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Zolboot N, Xiao Y, Du JX, Ghanem MM, Choi SY, Junn MJ, Zampa F, Huang Z, MacRae IJ, Lippi G. MicroRNAs are necessary for the emergence of Purkinje cell identity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560023. [PMID: 37808721 PMCID: PMC10557743 DOI: 10.1101/2023.09.28.560023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Brain computations are dictated by the unique morphology and connectivity of neuronal subtypes, features established by closely timed developmental events. MicroRNAs (miRNAs) are critical for brain development, but current technologies lack the spatiotemporal resolution to determine how miRNAs instruct the steps leading to subtype identity. Here, we developed new tools to tackle this major gap. Fast and reversible miRNA loss-of-function revealed that miRNAs are necessary for cerebellar Purkinje cell (PC) differentiation, which previously appeared miRNA-independent, and resolved distinct miRNA critical windows in PC dendritogenesis and climbing fiber synaptogenesis, key determinants of PC identity. To identify underlying mechanisms, we generated a mouse model, which enables precise mapping of miRNAs and their targets in rare cell types. With PC-specific maps, we found that the PC-enriched miR-206 drives exuberant dendritogenesis and modulates synaptogenesis. Our results showcase vastly improved approaches for dissecting miRNA function and reveal that many critical miRNA mechanisms remain largely unexplored. Highlights Fast miRNA loss-of-function with T6B impairs postnatal Purkinje cell developmentReversible T6B reveals critical miRNA windows for dendritogenesis and synaptogenesisConditional Spy3-Ago2 mouse line enables miRNA-target network mapping in rare cellsPurkinje cell-enriched miR-206 regulates its unique dendritic and synaptic morphology.
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2
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Prodromidou K, Matsas R. Evolving features of human cortical development and the emerging roles of non-coding RNAs in neural progenitor cell diversity and function. Cell Mol Life Sci 2021; 79:56. [PMID: 34921638 PMCID: PMC11071749 DOI: 10.1007/s00018-021-04063-7] [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: 04/02/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
The human cerebral cortex is a uniquely complex structure encompassing an unparalleled diversity of neuronal types and subtypes. These arise during development through a series of evolutionary conserved processes, such as progenitor cell proliferation, migration and differentiation, incorporating human-associated adaptations including a protracted neurogenesis and the emergence of novel highly heterogeneous progenitor populations. Disentangling the unique features of human cortical development involves elucidation of the intricate developmental cell transitions orchestrated by progressive molecular events. Crucially, developmental timing controls the fine balance between cell cycle progression/exit and the neurogenic competence of precursor cells, which undergo morphological transitions coupled to transcriptome-defined temporal states. Recent advances in bulk and single-cell transcriptomic technologies suggest that alongside protein-coding genes, non-coding RNAs exert important regulatory roles in these processes. Interestingly, a considerable number of novel long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have appeared in human and non-human primates suggesting an evolutionary role in shaping cortical development. Here, we present an overview of human cortical development and highlight the marked diversification and complexity of human neuronal progenitors. We further discuss how lncRNAs and miRNAs constitute critical components of the extended epigenetic regulatory network defining intermediate states of progenitors and controlling cell cycle dynamics and fate choices with spatiotemporal precision, during human neurodevelopment.
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Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece.
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece
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3
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Zolboot N, Du JX, Zampa F, Lippi G. MicroRNAs Instruct and Maintain Cell Type Diversity in the Nervous System. Front Mol Neurosci 2021; 14:646072. [PMID: 33994943 PMCID: PMC8116551 DOI: 10.3389/fnmol.2021.646072] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Characterizing the diverse cell types that make up the nervous system is essential for understanding how the nervous system is structured and ultimately how it functions. The astonishing range of cellular diversity found in the nervous system emerges from a small pool of neural progenitor cells. These progenitors and their neuronal progeny proceed through sequential gene expression programs to produce different cell lineages and acquire distinct cell fates. These gene expression programs must be tightly regulated in order for the cells to achieve and maintain the proper differentiated state, remain functional throughout life, and avoid cell death. Disruption of developmental programs is associated with a wide range of abnormalities in brain structure and function, further indicating that elucidating their contribution to cellular diversity will be key to understanding brain health. A growing body of evidence suggests that tight regulation of developmental genes requires post-transcriptional regulation of the transcriptome by microRNAs (miRNAs). miRNAs are small non-coding RNAs that function by binding to mRNA targets containing complementary sequences and repressing their translation into protein, thereby providing a layer of precise spatial and temporal control over gene expression. Moreover, the expression profiles and targets of miRNAs show great specificity for distinct cell types, brain regions and developmental stages, suggesting that they are an important parameter of cell type identity. Here, we provide an overview of miRNAs that are critically involved in establishing neural cell identities, focusing on how miRNA-mediated regulation of gene expression modulates neural progenitor expansion, cell fate determination, cell migration, neuronal and glial subtype specification, and finally cell maintenance and survival.
