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Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. Nat Biotechnol 2022; 40:741-750. [PMID: 35013600 DOI: 10.1038/s41587-021-01136-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/26/2021] [Indexed: 02/06/2023]
Abstract
The accuracy of methods for assembling transcripts from short-read RNA sequencing data is limited by the lack of long-range information. Here we introduce Ladder-seq, an approach that separates transcripts according to their lengths before sequencing and uses the additional information to improve the quantification and assembly of transcripts. Using simulated data, we show that a kallisto algorithm extended to process Ladder-seq data quantifies transcripts of complex genes with substantially higher accuracy than conventional kallisto. For reference-based assembly, a tailored scheme based on the StringTie2 algorithm reconstructs a single transcript with 30.8% higher precision than its conventional counterpart and is more than 30% more sensitive for complex genes. For de novo assembly, a similar scheme based on the Trinity algorithm correctly assembles 78% more transcripts than conventional Trinity while improving precision by 78%. In experimental data, Ladder-seq reveals 40% more genes harboring isoform switches compared to conventional RNA sequencing and unveils widespread changes in isoform usage upon m6A depletion by Mettl14 knockout.
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Aiken J, Holzbaur ELF. Cytoskeletal regulation guides neuronal trafficking to effectively supply the synapse. Curr Biol 2021; 31:R633-R650. [PMID: 34033795 DOI: 10.1016/j.cub.2021.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The development and proper function of the brain requires the formation of highly complex neuronal circuitry. These circuits are shaped from synaptic connections between neurons and must be maintained over a lifetime. The formation and continued maintenance of synapses requires accurate trafficking of presynaptic and postsynaptic components along the axon and dendrite, respectively, necessitating deliberate and specialized delivery strategies to replenish essential synaptic components. Maintenance of synaptic transmission also requires readily accessible energy stores, produced in part by localized mitochondria, that are tightly regulated with activity level. In this review, we focus on recent developments in our understanding of the cytoskeletal environment of axons and dendrites, examining how local regulation of cytoskeletal dynamics and organelle trafficking promotes synapse-specific delivery and plasticity. These new insights shed light on the complex and coordinated role that cytoskeletal elements play in establishing and maintaining neuronal circuitry.
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Affiliation(s)
- Jayne Aiken
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Ravnik-Glavač M, Glavač D. Circulating RNAs as Potential Biomarkers in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2020; 21:ijms21051714. [PMID: 32138249 PMCID: PMC7084402 DOI: 10.3390/ijms21051714] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex multi-system neurodegenerative disorder with currently limited diagnostic and no therapeutic options. Despite the intense efforts no clinically applicable biomarkers for ALS are yet established. Most current research is thus focused, in particular, in identifying potential non-invasive circulating biomarkers for more rapid and accurate diagnosis and monitoring of the disease. In this review, we have focused on messenger RNA (mRNA), non-coding RNAs (lncRNAs), micro RNAs (miRNAs) and circular RNA (circRNAs) as potential biomarkers for ALS in peripheral blood serum, plasma and cells. The most promising miRNAs include miR-206, miR-133b, miR-27a, mi-338-3p, miR-183, miR-451, let-7 and miR-125b. To test clinical potential of this miRNA panel, a useful approach may be to perform such analysis on larger multi-center scale using similar experimental design. However, other types of RNAs (lncRNAs, circRNAs and mRNAs) that, together with miRNAs, represent RNA networks, have not been yet extensively studied in blood samples of patients with ALS. Additional research has to be done in order to find robust circulating biomarkers and therapeutic targets that will distinguish key RNA interactions in specific ALS-types to facilitate diagnosis, predict progression and design therapy.
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Affiliation(s)
- Metka Ravnik-Glavač
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
- Correspondence: (M.R.-G.); (D.G.)
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
- Correspondence: (M.R.-G.); (D.G.)
