
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | | | - Kun Ma
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China.
| | - Shiping Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, 518100, China.
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Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci 2020; 77:3991-4014. [PMID: 32303790 PMCID: PMC11105112 DOI: 10.1007/s00018-020-03518-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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Salzberg Y, Gat A, Oren-Suissa M. One template, two outcomes: How does the sex-shared nervous system generate sex-specific behaviors? Curr Top Dev Biol 2020; 144:245-268. [PMID: 33992155 DOI: 10.1016/bs.ctdb.2020.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Sex-specific behaviors are common in nature and are crucial for reproductive fitness and species survival. A key question in the field of sex/gender neurobiology is whether and to what degree the sex-shared nervous system differs between the sexes in the anatomy, connectivity and molecular identity of its components. An equally intriguing issue is how does the same sex-shared neuronal template diverge to mediate distinct behavioral outputs in females and males. This chapter aims to present the most up-to-date understanding of how this task is achieved in C. elegans. The vast majority of neurons in C. elegans are shared among the two sexes in terms of their lineage history, anatomical position and neuronal identity. Yet a substantial amount of evidence points to the hermaphrodite-male counterparts of some neurons expressing different genes and forming different synaptic connections. This, in turn, enables the same cells and circuits to transmit discrete signals in the two sexes and ultimately execute different functions. We review the various sex-shared behavioral paradigms that have been shown to be sexually dimorphic in recent years, discuss the mechanisms that underlie these examples, refer to the developmental regulation of neuronal dimorphism and suggest evolutionary concepts that emerge from the data.
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Affiliation(s)
- Yehuda Salzberg
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Asaf Gat
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Meital Oren-Suissa
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.
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26
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Ledesma-Durán A, Ortiz-Durán EA, Aragón JL, Santamaría-Holek I. Eckhaus selection: The mechanism of pattern persistence in a reaction-diffusion system. Phys Rev E 2020; 102:032214. [PMID: 33076036 DOI: 10.1103/physreve.102.032214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/01/2020] [Indexed: 11/07/2022]
Abstract
In this work, we show theoretically and numerically that a one-dimensional reaction-diffusion system, near the Turing bifurcation, produces different number of stripes when, in addition to random noise, the Fourier mode of a prepattern used to initialize the system changes. We also show that the Fourier modes that persist are inside the Eckhaus stability regions, while those outside this region follow a wave number selection process not predicted by the linear analysis. To test our results, we use the Brusselator reaction-diffusion system obtaining an excellent agreement between the weakly nonlinear predictions of the real Ginzburg-Landau equations and the numerical solutions near the bifurcation. Although the persistence of patterns is not relevant as a simple generating mechanism of self-organization, it is crucial to understand the formation of patterns that occurs in multiple stages. In this work, we discuss the relevance of our results on the robustness and diversity of solutions in multiple-steps mechanisms of biological pattern formation and auto-organization in growing domains.
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Affiliation(s)
- Aldo Ledesma-Durán
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla, 76230 Querétaro, Mexico
| | - E A Ortiz-Durán
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla, 76230 Querétaro, Mexico
| | - J L Aragón
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla, 76230 Querétaro, Mexico
| | - Iván Santamaría-Holek
- Unidad Multidiciplinaria de Docencia e Investigación, Facutad de Ciencias, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla, 76230 Querétaro, Mexico
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Li ML, Tang H, Shao Y, Wang MS, Xu HB, Wang S, Irwin DM, Adeola AC, Zeng T, Chen L, Li Y, Wu DD. Evolution and transition of expression trajectory during human brain development. BMC Evol Biol 2020; 20:72. [PMID: 32576137 PMCID: PMC7310562 DOI: 10.1186/s12862-020-01633-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/26/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The remarkable abilities of the human brain are distinctive features that set us apart from other animals. However, our understanding of how the brain has changed in the human lineage remains incomplete, but is essential for understanding cognition, behavior, and brain disorders in humans. Here, we compared the expression trajectory in brain development between humans and rhesus macaques (Macaca mulatta) to explore their divergent transcriptome profiles. RESULTS Results showed that brain development could be divided into two stages, with a demarcation date in a range between 25 and 26 postconception weeks (PCW) for humans and 17-23PCWfor rhesus macaques, rather than birth time that have been widely used as a uniform demarcation time of neurodevelopment across species. Dynamic network biomarker (DNB) analysis revealed that the two demarcation dates were transition phases during brain development, after which the brain transcriptome profiles underwent critical transitions characterized by highly fluctuating DNB molecules. We also found that changes between early and later brain developmental stages (as defined by the demarcation points) were substantially greater in the human brain than in the macaque brain. To explore the molecular mechanism underlying prolonged timing during early human brain development, we carried out expression heterochrony tests. Results demonstrated that compared to macaques, more heterochronic genes exhibited neoteny during early human brain development, consistent with the delayed demarcation time in the human lineage, and proving that neoteny in human brain development could be traced to the prenatal period. We further constructed transcriptional networks to explore the profile of early human brain development and identified the hub gene RBFOX1 as playing an important role in regulating early brain development. We also found RBFOX1 evolved rapidly in its non-coding regions, indicating that this gene played an important role in human brain evolution. Our findings provide evidence that RBFOX1 is a likely key hub gene in early human brain development and evolution. CONCLUSIONS By comparing gene expression profiles between humans and macaques, we found divergent expression trajectories between the two species, which deepens our understanding of the evolution of the human brain.