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Affiliation(s)
- Norjin Zolboot
- The Scripps Research Institute, La Jolla, CA, United States
| | - Jessica X. Du
- The Scripps Research Institute, La Jolla, CA, United States
- Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Federico Zampa
- The Scripps Research Institute, La Jolla, CA, United States
| | - Giordano Lippi
- The Scripps Research Institute, La Jolla, CA, United States
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4
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An evolutionarily acquired microRNA shapes development of mammalian cortical projections. Proc Natl Acad Sci U S A 2020; 117:29113-29122. [PMID: 33139574 PMCID: PMC7682328 DOI: 10.1073/pnas.2006700117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mammalian central nervous system contains unique projections from the cerebral cortex thought to underpin complex motor and cognitive skills, including the corticospinal tract and corpus callosum. The neurons giving rise to these projections—corticospinal and callosal projection neurons—develop from the same progenitors, but acquire strikingly different fates. The broad evolutionary conservation of known genes controlling cortical projection neuron fates raises the question of how the more narrowly conserved corticospinal and callosal projections evolved. We identify a microRNA cluster selectively expressed by corticospinal projection neurons and exclusive to placental mammals. One of these microRNAs promotes corticospinal fate via regulation of the callosal gene LMO4, suggesting a mechanism whereby microRNA regulation during development promotes evolution of neuronal diversity. The corticospinal tract is unique to mammals and the corpus callosum is unique to placental mammals (eutherians). The emergence of these structures is thought to underpin the evolutionary acquisition of complex motor and cognitive skills. Corticospinal motor neurons (CSMN) and callosal projection neurons (CPN) are the archetypal projection neurons of the corticospinal tract and corpus callosum, respectively. Although a number of conserved transcriptional regulators of CSMN and CPN development have been identified in vertebrates, none are unique to mammals and most are coexpressed across multiple projection neuron subtypes. Here, we discover 17 CSMN-enriched microRNAs (miRNAs), 15 of which map to a single genomic cluster that is exclusive to eutherians. One of these, miR-409-3p, promotes CSMN subtype identity in part via repression of LMO4, a key transcriptional regulator of CPN development. In vivo, miR-409-3p is sufficient to convert deep-layer CPN into CSMN. This is a demonstration of an evolutionarily acquired miRNA in eutherians that refines cortical projection neuron subtype development. Our findings implicate miRNAs in the eutherians’ increase in neuronal subtype and projection diversity, the anatomic underpinnings of their complex behavior.
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5
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Chevalier RL. Evolution, kidney development, and chronic kidney disease. Semin Cell Dev Biol 2019; 91:119-131. [PMID: 29857053 PMCID: PMC6281795 DOI: 10.1016/j.semcdb.2018.05.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/29/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]
Abstract
There is a global epidemic of chronic kidney disease (CKD) characterized by a progressive loss of nephrons, ascribed in large part to a rising incidence of hypertension, metabolic syndrome, and type 2 diabetes mellitus. There is a ten-fold variation in nephron number at birth in the general population, and a 50% overall decrease in nephron number in the last decades of life. The vicious cycle of nephron loss stimulating hypertrophy by remaining nephrons and resulting in glomerulosclerosis has been regarded as maladaptive, and only partially responsive to angiotensin inhibition. Advances over the past century in kidney physiology, genetics, and development have elucidated many aspects of nephron formation, structure and function. Parallel advances have been achieved in evolutionary biology, with the emergence of evolutionary medicine, a discipline that promises to provide new insight into the treatment of chronic disease. This review provides a framework for understanding the origins of contemporary developmental nephrology, and recent progress in evolutionary biology. The establishment of evolutionary developmental biology (evo-devo), ecological developmental biology (eco-devo), and developmental origins of health and disease (DOHaD) followed the discovery of the hox gene family, the recognition of the contribution of cumulative environmental stressors to the changing phenotype over the life cycle, and mechanisms of epigenetic regulation. The maturation of evolutionary medicine has contributed to new investigative approaches to cardiovascular disease, cancer, and infectious disease, and promises the same for CKD. By incorporating these principles, developmental nephrology is ideally positioned to answer important questions regarding the fate of nephrons from embryo through senescence.
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Affiliation(s)
- Robert L Chevalier
- Department of Pediatrics, The University of Virginia, P.O. Box 800386, Charlottesville, VA, United States.
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6
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Zhao X, Bhattacharyya A. Human Models Are Needed for Studying Human Neurodevelopmental Disorders. Am J Hum Genet 2018; 103:829-857. [PMID: 30526865 DOI: 10.1016/j.ajhg.2018.10.009] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/09/2018] [Indexed: 12/19/2022] Open
Abstract
The analysis of animal models of neurological disease has been instrumental in furthering our understanding of neurodevelopment and brain diseases. However, animal models are limited in revealing some of the most fundamental aspects of development, genetics, pathology, and disease mechanisms that are unique to humans. These shortcomings are exaggerated in disorders that affect the brain, where the most significant differences between humans and animal models exist, and could underscore failures in targeted therapeutic interventions in affected individuals. Human pluripotent stem cells have emerged as a much-needed model system for investigating human-specific biology and disease mechanisms. However, questions remain regarding whether these cell-culture-based models are sufficient or even necessary. In this review, we summarize human-specific features of neurodevelopment and the most common neurodevelopmental disorders, present discrepancies between animal models and human diseases, demonstrate how human stem cell models can provide meaningful information, and discuss the challenges that exist in our pursuit to understand distinctively human aspects of neurodevelopment and brain disease. This information argues for a more thoughtful approach to disease modeling through consideration of the valuable features and limitations of each model system, be they human or animal, to mimic disease characteristics.