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Yoo KS, Lee K, Oh JY, Lee H, Park H, Park YS, Kim HK. Postsynaptic density protein 95 (PSD-95) is transported by KIF5 to dendritic regions. Mol Brain 2019; 12:97. [PMID: 31753031 PMCID: PMC6873588 DOI: 10.1186/s13041-019-0520-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/04/2019] [Indexed: 11/18/2022] Open
Abstract
Postsynaptic density protein 95 (PSD-95) is a pivotal postsynaptic scaffolding protein in excitatory neurons. Although the transport and regulation of PSD-95 in synaptic regions is well understood, dendritic transport of PSD-95 before synaptic localization still remains to be clarified. To evaluate the role of KIF5, conventional kinesin, in the dendritic transport of PSD-95 protein, we expressed a transport defective form of KIF5A (ΔMD) that does not contain the N-terminal motor domain. Expression of ΔMD significantly decreased PSD-95 level in the dendrites. Consistently, KIF5 was associated with PSD-95 in in vitro and in vivo assays. This interaction was mediated by the C-terminal tail regions of KIF5A and the third PDZ domain of PSD-95. Additionally, the ADPDZ3 (the association domain of NMDA receptor and PDZ3 domain) expression significantly reduced the levels of PSD-95, glutamate receptor 1 (GluA1) in dendrites. The association between PSD-95 and KIF5A was dose-dependent on Staufen protein, suggesting that the Staufen plays a role as a regulatory role in the association. Taken together, our data suggest a new mechanism for dendritic transport of the AMPA receptor-PSD-95.
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Affiliation(s)
- Ki-Seo Yoo
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, South Korea
| | - Kina Lee
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, South Korea
| | - Jun-Young Oh
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, South Korea.,Department of Structure and Function of Neural Network, Korea Brain Research Institute, 61 Cheomdan-ro, Dong-gu, Daegu, 41068, South Korea
| | - Hyoeun Lee
- Department of Structure and Function of Neural Network, Korea Brain Research Institute, 61 Cheomdan-ro, Dong-gu, Daegu, 41068, South Korea
| | - Hyungju Park
- Department of Structure and Function of Neural Network, Korea Brain Research Institute, 61 Cheomdan-ro, Dong-gu, Daegu, 41068, South Korea
| | - Young Seok Park
- Department of Neurosurgery, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, South Korea
| | - Hyong Kyu Kim
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, South Korea.
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Abstract
SIGNIFICANCE Mitochondrial dynamics describes the continuous change in the position, size, and shape of mitochondria within cells. The morphological and functional complexity of neurons, the remarkable length of their processes, and the rapid changes in metabolic requirements arising from their intrinsic excitability render these cells particularly dependent on effective mitochondrial function and positioning. The rules that govern these changes and their functional significance are not fully understood, yet the dysfunction of mitochondrial dynamics has been implicated as a pathogenetic factor in a number of diseases, including disorders of the central and peripheral nervous systems. RECENT ADVANCES In recent years, a number of mutations of genes encoding proteins that play important roles in mitochondrial dynamics and function have been discovered in patients with Charcot-Marie-Tooth (CMT) disease, a hereditary peripheral neuropathy. These findings have directly linked mitochondrial pathology to the pathology of peripheral nerve and have identified certain aspects of mitochondrial dynamics as potential early events in the pathogenesis of CMT. In addition, mitochondrial dysfunction has now been implicated in the pathogenesis of noninherited neuropathies, including diabetic and inflammatory neuropathies. CRITICAL ISSUES The role of mitochondria in peripheral nerve diseases has been mostly examined in vitro, and less so in animal models. FUTURE DIRECTIONS This review examines available evidence for the role of mitochondrial dynamics in the pathogenesis of peripheral neuropathies, their relevance in human diseases, and future challenges for research in this field.