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Affiliation(s)
- Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Hui Tang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Hai-Bo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, Ontario, M5G 2C4, Canada
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Tao Zeng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, 650091, Yunnan, China.
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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Abete-Luzi P, Fukushige T, Yun S, Krause MW, Eisenmann DM. New Roles for the Heterochronic Transcription Factor LIN-29 in Cuticle Maintenance and Lipid Metabolism at the Larval-to-Adult Transition in Caenorhabditis elegans. Genetics 2020; 214:669-690. [PMID: 31974205 PMCID: PMC7054012 DOI: 10.1534/genetics.119.302860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/21/2020] [Indexed: 11/18/2022] Open
Abstract
Temporal regulation of gene expression is a crucial aspect of metazoan development. In the roundworm Caenorhabditis elegans, the heterochronic pathway controls multiple developmental events in a time-specific manner. The most downstream effector of this pathway, the zinc-finger transcription factor LIN-29, acts in the last larval stage (L4) to regulate elements of the larval-to-adult switch. Here, we explore new LIN-29 targets and their implications for this developmental transition. We used RNA-sequencing to identify genes differentially expressed between animals misexpressing LIN-29 at an early time point and control animals. Among 230 LIN-29-activated genes, we found that genes encoding cuticle collagens were overrepresented. Interestingly, expression of lin-29 and some of these collagens was increased in adults with cuticle damage, suggesting a previously unknown function for LIN-29 in adult cuticle maintenance. On the other hand, genes involved in fat metabolism were enriched among 350 LIN-29-downregulated targets. We used mass spectrometry to assay lipid content in animals overexpressing LIN-29 and observed reduced fatty acid levels. Many LIN-29-repressed genes are normally expressed in the intestine, suggesting cell-nonautonomous regulation. We identified several LIN-29 upregulated genes encoding signaling molecules that may act as mediators in the regulation of intestinally expressed genes encoding fat metabolic enzymes and vitellogenins. Overall, our results support the model of LIN-29 as a major regulator of adult cuticle synthesis and integrity, and as the trigger for metabolic changes that take place at the important transition from rapid growth during larval life to slower growth and offspring production during adulthood.
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Affiliation(s)
- Patricia Abete-Luzi
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Sijung Yun
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael W Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - David M Eisenmann
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250
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29
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Does Birth Trigger Cell Death in the Developing Brain? eNeuro 2020; 7:ENEURO.0517-19.2020. [PMID: 32015098 PMCID: PMC7031855 DOI: 10.1523/eneuro.0517-19.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/27/2022] Open
Abstract
Developmental cell death eliminates half of the neurons initially generated in the mammalian brain, and occurs perinatally in many species. It is possible that the timing of neuronal cell death is developmentally programmed, and only coincidentally associated with birth. Alternatively, birth may play a role in shaping cell death. To test these competing hypotheses, we experimentally advanced or delayed birth by 1 d in mice (within the normal range of gestation for the species) and examined effects on the temporal pattern and magnitude (amount) of neuronal cell death, using immunohistochemical detection of activated caspase-3 as a cell death marker. In order to detect effects of subtle changes in birth timing, we focused on brain areas that exhibit sharp postnatal peaks in cell death. We find that advancing birth advances peak cell death, supporting the hypothesis that birth triggers cell death. However, a delay of birth does not delay cell death. Thus, birth can advance cell death, but if postponed, a developmental program governs. Advancing or delaying birth also caused region-specific changes in the overall magnitude of cell death. Our findings shed light on the long-standing question of what controls the timing and magnitude of developmental neuronal cell death, and position birth as an orchestrator of brain development. Because humans across the world now routinely alter birth timing, these findings may have implications for current obstetric practices.
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Chambers CB, Gross J, Pratt K, Guo X, Byrnes C, Lee YT, Lavelle D, Dean A, Miller JL, Wilber A. The mRNA-Binding Protein IGF2BP1 Restores Fetal Hemoglobin in Cultured Erythroid Cells from Patients with β-Hemoglobin Disorders. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:429-440. [PMID: 32154328 PMCID: PMC7056608 DOI: 10.1016/j.omtm.2020.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/22/2020] [Indexed: 12/12/2022]
Abstract
Sickle cell disease (SCD) and β-thalassemia are caused by structural abnormality or inadequate production of adult hemoglobin (HbA, α2β2), respectively. Individuals with either disorder are asymptomatic before birth because fetal hemoglobin (HbF, α2γ2) is unaffected. Thus, reversal of the switch from HbF to HbA could reduce or even prevent symptoms these disorders. In this study, we show that insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) is one factor that could accomplish this goal. IGF2BP1 is a fetal factor that undergoes a transcriptional switch consistent with the transition from HbF to HbA. Lentivirus delivery of IGF2BP1 to CD34+ cells of healthy adult donors reversed hemoglobin production toward the fetal type in culture-differentiated erythroid cells. Analogous studies using patient-derived CD34+ cells revealed that IGF2BP1-dependent HbF induction could ameliorate the chain imbalance in β-thalassemia or potently suppress expression of sickle β-globin in SCD. In all cases, fetal γ-globin mRNA increased and adult β-globin decreased due, in part, to formation of contacts between the locus control region (LCR) and γ-globin genes. We conclude that expression of IGF2BP1 in adult erythroid cells has the potential to maximize HbF expression in patients with severe β-hemoglobin disorders by reversing the developmental γ- to β-globin switch.