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Affiliation(s)
- Xinyu Zhao
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA.
| | - Anita Bhattacharyya
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA.
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7
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Abstract
The noncoding portion of the genome, including microRNAs, has been fertile evolutionary soil for cortical development in primates. A major contribution to cortical expansion in primates is the generation of novel precursor cell populations. Because miRNA expression profiles track closely with cell identity, it is likely that numerous novel microRNAs have contributed to cellular diversity in the brain. The tools to determine the genomic context within which novel microRNAs emerge and how they become integrated into molecular circuitry are now in hand.
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Affiliation(s)
- Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Tomasz Nowakowski
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143, USA.,Department of Anatomy, University of California, San Francisco, California 94158, USA
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8
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Sasidharan V, Marepally S, Elliott SA, Baid S, Lakshmanan V, Nayyar N, Bansal D, Sánchez Alvarado A, Vemula PK, Palakodeti D. The miR-124 family of microRNAs is crucial for regeneration of the brain and visual system in the planarian Schmidtea mediterranea. Development 2017; 144:3211-3223. [PMID: 28807895 PMCID: PMC5612250 DOI: 10.1242/dev.144758] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 08/01/2017] [Indexed: 01/15/2023]
Abstract
Brain regeneration in planarians is mediated by precise spatiotemporal control of gene expression and is crucial for multiple aspects of neurogenesis. However, the mechanisms underpinning the gene regulation essential for brain regeneration are largely unknown. Here, we investigated the role of the miR-124 family of microRNAs in planarian brain regeneration. The miR-124 family (miR-124) is highly conserved in animals and regulates neurogenesis by facilitating neural differentiation, yet its role in neural wiring and brain organization is not known. We developed a novel method for delivering anti-miRs using liposomes for the functional knockdown of microRNAs. Smed-miR-124 knockdown revealed a key role for these microRNAs in neuronal organization during planarian brain regeneration. Our results also demonstrated an essential role for miR-124 in the generation of eye progenitors. Additionally, miR-124 regulates Smed-slit-1, which encodes an axon guidance protein, either by targeting slit-1 mRNA or, potentially, by modulating the canonical Notch pathway. Together, our results reveal a role for miR-124 in regulating the regeneration of a functional brain and visual system. Summary:miR-124 is required during de novo regeneration of the cephalic ganglion and visual system in planarians, as well as in slit-1 expression in the midline of anterior regenerating tissue via canonical Notch signaling.
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Affiliation(s)
- Vidyanand Sasidharan
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India.,Manipal University, Manipal, Karnataka 576104, India
| | - Srujan Marepally
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India
| | - Sarah A Elliott
- Stowers Institute for Medical Research and Howard Hughes Medical Institute, Kansas City, MO 64110, USA.,Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Srishti Baid
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India
| | - Vairavan Lakshmanan
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India
| | - Nishtha Nayyar
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India
| | - Dhiru Bansal
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India.,Manipal University, Manipal, Karnataka 576104, India
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research and Howard Hughes Medical Institute, Kansas City, MO 64110, USA.,Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Praveen Kumar Vemula
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India
| | - Dasaradhi Palakodeti
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK campus, Bangalore, Karnataka 560065, India
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9
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Grimaldi A, Zarone MR, Irace C, Zappavigna S, Lombardi A, Kawasaki H, Caraglia M, Misso G. Non-coding RNAs as a new dawn in tumor diagnosis. Semin Cell Dev Biol 2017; 78:37-50. [PMID: 28765094 DOI: 10.1016/j.semcdb.2017.07.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/12/2022]
Abstract
The current knowledge about non-coding RNAs (ncRNAs) as important regulators of gene expression in both physiological and pathological conditions, has been the main engine for the design of innovative platforms to finalize the pharmacological application of ncRNAs as either therapeutic tools or as molecular biomarkers in cancer. Biochemical alterations of cancer cells are, in fact, largely supported by ncRNA disregulation in the tumor site, which, in turn, reflects the cancer-associated specific modification of circulating ncRNA expression pattern. The aim of this review is to describe the state of the art of pre-clinical and clinical studies that analyze the involvement of miRNAs and lncRNAs in cancer-related processes, such as proliferation, invasion and metastases, giving emphasis to their functional role. A central node of our work has been also the examination of advantages and criticisms correlated with the clinical use of ncRNAs, taking into account the pressing need to refine the profiling methods aimed at identify novel diagnostic and prognostic markers and the request to optimize the delivery of such nucleic acids for a therapeutic use in an imminent future.