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Affiliation(s)
- Christopher B Chambers
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
| | - Jeffrey Gross
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
| | - Katherine Pratt
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
| | - Xiang Guo
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Colleen Byrnes
- Genetics of Development and Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Y Terry Lee
- Genetics of Development and Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Donald Lavelle
- Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.,Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffery L Miller
- Genetics of Development and Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew Wilber
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL 62702, USA.,Simmons Cancer Institute, Springfield, IL 62702, USA
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31
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van der Horst SEM, Cravo J, Woollard A, Teapal J, van den Heuvel S. C. elegans Runx/CBFβ suppresses POP-1 TCF to convert asymmetric to proliferative division of stem cell-like seam cells. Development 2019; 146:dev.180034. [PMID: 31740621 PMCID: PMC6899014 DOI: 10.1242/dev.180034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/18/2019] [Indexed: 01/04/2023]
Abstract
A correct balance between proliferative and asymmetric cell divisions underlies normal development, stem cell maintenance and tissue homeostasis. What determines whether cells undergo symmetric or asymmetric cell division is poorly understood. To gain insight into the mechanisms involved, we studied the stem cell-like seam cells in the Caenorhabditis elegans epidermis. Seam cells go through a reproducible pattern of asymmetric divisions, instructed by divergent canonical Wnt/β-catenin signaling, and symmetric divisions that increase the seam cell number. Using time-lapse fluorescence microscopy we observed that symmetric cell divisions maintain asymmetric localization of Wnt/β-catenin pathway components. Our observations, based on lineage-specific knockout and GFP-tagging of endogenous pop-1, support the model that POP-1TCF induces differentiation at a high nuclear level, whereas low nuclear POP-1 promotes seam cell self-renewal. Before symmetric division, the transcriptional regulator RNT-1Runx and cofactor BRO-1CBFβ temporarily bypass Wnt/β-catenin asymmetry by downregulating pop-1 expression. Thereby, RNT-1/BRO-1 appears to render POP-1 below the level required for its repressor function, which converts differentiation into self-renewal. Thus, we found that conserved Runx/CBFβ-type stem cell regulators switch asymmetric to proliferative cell division by opposing TCF-related transcriptional repression. Summary: To switch asymmetric to proliferative cell division, the C. elegans RNT-1/BRO-1 transcriptional repressor opposes POP-1 TCF expression in seam stem cells, which turns POP-1-induced differentiation into self-renewal.
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Affiliation(s)
- Suzanne E M van der Horst
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Janine Cravo
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alison Woollard
- Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK
| | - Juliane Teapal
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sander van den Heuvel
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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32
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Axin Family of Scaffolding Proteins in Development: Lessons from C. elegans. J Dev Biol 2019; 7:jdb7040020. [PMID: 31618970 PMCID: PMC6956378 DOI: 10.3390/jdb7040020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022] Open
Abstract
Scaffold proteins serve important roles in cellular signaling by integrating inputs from multiple signaling molecules to regulate downstream effectors that, in turn, carry out specific biological functions. One such protein, Axin, represents a major evolutionarily conserved scaffold protein in metazoans that participates in the WNT pathway and other pathways to regulate diverse cellular processes. This review summarizes the vast amount of literature on the regulation and functions of the Axin family of genes in eukaryotes, with a specific focus on Caenorhabditis elegans development. By combining early studies with recent findings, the review is aimed to serve as an updated reference for the roles of Axin in C. elegans and other model systems.