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Affiliation(s)
- Anna Grimaldi
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Mayra Rachele Zarone
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Carlo Irace
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Silvia Zappavigna
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Angela Lombardi
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Hiromichi Kawasaki
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy; Wakunaga Pharmaceutical Co. LTD, 4-5-36 Miyahara, Yodogawa-ku, Osaka 532-0003 Japan
| | - Michele Caraglia
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
| | - Gabriella Misso
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
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10
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Chevalier RL. The proximal tubule is the primary target of injury and progression of kidney disease: role of the glomerulotubular junction. Am J Physiol Renal Physiol 2016; 311:F145-61. [PMID: 27194714 PMCID: PMC4967168 DOI: 10.1152/ajprenal.00164.2016] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/03/2016] [Indexed: 12/16/2022] Open
Abstract
There is an alarming global increase in the incidence of end-stage kidney disease, for which early biomarkers and effective treatment options are lacking. Largely based on the histology of the end-stage kidney and on the model of unilateral ureteral obstruction, current investigation is focused on the pathogenesis of renal interstitial fibrosis as a central mechanism in the progression of chronic kidney disease (CKD). It is now recognized that cumulative episodes of acute kidney injury (AKI) can lead to CKD, and, conversely, CKD is a risk factor for AKI. Based on recent and historic studies, this review shifts attention from the glomerulus and interstitium to the proximal tubule as the primary sensor and effector in the progression of CKD as well as AKI. Packed with mitochondria and dependent on oxidative phosphorylation, the proximal tubule is particularly vulnerable to injury (obstructive, ischemic, hypoxic, oxidative, metabolic), resulting in cell death and ultimately in the formation of atubular glomeruli. Animal models of human glomerular and tubular disorders have provided evidence for a broad repertoire of morphological and functional responses of the proximal tubule, revealing processes of degeneration and repair that may lead to new therapeutic strategies. Most promising are studies that encompass the entire life cycle from fetus to senescence, recognizing epigenetic factors. The application of techniques in molecular characterization of tubule segments and the development of human kidney organoids may provide new insights into the mammalian kidney subjected to stress or injury, leading to biomarkers of early CKD and new therapies.
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Affiliation(s)
- Robert L Chevalier
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
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11
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MiR-124 is differentially expressed in derivatives of the sympathoadrenal cell lineage and promotes neurite elongation in chromaffin cells. Cell Tissue Res 2016; 365:225-32. [DOI: 10.1007/s00441-016-2395-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/09/2016] [Indexed: 01/02/2023]
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12
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Abstract
MicroRNAs (miRs) are a group of small RNAs that play a major role in post-transcriptional regulation of gene expression. In animals, many of the miRs are expressed in a conserved spatiotemporal manner. Muscle tissues, the major cellular systems involved in the locomotion and physiological functions of animals, have been one of the main sites for verification of miR targets and analysis of their developmental functions. During the determination and differentiation of muscle cells, numerous miRs bind to and repress target mRNAs in a highly specific but redundant manner. Interspecific comparisons of the sequences and expression of miRs have suggested that miR regulation became increasingly important during the course of vertebrate evolution. However, the detailed molecular interactions that have led to the highly complex morphological structures still await investigation. In this review, we will summarize the recent findings on the functional and developmental characteristics of miRs that have played major roles in vertebrate myogenesis, and discuss how the evolution of miRs is related to the morphological complexity of the vertebrates.
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13
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Kianianmomeni A. Potential impact of gene regulatory mechanisms on the evolution of multicellularity in the volvocine algae. Commun Integr Biol 2015; 8:e1017175. [PMID: 26479715 PMCID: PMC4594364 DOI: 10.1080/19420889.2015.1017175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 01/22/2015] [Accepted: 01/22/2015] [Indexed: 01/23/2023] Open
Abstract
A fundamental question in biology is how multicellular organisms can arise from their single-celled precursors. The evolution of multicellularity requires the adoption of new traits in unicellular ancestors that allows the generation of form by, for example, increasing the size and developing new cell types. But what are the genetic, cellular and biochemical bases underlying the evolution of multicellularity? Recent advances in evolutionary developmental biology suggest that the regulation of gene expression by cis-regulatory factors, gene duplication and alternative splicing contribute to phenotypic evolution. These mechanisms enable different degrees of phenotypic divergence and complexity with variation in traits from genomes with similar gene contents. In addition, signaling pathways specific to cell types are developed to guarantee the modulation of cellular and developmental processes matched to the cell types as well as the maintenance of multicellularity.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants; University of Bielefeld ; Bielefeld, Germany
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14
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Dehay C, Kennedy H, Kosik KS. The outer subventricular zone and primate-specific cortical complexification. Neuron 2015; 85:683-94. [PMID: 25695268 DOI: 10.1016/j.neuron.2014.12.060] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Evolutionary expansion and complexification of the primate cerebral cortex are largely linked to the emergence of the outer subventricular zone (OSVZ), a uniquely structured germinal zone that generates the expanded primate supragranular layers. The primate OSVZ departs from rodent germinal zones in that it includes a higher diversity of precursor types, inter-related in bidirectional non-hierarchical lineages. In addition, primate-specific regulatory mechanisms are operating in primate cortical precursors via the occurrence of novel miRNAs. Here, we propose that the origin and evolutionary importance of the OSVZ is related to genetic changes in multiple regulatory loops and that cell-cycle regulation is a favored target for evolutionary adaptation of the cortex.