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Komarovsky Gulman N, Armon L, Shalit T, Urbach A. Heterochronic regulation of lung development via the Lin28-Let-7 pathway. FASEB J 2019; 33:12008-12018. [PMID: 31373834 DOI: 10.1096/fj.201802702r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The heterochronic gene Lin28 regulates diverse developmental processes. It was shown previously that global Lin28A overexpression during mouse embryogenesis results in perinatal lethality. However, the reason for this early lethality has not been elucidated. Here, we showed that Lin28A overexpression prevents normal lung development via the inhibition of the Let-7 micro RNAs, thus causing the perinatal lethality. We further found that Lin28A overexpression in lung mesenchymal cells, but not epithelial cells, is sufficient to recapitulate the lung phenotype. Moreover, we defined the specific time window wherein Lin28A expression exerts its effect. Deep characterization of the transgenic lungs suggests that the Lin28A-Let-7 pathway delays the transition from one developmental stage to another but does not completely abrogate the differentiation capacity of the lung progenitor cells. Finally, we suggested that the effect of Lin28A-Let-7 on embryonic lung development is mediated at least in part through the TGF-β1-signaling pathway. Altogether, these findings define for the first time the Lin28-Let-7 pathway as a critical heterochronic regulator of lung development.-Komarovsky Gulman, N., Armon, L., Shalit, T., Urbach, A. Heterochronic regulation of lung development via the Lin28-Let-7 pathway.
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Affiliation(s)
- Nelly Komarovsky Gulman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Leah Armon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tali Shalit
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Achia Urbach
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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Repressive Gene Regulation Synchronizes Development with Cellular Metabolism. Cell 2019; 178:980-992.e17. [PMID: 31353220 DOI: 10.1016/j.cell.2019.06.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/06/2019] [Accepted: 06/12/2019] [Indexed: 01/06/2023]
Abstract
Metabolic conditions affect the developmental tempo of animals. Developmental gene regulatory networks (GRNs) must therefore synchronize their dynamics with a variable timescale. We find that layered repression of genes couples GRN output with variable metabolism. When repressors of transcription or mRNA and protein stability are lost, fewer errors in Drosophila development occur when metabolism is lowered. We demonstrate the universality of this phenomenon by eliminating the entire microRNA family of repressors and find that development to maturity can be largely rescued when metabolism is reduced. Using a mathematical model that replicates GRN dynamics, we find that lowering metabolism suppresses the emergence of developmental errors by curtailing the influence of auxiliary repressors on GRN output. We experimentally show that gene expression dynamics are less affected by loss of repressors when metabolism is reduced. Thus, layered repression provides robustness through error suppression and may provide an evolutionary route to a shorter reproductive cycle.
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Regulation of Caenorhabditis elegans neuronal polarity by heterochronic genes. Proc Natl Acad Sci U S A 2019; 116:12327-12336. [PMID: 31164416 DOI: 10.1073/pnas.1820928116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many neurons display characteristic patterns of synaptic connections that are under genetic control. The Caenorhabditis elegans DA cholinergic motor neurons form synaptic connections only on their dorsal axons. We explored the genetic pathways that specify this polarity by screening for gene inactivations and mutations that disrupt this normal polarity of a DA motorneuron. A RAB-3::GFP fusion protein that is normally localized to presynaptic terminals along the dorsal axon of the DA9 motorneuron was used to screen for gene inactivations that disrupt the DA9 motorneuron polarity. This screen identified heterochronic genes as major regulators of DA neuron presynaptic polarity. In many heterochronic mutants, presynapses of this cholinergic motoneuron are mislocalized to the dendrite at the ventral side: inactivation of the blmp-1 transcription factor gene, the lin-29/Zn finger transcription factor, lin-28/RNA binding protein, and the let-7miRNA gene all disrupt the presynaptic polarity of this DA cholinergic neuron. We also show that the dre-1/F box heterochronic gene functions early in development to control maintenance of polarity at later stages, and that a mutation in the let-7 heterochronic miRNA gene causes dendritic misplacement of RAB-3 presynaptic markers that colocalize with muscle postsynaptic terminals ectopically. We propose that heterochronic genes are components in the UNC-6/Netrin pathway of synaptic polarity of these neurons. These findings highlight the role of heterochronic genes in postmitotic neuronal patterning events.
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Farahani R, Rezaei-Lotfi S, Simonian M, Hunter N. Bi-modal reprogramming of cell cycle by MiRNA-4673 amplifies human neurogenic capacity. Cell Cycle 2019; 18:848-868. [PMID: 30907228 DOI: 10.1080/15384101.2019.1595873] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Molecular mechanisms that inform heterochronic adaptations of neurogenesis in Homo sapiens remain largely unknown. Here, we uncover a signature in the cell cycle that amplifies the proliferative capacity of human neural progenitors by input from microRNA4673 encoded in Notch-1. The miRNA instructs bimodal reprogramming of the cell cycle, leading to initial synchronization of neural precursors at the G0 phase of the cell cycle followed by accelerated progression through interphase. The key event in G0 synchronization is transient inhibition by miR4673 of cyclin-dependent kinase-18, a member of an ancient family of cyclins that license M-G1 transition. In parallel, autophagic degradation of p53/p21 and transcriptional silencing of XRCC3/BRCA2 relax G1/S cell cycle checkpoint and accelerate interphase by ≈2.8-fold. The resultant reprogrammed cell cycle amplifies the proliferative capacity and delays the differentiation of human neural progenitors.