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Affiliation(s)
- Colette Dehay
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003, Lyon, France.
| | - Henry Kennedy
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003, Lyon, France.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Dept Cellular Molecular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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15
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miR-92a regulates expression of synaptic GluA1-containing AMPA receptors during homeostatic scaling. Nat Neurosci 2014; 17:1040-2. [PMID: 25017011 DOI: 10.1038/nn.3762] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022]
Abstract
We investigated whether microRNAs could regulate AMPA receptor expression during activity blockade. miR-92a strongly repressed the translation of GluA1 receptors by binding the 3' untranslated region of rat GluA1 (also known as Gria1) mRNA and was downregulated in rat hippocampal neurons after treatment with tetrodotoxin and AP5. Deleting the seed region in GluA1 or overexpressing miR-92a blocked homeostatic scaling, indicating that miR-92a regulates the translation and synaptic incorporation of new GluA1-containing AMPA receptors.
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16
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Della Pina S, Souer E, Koes R. Arguments in the evo-devo debate: say it with flowers! JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2231-42. [PMID: 24648567 DOI: 10.1093/jxb/eru111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A key question in evolutionary developmental biology is how DNA sequence changes have directed the evolution of morphological diversity. The widely accepted view was that morphological changes resulted from differences in number and/or type of transcription factors, or even from small changes in the amino acid sequence of similar proteins. Research over the last two decades indicated that most of the developmental and genetic mechanisms that produce new structures involve proteins that are deeply conserved. These proteins are encoded by a type of genes known as 'toolkit' genes that control a plethora of processes essential for the correct development of the organism. Mutations in these toolkit genes produce deleterious pleiotropic effects. In contrast, alterations in regulatory regions affect their expression only at specific sites in the organism, facilitating morphological change at the tissue and organ levels. However, some examples from the animal and plant fields indicate that coding mutations also contributed to phenotypic evolution. Therefore, the main question at this point is to what extent these mechanisms have contributed to the evolution of morphological diversity. Today, an increasing amount of data, especially from the plant field, implies that changes in cis-regulatory sequences in fact played a major role in evolution.
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Affiliation(s)
- Serena Della Pina
- Department of Molecular Cell Biology, Graduate School of Experimental Plant Sciences, VU University, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Erik Souer
- Department of Molecular Cell Biology, Graduate School of Experimental Plant Sciences, VU University, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ronald Koes
- Department of Molecular Cell Biology, Graduate School of Experimental Plant Sciences, VU University, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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Arcila ML, Betizeau M, Cambronne XA, Guzman E, Doerflinger N, Bouhallier F, Zhou H, Wu B, Rani N, Bassett DS, Borello U, Huissoud C, Goodman RH, Dehay C, Kosik KS. Novel primate miRNAs coevolved with ancient target genes in germinal zone-specific expression patterns. Neuron 2014; 81:1255-1262. [PMID: 24583023 DOI: 10.1016/j.neuron.2014.01.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 01/15/2023]
Abstract
Major nonprimate-primate differences in cortico-genesis include the dimensions, precursor lineages, and developmental timing of the germinal zones (GZs). microRNAs (miRNAs) of laser-dissected GZ compartments and cortical plate (CP) from embryonic E80 macaque visual cortex were deep sequenced. The CP and the GZ including ventricular zone (VZ) and outer and inner subcompartments of the outer subventricular zone (OSVZ) in area 17 displayed unique miRNA profiles. miRNAs present in primate, but absent in rodent, contributed disproportionately to the differential expression between GZ subregions. Prominent among the validated targets of these miRNAs were cell-cycle and neurogenesis regulators. Coevolution between the emergent miRNAs and their targets suggested that novel miRNAs became integrated into ancient gene circuitry to exert additional control over proliferation. We conclude that multiple cell-cycle regulatory events contribute to the emergence of primate-specific cortical features, including the OSVZ, generated enlarged supragranular layers, largely responsible for the increased primate cortex computational abilities.
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Affiliation(s)
- Mary L Arcila
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Marion Betizeau
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Xiaolu A Cambronne
- Vollum Institute, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97068, USA
| | - Elmer Guzman
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Nathalie Doerflinger
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Frantz Bouhallier
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Hongjun Zhou
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Bian Wu
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Neha Rani
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Danielle S Bassett
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ugo Borello
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Cyril Huissoud
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France; Service de gynécologie-obstétrique, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, 69004 Lyon, France
| | - Richard H Goodman
- Vollum Institute, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97068, USA
| | - Colette Dehay
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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Hill JM, Lukiw WJ. Comparing miRNAs and viroids; highly conserved molecular mechanisms for the transmission of genetic information. Front Cell Neurosci 2014; 8:45. [PMID: 24600348 PMCID: PMC3929837 DOI: 10.3389/fncel.2014.00045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/01/2014] [Indexed: 12/29/2022] Open
Affiliation(s)
- James M Hill
- LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Microbiology, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Ophthalmology, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Pharmacology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Microbiology, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Neurology, Louisiana State University Health Sciences Center New Orleans, LA, USA
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Hill JM, Zhao Y, Bhattacharjee S, Lukiw WJ. miRNAs and viroids utilize common strategies in genetic signal transfer. Front Mol Neurosci 2014; 7:10. [PMID: 24574963 PMCID: PMC3918644 DOI: 10.3389/fnmol.2014.00010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/22/2014] [Indexed: 12/29/2022] Open
Affiliation(s)
- James M Hill
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Ophthalmology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Microbiology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
| | - Yuhai Zhao
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
| | - Surjyadipta Bhattacharjee
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
| | - Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Ophthalmology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA ; Department of Neurology, Louisiana State University Health Sciences Center, Louisiana State University New Orleans, LA, USA
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20
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Tani S, Kuraku S, Sakamoto H, Inoue K, Kusakabe R. Developmental expression and evolution of muscle-specific microRNAs conserved in vertebrates. Evol Dev 2013; 15:293-304. [DOI: 10.1111/ede.12039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Saori Tani
- Department of Biology; Graduate School of Science; Kobe University; 1-1 Rokkodaicho; Nada-Ku, Kobe; 657-8501; Japan
| | - Shigehiro Kuraku
- Genome Resource and Analysis Unit; RIKEN Center for Developmental Biology; 2-2-3 Minatojima-Minami; Chuo-Ku, Kobe; 650-0047; Japan
| | - Hiroshi Sakamoto
- Department of Biology; Graduate School of Science; Kobe University; 1-1 Rokkodaicho; Nada-Ku, Kobe; 657-8501; Japan
| | - Kunio Inoue
- Department of Biology; Graduate School of Science; Kobe University; 1-1 Rokkodaicho; Nada-Ku, Kobe; 657-8501; Japan
| | - Rie Kusakabe
- Department of Biology; Graduate School of Science; Kobe University; 1-1 Rokkodaicho; Nada-Ku, Kobe; 657-8501; Japan
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21
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Chao YL, Chen CH. An introduction to microRNAs and their dysregulation in psychiatric disorders. Tzu Chi Med J 2013. [DOI: 10.1016/j.tcmj.2012.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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22
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Carroll AP, Tooney PA, Cairns MJ. Context-specific microRNA function in developmental complexity. J Mol Cell Biol 2013; 5:73-84. [PMID: 23362311 DOI: 10.1093/jmcb/mjt004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Since their discovery, microRNAs (miRNA) have been implicated in a vast array of biological processes in animals, from fundamental developmental functions including cellular proliferation and differentiation, to more complex and specialized roles such as long-term potentiation and synapse-specific modifications in neurons. This review recounts the history behind this paradigm shift, which has seen small non-coding RNA molecules coming to the forefront of molecular biology, and introduces their role in establishing developmental complexity in animals. The fundamental mechanisms of miRNA biogenesis and function are then considered, leading into a discussion of recent discoveries transforming our understanding of how these molecules regulate gene network behaviour throughout developmental and pathophysiological processes. The emerging complexity of this mechanism is also examined with respect to the influence of cellular context on miRNA function. This discussion highlights the absolute imperative for experimental designs to appreciate the significance of context-specific factors when determining what genes are regulated by a particular miRNA. Moreover, by establishing the timing, location, and mechanism of these regulatory events, we may ultimately understand the true biological function of a specific miRNA in a given cellular environment.
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Affiliation(s)
- Adam P Carroll
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW, Australia
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23
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Maxwell EK, Ryan JF, Schnitzler CE, Browne WE, Baxevanis AD. MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics 2012; 13:714. [PMID: 23256903 PMCID: PMC3563456 DOI: 10.1186/1471-2164-13-714] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/30/2012] [Indexed: 01/21/2023] Open
Abstract
Background MicroRNAs play a vital role in the regulation of gene expression and have been identified in every animal with a sequenced genome examined thus far, except for the placozoan Trichoplax. The genomic repertoires of metazoan microRNAs have become increasingly endorsed as phylogenetic characters and drivers of biological complexity. Results In this study, we report the first investigation of microRNAs in a species from the phylum Ctenophora. We use short RNA sequencing and the assembled genome of the lobate ctenophore Mnemiopsis leidyi to show that this species appears to lack any recognizable microRNAs, as well as the nuclear proteins Drosha and Pasha, which are critical to canonical microRNA biogenesis. This finding represents the first reported case of a metazoan lacking a Drosha protein. Conclusions Recent phylogenomic analyses suggest that Mnemiopsis may be the earliest branching metazoan lineage. If this is true, then the origins of canonical microRNA biogenesis and microRNA-mediated gene regulation may postdate the last common metazoan ancestor. Alternatively, canonical microRNA functionality may have been lost independently in the lineages leading to both Mnemiopsis and the placozoan Trichoplax, suggesting that microRNA functionality was not critical until much later in metazoan evolution.
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Affiliation(s)
- Evan K Maxwell
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Chen CY, Chen ST, Juan HF, Huang HC. Lengthening of 3'UTR increases with morphological complexity in animal evolution. ACTA ACUST UNITED AC 2012; 28:3178-81. [PMID: 23080117 DOI: 10.1093/bioinformatics/bts623] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
MOTIVATION Evolutionary expansion of gene regulatory circuits seems to boost morphological complexity. However, the expansion patterns and the quantification relationships have not yet been identified. In this study, we focus on the regulatory circuits at the post-transcriptional level, investigating whether and how this principle may apply. RESULTS By analysing the structure of mRNA transcripts in multiple metazoan species, we observed a striking exponential correlation between the length of 3' untranslated regions (3'UTR) and morphological complexity as measured by the number of cell types in each organism. Cellular diversity was similarly associated with the accumulation of microRNA genes and their putative targets. We propose that the lengthening of 3'UTRs together with a commensurate exponential expansion in post-transcriptional regulatory circuits can contribute to the emergence of new cell types during animal evolution.