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Affiliation(s)
- Ramin Farahani
- a IDR/Westmead Institute for Medical Research , Sydney , NSW , Australia.,b Department of Life Sciences, Faculty of Medicine and Health Sciences , University of Sydney , Sydney , NSW , Australia
| | - Saba Rezaei-Lotfi
- b Department of Life Sciences, Faculty of Medicine and Health Sciences , University of Sydney , Sydney , NSW , Australia
| | - Mary Simonian
- a IDR/Westmead Institute for Medical Research , Sydney , NSW , Australia
| | - Neil Hunter
- a IDR/Westmead Institute for Medical Research , Sydney , NSW , Australia.,b Department of Life Sciences, Faculty of Medicine and Health Sciences , University of Sydney , Sydney , NSW , Australia
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Wersebe M, Blackwood P, Guo YT, Jaeger J, May D, Meindl G, Ryan SN, Wong V, Hua J. The effects of different cold-temperature regimes on development, growth, and susceptibility to an abiotic and biotic stressor. Ecol Evol 2019; 9:3355-3366. [PMID: 30962897 PMCID: PMC6434568 DOI: 10.1002/ece3.4957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/19/2018] [Accepted: 01/08/2019] [Indexed: 11/05/2022] Open
Abstract
Global climate change is expected to both increase average temperatures as well as temperature variability.Increased average temperatures have led to earlier breeding in many spring-breeding organisms. However, individuals breeding earlier will also face increased temperature fluctuations, including exposure to potentially harmful cold-temperature regimes during early developmental stages.Using a model spring-breeding amphibian, we investigated how embryonic exposure to different cold-temperature regimes (control, cold-pulse, and cold-press) affected (a) compensatory larval development and growth, (b) larval susceptibility to a common contaminant, and (c) larval susceptibility to parasites.We found: (a) no evidence of compensatory development or growth, (b) larvae exposed to the cold-press treatment were more susceptible to NaCl at 4-days post-hatching but recovered by 17-days post-hatching, and (c) larvae exposed to both cold treatments were less susceptible to parasites.These results demonstrate that variation in cold-temperature regimes can lead to unique direct and indirect effects on larval growth, development, and response to stressors. This underscores the importance of considering cold-temperature variability and not just increased average temperatures when examining the impacts of climate disruption.
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Affiliation(s)
- Matthew Wersebe
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - Paradyse Blackwood
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - Ying Tong Guo
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - Jared Jaeger
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - Dyllan May
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - George Meindl
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - Sean N. Ryan
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - Vivian Wong
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
| | - Jessica Hua
- Biological Sciences DepartmentBinghamton University (SUNY)BinghamtonNew York
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Robinton DA, Chal J, Lummertz da Rocha E, Han A, Yermalovich AV, Oginuma M, Schlaeger TM, Sousa P, Rodriguez A, Urbach A, Pourquié O, Daley GQ. The Lin28/let-7 Pathway Regulates the Mammalian Caudal Body Axis Elongation Program. Dev Cell 2019; 48:396-405.e3. [DOI: 10.1016/j.devcel.2018.12.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 08/13/2018] [Accepted: 12/17/2018] [Indexed: 02/09/2023]
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Tang M, Bai X, Niu LJ, Chai X, Chen MS, Xu ZF. miR172 Regulates both Vegetative and Reproductive Development in the Perennial Woody Plant Jatropha curcas. PLANT & CELL PHYSIOLOGY 2018; 59:2549-2563. [PMID: 30541045 PMCID: PMC6290486 DOI: 10.1093/pcp/pcy175] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/21/2018] [Indexed: 05/04/2023]
Abstract
Jatropha curcas is a promising feedstock for biofuel production because its oil is highly suitable for processing bio-jet fuels and biodiesel. However, Jatropha exhibits a long juvenile stage in subtropical areas. miR172, a conserved small non-protein-coding RNA molecule with 21 nucleotides, regulates a wide range of developmental processes. To date, however, no studies have examined the function of miR172 in Jatropha. There are five miR172 precursors encoding two mature miR172s in Jatropha, which are expressed in all tissues, with the highest expression level in leaves, and the levels are up-regulated with age. Overexpression of JcmiR172a resulted in early flowering, abnormal flowers, and altered leaf morphology in transgenic Arabidopsis and Jatropha. The expression levels of miR172 target genes were down-regulated, and the flower identity genes were up-regulated in the JcmiR172a-overexpressing transgenic plants. Interestingly, we showed that JcmiR172 might be involved in regulation of stem vascular development through manipulating the expression of cellulose and lignin biosynthesis genes. Overexpression of JcmiR172a enhanced xylem development and reduced phloem and pith development. This study helped elucidate the functions of miR172 in perennial plants, a known age-related miRNA involved in the regulation of perennial plant phase change and organ development.