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Affiliation(s)
- Cho-Yi Chen
- Genome and Systems Biology Degree Program, Department of Life Science, Institute of Molecular and Cellular Biology, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 116, Taiwan
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25
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MicroRNA regulation of the synaptic plasticity-related gene Arc. PLoS One 2012; 7:e41688. [PMID: 22844515 PMCID: PMC3406043 DOI: 10.1371/journal.pone.0041688] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 06/25/2012] [Indexed: 02/04/2023] Open
Abstract
Expression of activity-regulated cytoskeleton associated protein (Arc) is crucial for diverse types of experience-dependent synaptic plasticity and long-term memory in mammals. However, the mechanisms governing Arc-specific translation are little understood. Here, we asked whether Arc translation is regulated by microRNAs. Bioinformatic analysis predicted numerous candidate miRNA binding sites within the Arc 3′-untranslated region (UTR). Transfection of the corresponding microRNAs in human embryonic kidney cells inhibited expression of an Arc 3′UTR luciferase reporter from between 10 to 70% across 16 microRNAs tested. Point mutation and deletion of the microRNA-binding seed-region for miR-34a, miR-326, and miR-19a partially or fully rescued reporter expression. In addition, expression of specific microRNA pairs synergistically modulated Arc reporter expression. In primary rat hippocampal neuronal cultures, ectopic expression of miR-34a, miR-193a, or miR-326, downregulated endogenous Arc protein expression in response to BDNF treatment. Conversely, treatment of neurons with cell-penetrating, peptide nucleic acid (PNA) inhibitors of miR-326 enhanced Arc mRNA expression. BDNF dramatically upregulated neuronal expression of Arc mRNA and miR-132, a known BDNF-induced miRNA, without affecting expression of Arc-targeting miRNAs. Developmentally, miR-132 was upregulated at day 10 in vitro whereas Arc-targeting miRNAs were downregulated. In the adult brain, LTP induction in the dentate gyrus triggered massive upregulation of Arc and upregulation of miR-132 without affecting levels of mature Arc-targeting miRNAs. Turning to examine miRNA localization, qPCR analysis of dentate gyrus synaptoneurosome and total lysates fractions demonstrated synaptic enrichment relative to small nucleolar RNA. In conclusion, we find that Arc is regulated by multiple miRNAs and modulated by specific miRNA pairs in vitro. Furthermore, we show that, in contrast to miR-132, steady state levels of Arc-targeting miRNAs do not change in response to activity-dependent expression of Arc in hippocampal neurons in vitro or during LTP in vivo.
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26
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Duroux-Richard I, Jorgensen C, Apparailly F. What do microRNAs mean for rheumatoid arthritis? ACTA ACUST UNITED AC 2012; 64:11-20. [PMID: 21898352 DOI: 10.1002/art.30651] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Abstract
Brain regions and their highly neuroplastic long axonal connections that expanded rapidly during hominid evolution are preferentially affected by Alzheimer disease. There is no natural animal model with full disease pathology (neurofibrillary tangles and neuritic amyloid plaques of a severity seen in Alzheimer's disease brains). Biomarkers such as reduced glucose metabolism in association neocortex, defects in long white matter tracts, RNA neurochemical changes, and high CSF levels of total and phosphorylated tau protein, which are helpful to identify MCI and preclinical Alzheimer disease patients, may also provide insights into what brain changes led to this disease being introduced during hominid evolution.
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28
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Witkos TM, Koscianska E, Krzyzosiak WJ. Practical Aspects of microRNA Target Prediction. Curr Mol Med 2011; 11:93-109. [PMID: 21342132 PMCID: PMC3182075 DOI: 10.2174/156652411794859250] [Citation(s) in RCA: 358] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Accepted: 11/27/2010] [Indexed: 12/19/2022]
Abstract
microRNAs (miRNAs) are endogenous non-coding RNAs that control gene expression at the posttranscriptional level. These small regulatory molecules play a key role in the majority of biological processes and their expression is also tightly regulated. Both the deregulation of genes controlled by miRNAs and the altered miRNA expression have been linked to many disorders, including cancer, cardiovascular, metabolic and neurodegenerative diseases. Therefore, it is of particular interest to reliably predict potential miRNA targets which might be involved in these diseases. However, interactions between miRNAs and their targets are complex and very often there are numerous putative miRNA recognition sites in mRNAs. Many miRNA targets have been computationally predicted but only a limited number of these were experimentally validated. Although a variety of miRNA target prediction algorithms are available, results of their application are often inconsistent. Hence, finding a functional miRNA target is still a challenging task. In this review, currently available and frequently used computational tools for miRNA target prediction, i.e., PicTar, TargetScan, DIANA-microT, miRanda, rna22 and PITA are outlined and various practical aspects of miRNA target analysis are extensively discussed. Moreover, the performance of three algorithms (PicTar, TargetScan and DIANA-microT) is both demonstrated and evaluated by performing an in-depth analysis of miRNA interactions with mRNAs derived from genes triggering hereditary neurological disorders known as trinucleotide repeat expansion diseases (TREDs), such as Huntington’s disease (HD), a number of spinocerebellar ataxias (SCAs), and myotonic dystrophy type 1 (DM1).