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Affiliation(s)
- Mingyong Tang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Xue Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Long-Jian Niu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Xia Chai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
- Corresponding author: E-mail, ; Fax, +86-691-8715070
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40
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Sun L, Sang M, Zheng C, Wang D, Shi H, Liu K, Guo Y, Cheng T, Zhang Q, Wu R. The genetic architecture of heterochrony as a quantitative trait: lessons from a computational model. Brief Bioinform 2018; 19:1430-1439. [PMID: 28575183 DOI: 10.1093/bib/bbx056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Indexed: 11/14/2022] Open
Abstract
Heterochrony is known as a developmental change in the timing or rate of ontogenetic events across phylogenetic lineages. It is a key concept synthesizing development into ecology and evolution to explore the mechanisms of how developmental processes impact on phenotypic novelties. A number of molecular experiments using contrasting organisms in developmental timing have identified specific genes involved in heterochronic variation. Beyond these classic approaches that can only identify single genes or pathways, quantitative models derived from current next-generation sequencing data serve as a more powerful tool to precisely capture heterochronic variation and systematically map a complete set of genes that contribute to heterochronic processes. In this opinion note, we discuss a computational framework of genetic mapping that can characterize heterochronic quantitative trait loci that determine the pattern and process of development. We propose a unifying model that charts the genetic architecture of heterochrony that perceives and responds to environmental perturbations and evolves over geologic time. The new model may potentially enhance our understanding of the adaptive value of heterochrony and its evolutionary origins, providing a useful context for designing new organisms that can best use future resources.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Mengmeng Sang
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Chenfei Zheng
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Dongyang Wang
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Hexin Shi
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Kaiyue Liu
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Yanfang Guo
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Tangren Cheng
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Rongling Wu
- Center for Computational Biology at Beijing Forestry University
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Abstract
Biology is dynamic. Timescales range from frenetic sub-second ion fluxes and enzymatic reactions to the glacial millions of years of evolutionary change. Falling somewhere in the middle of this range are the processes we usually study in development: cell division and differentiation, gene expression, cell-cell signalling, and morphogenesis. But what sets the tempo and manages the order of developmental events? Are the order and tempo different between species? How is the sequence of multiple events coordinated? Here, we discuss the importance of time for developing embryos, highlighting the necessity for global as well as cell-autonomous control. New reagents and tools in imaging and genomic engineering, combined with in vitro culture, are beginning to offer fresh perspectives and molecular insight into the origin and mechanisms of developmental time.
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Affiliation(s)
- Miki Ebisuya
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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Precocious Puberty and the Lin28/Let7 Pathway: The Therapeutic Effect of the Nourishing "Yin" and Purging "Fire" Traditional Chinese Medicine Mixture in a Rat Model. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:4868045. [PMID: 30046338 PMCID: PMC6038664 DOI: 10.1155/2018/4868045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022]
Abstract
The present study aims to investigate the effects of the nourishing “Yin” and purging “Fire” Traditional Chinese Medicine (TCM) herb mixture on precocious puberty and TCM may act through hypothalamic Lin28/let7 pathway expression in the precocious puberty model rats. Meanwhile, to confirm the relationship between Lin28/let7 pathway and puberty by overexpression Lin28a, in the first part of this study, female rats were randomly allocated into untreated controls, the precocious puberty (PP) model group, the PP control group, and the PP + TCM group. Rats on postnatal day 5 were injected danazol to establish the PP model. From days 15 to 35, the rats in the TCM group were given the TCM twice daily. Vaginal opening, sex-related hormones, and body and reproductive organ weights were measured, and the expressions of hypothalamic Lin28a and Lin28b mRNA and let7a and let7b miRNA were detected. In addition, in the second part, the effects of overexpression of Lin28a on the vaginal opening time were evaluated. In the two parts of the study, we found that, at the onset of puberty, a decrease in ovary weight, an increase in the serum levels of luteinizing hormone and progesterone, and increased expression levels of hypothalamic Lin28b mRNA were observed in the PP + TCM group compared to the PP model group. The vaginal opening time was significantly delayed upon overexpression of Lin28a. Above all, the mechanism by which the TCM treats precocious puberty is thus likely to be associated with inhibition of the hypothalamic Lin28/let7 signaling pathway and our findings provide in-depth insight into the relationship between the overexpression of Lin28a gene in the hypothalamus and the onset of puberty.
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43
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Abete-Luzi P, Eisenmann DM. Regulation ofC. elegansL4 cuticle collagen genes by the heterochronic protein LIN-29. Genesis 2018; 56. [DOI: 10.1002/dvg.23106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/12/2018] [Accepted: 03/27/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Patricia Abete-Luzi
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland 21250
| | - David M. Eisenmann
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland 21250
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Fu Y, Gao L, Shi Z, You F, Zhang J, Li W. Characterization and expression of lin-28a involved in lin28/let-7signal pathway during early development of P. olivaceus. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:451-463. [PMID: 29218439 DOI: 10.1007/s10695-017-0445-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
Heterochronic lin-28 is a conserved RNA-binding protein that plays a key role in the timing of developmental events in organisms. As a crucial heterochronic gene, the protein controls developmental events of the second of four larval stages in Caenorhabditi elegans. Heterochronic let-7 miRNAs are often present in various species and highly conserved in sequence and biological function and are required for various biological processes. Previous studies showed that ten let-7 miRNAs were identified in the Japanese flounder (Paralichthys olivaceus) and that they were primarily expressed during metamorphosis. In this study, we clone and characterize the lin-28a gene from P. olivaceus and exhibit its dynamic expression pattern at different developmental stages and various adult tissues. The results show that the P. olivaceus lin-28a gene has high sequence similarity with other species and is highly expressed in the embryonic stage but weakly expressed in the larval stage. In addition, lin-28a overexpression causes cell proliferation and significantly promotes the levels of pre-let-7a and pre-let-7d while markedly depressing let-7a and let-7d expression in FEC (Flounder Embryonic Cell), which indicate that lin-28 possibly blocks the maturation of let-7 miRNAs. Additionally, lin-28a is identified as a target gene of let-7 miRNAs, and let-7 miRNAs directly regulate lin-28a expression by targeting its 3' UTR. Taken together, lin-28a along with let-7 miRNA participates in a lin-28/let-7 axis pathway that regulates cell division and timing of embryonic and metamorphic events in P. olivaceus.
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Affiliation(s)
- Yuanshuai Fu
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, 999, Hu-Cheng-Huan Road, Lingang New City, Shanghai, 201306, China
| | - Lina Gao
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, 999, Hu-Cheng-Huan Road, Lingang New City, Shanghai, 201306, China
| | - Zhiyi Shi
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, 999, Hu-Cheng-Huan Road, Lingang New City, Shanghai, 201306, China.
| | - Feng You
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Junling Zhang
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, 999, Hu-Cheng-Huan Road, Lingang New City, Shanghai, 201306, China
| | - Wenjuan Li
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Ministry of Agriculture, 999, Hu-Cheng-Huan Road, Lingang New City, Shanghai, 201306, China
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Metheetrairut C, Ahuja Y, Slack FJ. acn-1, a C. elegans homologue of ACE, genetically interacts with the let-7 microRNA and other heterochronic genes. Cell Cycle 2017; 16:1800-1809. [PMID: 28933985 DOI: 10.1080/15384101.2017.1344798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The heterochronic pathway in C. elegans controls the relative timing of cell fate decisions during post-embryonic development. It includes a network of microRNAs (miRNAs), such as let-7, and protein-coding genes, such as the stemness factors, LIN-28 and LIN-41. Here we identified the acn-1 gene, a homologue of mammalian angiotensin-converting enzyme (ACE), as a new suppressor of the stem cell developmental defects of let-7 mutants. Since acn-1 null mutants die during early larval development, we used RNAi to characterize the role of acn-1 in C. elegans seam cell development, and determined its interaction with heterochronic factors, including let-7 and its downstream interactors - lin-41, hbl-1, and apl-1. We demonstrate that although RNAi knockdown of acn-1 is insufficient to cause heterochronic defects on its own, loss of acn-1 suppresses the retarded phenotypes of let-7 mutants and enhances the precocious phenotypes of hbl-1, though not lin-41, mutants. Conversely, the pattern of acn-1 expression, which oscillates during larval development, is disrupted by lin-41 mutants but not by hbl-1 mutants. Finally, we show that acn-1(RNAi) enhances the let-7-suppressing phenotypes caused by loss of apl-1, a homologue of the Alzheimer's disease-causing amyloid precursor protein (APP), while significantly disrupting the expression of apl-1 during the L4 larval stage. In conclusion, acn-1 interacts with heterochronic genes and appears to function downstream of let-7 and its target genes, including lin-41 and apl-1.
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Affiliation(s)
- Chanatip Metheetrairut
- a Department of Molecular, Cellular, and Developmental Biology , Yale University , New Haven , CT , USA
| | - Yuri Ahuja
- a Department of Molecular, Cellular, and Developmental Biology , Yale University , New Haven , CT , USA
| | - Frank J Slack
- a Department of Molecular, Cellular, and Developmental Biology , Yale University , New Haven , CT , USA
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Comparative proteome analysis between C . briggsae embryos and larvae reveals a role of chromatin modification proteins in embryonic cell division. Sci Rep 2017; 7:4296. [PMID: 28655887 PMCID: PMC5487359 DOI: 10.1038/s41598-017-04533-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/16/2017] [Indexed: 11/12/2022] Open
Abstract
Caenorhabditis briggsae has emerged as a model for comparative biology against model organism C. elegans. Most of its cell fate specifications are completed during embryogenesis whereas its cell growth is achieved mainly in larval stages. The molecular mechanism underlying the drastic developmental changes is poorly understood. To gain insights into the molecular changes between the two stages, we compared the proteomes between the two stages using iTRAQ. We identified a total of 2,791 proteins in the C. briggsae embryos and larvae, 247 of which undergo up- or down-regulation between the two stages. The proteins that are upregulated in the larval stages are enriched in the Gene Ontology categories of energy production, protein translation, and cytoskeleton; whereas those upregulated in the embryonic stage are enriched in the categories of chromatin dynamics and posttranslational modification, suggesting a more active chromatin modification in the embryos than in the larva. Perturbation of a subset of chromatin modifiers followed by cell lineage analysis suggests their roles in controlling cell division pace. Taken together, we demonstrate a general molecular switch from chromatin modification to metabolism during the transition from C. briggsae embryonic to its larval stages using iTRAQ approach. The switch might be conserved across metazoans.