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Affiliation(s)
- T M Witkos
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str. 61-704 Poznan, Poland
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Prochiantz A. Evolution of the nervous system: a critical evaluation of how genetic changes translate into morphological changes. DIALOGUES IN CLINICAL NEUROSCIENCE 2011. [PMID: 21319491 PMCID: PMC3181989 DOI: 10.31887/dcns.2010.12.4/aprochiantz] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Living creatures evolve, and this evolution allows them to adapt to an ever-changing milieu. Two main adaptive strategies coexist. The first involves genetic mutations taking place at the species level. The second strategy occurs at the individual level, and primarily involves changes in chromatin organization and brain circuits. We shall illustrate how the two modes of adaptation are interdependent, and will show the difference in their respective importance depending on the species. It will be proposed that changes in developmental strategies, genetically selected, can lead to more or less epigenetic freedom, sometimes with dramatic consequences. In particular it will be shown, taking chimpanzees and humans as examples, how minor genetic modifications can translate into nonlinear changes in brain structure and cultural practices, placing the two types of primates at a much greater distance than had been anticipated.
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Affiliation(s)
- Alain Prochiantz
- College de France, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Paris, France.
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Abstract
This Essay explores the notion that specialized cells have unique vulnerabilities to environmental contingencies that microRNAs help to counteract. Given the ease with which new microRNAs evolve, they may serve as ideal facilitators for the emergence of new cell types.
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Affiliation(s)
- Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular Cellular Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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31
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Barmack NH, Qian Z, Yakhnitsa V. Climbing fibers induce microRNA transcription in cerebellar Purkinje cells. Neuroscience 2010; 171:655-65. [PMID: 20875844 DOI: 10.1016/j.neuroscience.2010.09.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/21/2010] [Accepted: 09/22/2010] [Indexed: 12/26/2022]
Abstract
The coordinated expression of as many as 100 proteins may be required to sustain simple changes in synaptic transmission. While each protein may be regulated separately, the translation of multiple proteins could be regulated by microRNAs. MicroRNAs are short non-coding RNAs that translationally repress cognate sequences in targeted mRNAs. If these targeted sequences are shared across several genes, then a single microRNA could, effectively regulate the activity of several genes in parallel. Here we investigate whether microRNA transcription is influenced by naturally evoked synaptic activity at the climbing fiber-Purkinje cell synapse in the mouse cerebellar flocculus. Mice received 24 h of binocular horizontal optokinetic stimulation (HOKS) evoking sustained increases in climbing fiber activity to Purkinje cells in one flocculus and decreases to Purkinje cells in the other. Increased climbing fiber activity increased transcription of 12 microRNAs in the flocculus. The transcription of one of these microRNAs, miR335, was proportional to duration of stimulation, increasing 18-fold after 24 h of HOKS. We localized miR335 transcripts to Purkinje cells using hybridization histochemistry. Transcripts of miR335 decayed to baseline within 3 h after HOKS was stopped. We identified mRNA targets for miR335 using multiple screens: sequence analysis, microinjection of miR335 inhibitors and identification of mRNAs whose transcription decreased during HOKS. Two genes, calbindin and 14-3-3-θ passed these screens. Our data suggest that microRNA transcription could provide an important synaptic or homeostatic mechanism for the regulation of proteins that contribute to Purkinje cell plasticity.
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Affiliation(s)
- N H Barmack
- Department of Physiology and Pharmacology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA Translation and Stability by microRNAs. Annu Rev Biochem 2010; 79:351-79. [PMID: 20533884 DOI: 10.1146/annurev-biochem-060308-103103] [Citation(s) in RCA: 2335] [Impact Index Per Article: 166.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marc Robert Fabian
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland;
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Liston A, Linterman M, Lu LF. MicroRNA in the adaptive immune system, in sickness and in health. J Clin Immunol 2010; 30:339-46. [PMID: 20191314 DOI: 10.1007/s10875-010-9378-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Accepted: 02/05/2010] [Indexed: 12/19/2022]
Abstract
INTRODUCTION MicroRNA are emerging as key regulators of the development and function of adaptive immunity. These 19-24 nucleotide regulatory RNA molecules have essential roles in multiple faucets of adaptive immunity, from regulating the development of the key cellular players to the activation and function in immune responses. DISCUSSION MicroRNA are involved in T cell and B cell differentiation in the thymus and bone marrow, and subsequent peripheral homeostasis. The contribution of specific microRNA to the adaptive immune response becomes even more apparent during the effector phases: class switching and germinal centre formation in B cells, differentiation into functional lineages in T cells, and activation of antigen-presentation cells through pattern-recognition pathways. With the capacity of microRNA to alter the survival and death of T and B cells, control over microRNA expression is essential to prevent adaptive immune cells from unregulated proliferation. MicroRNA can act both as 'oncomirs' and tumour suppressors, and thus dysregulation of microRNA in lymphocytes can cause malignancies. CONCLUSION In this review, we will describe the role of microRNA in generating a productive adaptive response, and the consequences if microRNA-mediated repression of lymphocytes is perturbed.
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Affiliation(s)
- Adrian Liston
- VIB and University of Leuven, Leuven, 3000, Belgium.
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34
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Wiedemann C. Scaling with microRNAs. Nat Rev Neurosci 2009. [DOI: 10.1038/nrn2747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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