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47
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IGF2BP1 overexpression causes fetal-like hemoglobin expression patterns in cultured human adult erythroblasts. Proc Natl Acad Sci U S A 2017; 114:E5664-E5672. [PMID: 28652347 DOI: 10.1073/pnas.1609552114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we investigated in primary human erythroid tissues a downstream element of the heterochronic let-7 miRNA pathway, the insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), for its potential to affect the hemoglobin profiles in human erythroblasts. Comparison of adult bone marrow to fetal liver lysates demonstrated developmental silencing in IGF2BP1. Erythroid-specific overexpression of IGF2BP1 caused a nearly complete and pancellular reversal of the adult pattern of hemoglobin expression toward a more fetal-like phenotype. The reprogramming of hemoglobin expression was achieved at the transcriptional level by increased gamma-globin combined with decreased beta-globin transcripts resulting in gamma-globin rising to 90% of total beta-like mRNA. Delta-globin mRNA was reduced to barely detectable levels. Alpha-globin levels were not significantly changed. Fetal hemoglobin achieved levels of 68.6 ± 3.9% in the IGF2BP1 overexpression samples compared with 5.0 ± 1.8% in donor matched transduction controls. In part, these changes were mediated by reduced protein expression of the transcription factor BCL11A. mRNA stability and polysome studies suggest IGF2BP1 mediates posttranscriptional loss of BCL11A. These results suggest a mechanism for chronoregulation of fetal and adult hemoglobin expression in humans.
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48
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Lažetić V, Fay DS. Molting in C. elegans. WORM 2017; 6:e1330246. [PMID: 28702275 DOI: 10.1080/21624054.2017.1330246] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 12/21/2022]
Abstract
Molting is an essential developmental process for the majority of animal species on Earth. During the molting process, which is a specialized form of extracellular matrix (ECM) remodeling, the old apical ECM, or cuticle, is replaced with a new one. Many of the genes and pathways identified as important for molting in nematodes are highly conserved in vertebrates and include regulators and components of vesicular trafficking, steroid-hormone signaling, developmental timers, and hedgehog-like signaling. In this review, we discuss what is known about molting, with a focus on studies in Caenorhabditis elegans. We also describe the key structural elements of the cuticle that must be released, newly synthesized, or remodeled for proper molting to occur.
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Affiliation(s)
- Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, USA
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, USA
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Abstract
MicroRNAs (miRNAs) are involved in the regulation of a number of processes associated with metamorphosis, either in the less modified hemimetabolan mode or in the more modified holometabolan mode. The miR-100/let-7/miR-125 cluster has been studied extensively, especially in relation to wing morphogenesis in both hemimetabolan and holometabolan species. Other miRNAs also participate in wing morphogenesis, as well as in programmed cell and tissue death, neuromaturation, neuromuscular junction formation, and neuron cell fate determination, typically during the pupal stage of holometabolan species. A special case is the control of miR-2 over Kr-h1 transcripts, which determines adult morphogenesis in the hemimetabolan metamorphosis. This is an elegant example of how a single miRNA can control an entire process by acting on a crucial mediator; however, this is a quite exceptional mechanism that was apparently lost during the transition from hemimetaboly to holometaboly.
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Affiliation(s)
- Xavier Belles
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC)-Pompeu Fabra University (UPF), 08002 Barcelona, Spain;
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50
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Cohen-Fix O, Askjaer P. Cell Biology of the Caenorhabditis elegans Nucleus. Genetics 2017; 205:25-59. [PMID: 28049702 PMCID: PMC5216270 DOI: 10.1534/genetics.116.197160] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/09/2016] [Indexed: 12/25/2022] Open
Abstract
Studies on the Caenorhabditis elegans nucleus have provided fascinating insight to the organization and activities of eukaryotic cells. Being the organelle that holds the genetic blueprint of the cell, the nucleus is critical for basically every aspect of cell biology. The stereotypical development of C. elegans from a one cell-stage embryo to a fertile hermaphrodite with 959 somatic nuclei has allowed the identification of mutants with specific alterations in gene expression programs, nuclear morphology, or nuclear positioning. Moreover, the early C. elegans embryo is an excellent model to dissect the mitotic processes of nuclear disassembly and reformation with high spatiotemporal resolution. We review here several features of the C. elegans nucleus, including its composition, structure, and dynamics. We also discuss the spatial organization of chromatin and regulation of gene expression and how this depends on tight control of nucleocytoplasmic transport. Finally, the extensive connections of the nucleus with the cytoskeleton and their implications during development are described. Most processes of the C. elegans nucleus are evolutionarily conserved, highlighting the relevance of this powerful and versatile model organism to human biology.
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Affiliation(s)
- Orna Cohen-Fix
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Peter Askjaer
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
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