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Affiliation(s)
- Marija Sajic
- Department of Neuroinflammation, UCL Institute of Neurology , Queen Square, London, United Kingdom
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Maximino JR, de Oliveira GP, Alves CJ, Chadi G. Deregulated expression of cytoskeleton related genes in the spinal cord and sciatic nerve of presymptomatic SOD1(G93A) Amyotrophic Lateral Sclerosis mouse model. Front Cell Neurosci 2014; 8:148. [PMID: 24904291 PMCID: PMC4033281 DOI: 10.3389/fncel.2014.00148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/08/2014] [Indexed: 12/11/2022] Open
Abstract
Early molecular events related to cytoskeleton are poorly described in Amyotrophic Lateral Sclerosis (ALS), especially in the Schwann cell (SC), which offers strong trophic support to motor neurons. Database for Annotation, Visualization and Integrated Discovery (DAVID) tool identified cytoskeleton-related genes by employing the Cellular Component Ontology (CCO) in a large gene profiling of lumbar spinal cord and sciatic nerve of presymptomatic SOD1(G93A) mice. One and five CCO terms related to cytoskeleton were described from the spinal cord deregulated genes of 40 days (actin cytoskeleton) and 80 days (microtubule cytoskeleton, cytoskeleton part, actin cytoskeleton, neurofilament cytoskeleton, and cytoskeleton) old transgene mice, respectively. Also, four terms were depicted from the deregulated genes of sciatic nerve of 60 days old transgenes (actin cytoskeleton, cytoskeleton part, microtubule cytoskeleton and cytoskeleton). Kif1b was the unique deregulated gene in more than one studied region or presymptomatic age. The expression of Kif1b [quantitative polymerase chain reaction (qPCR)] elevated in the lumbar spinal cord (40 days old) and decreased in the sciatic nerve (60 days old) of presymptomatic ALS mice, results that were in line to microarray findings. Upregulation (24.8 fold) of Kif1b was seen in laser microdissected enriched immunolabeled motor neurons from the spinal cord of 40 days old presymptomatic SOD1(G93A) mice. Furthermore, Kif1b was dowregulated in the sciatic nerve Schwann cells of presymptomatic ALS mice (60 days old) that were enriched by means of cell microdissection (6.35 fold), cell sorting (3.53 fold), and primary culture (2.70 fold) technologies. The gene regulation of cytoskeleton molecules is an important occurrence in motor neurons and Schwann cells in presymptomatic stages of ALS and may be relevant in the dying back mechanisms of neuronal death. Furthermore, a differential regulation of Kif1b in the spinal cord and sciatic nerve cells emerged as key event in ALS.
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Affiliation(s)
- Jessica R Maximino
- Department of Neurology, Neuroregeneration Research Center, University of São Paulo School of Medicine São Paulo, Brazil
| | - Gabriela P de Oliveira
- Department of Neurology, Neuroregeneration Research Center, University of São Paulo School of Medicine São Paulo, Brazil
| | - Chrystian J Alves
- Department of Neurology, Neuroregeneration Research Center, University of São Paulo School of Medicine São Paulo, Brazil
| | - Gerson Chadi
- Department of Neurology, Neuroregeneration Research Center, University of São Paulo School of Medicine São Paulo, Brazil
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Kuźma-Kozakiewicz M, Chudy A, Gajewska B, Dziewulska D, Usarek E, Barańczyk-Kuźma A. Kinesin expression in the central nervous system of humans and transgenic hSOD1G93A mice with amyotrophic lateral sclerosis. NEURODEGENER DIS 2012; 12:71-80. [PMID: 23006449 DOI: 10.1159/000339529] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/10/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis is a fatal motor neuron degenerative disease. Most cases are sporadic (SALS), and approximately 10% are familial (FALS) among which over 20% are linked to the SOD1 mutation. Both SALS and FALS have been associated with retrograde axonal transport defects. Kinesins (KIFs) are motor proteins involved mainly in anterograde transport; however, some also participate in retrograde transport. OBJECTIVE The purpose of the study was to investigate and compare the expression of kinesins involved in anterograde (KIF5A, 5C) and retrograde (KIFC3/C2) axonal transport in SALS in humans and FALS in mice with the hSOD1G93A mutation. METHODS The studies were conducted on various parts of the CNS from autopsy specimens of SALS patients, and transgenic mice at presymptomatic and symptomatic stages using real-time quantitative PCR and reverse-transcription PCR. RESULTS All KIF expression in the motor cortex of individual SALS subjects was higher than in the adjacent sensory cortex, in contrast to the expression in control brains. It was also significantly higher in the frontal cortex of symptomatic but not presymptomatic mice compared to wild-type controls. However, the mean KIF expression in the SALS motor and sensory cortexes was lower than in control cortexes. To a lesser extent the decrease in KIF mean expression also occurred in human but not in mouse ALS spinal cords and in both human and mouse cerebella. CONCLUSION Disturbances in kinesin expression in the CNS may dysregulate both anterograde and retrograde axonal transports leading to motor neuron degeneration.
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Chen SC, Lu G, Chan CY, Chen Y, Wang H, Yew DTW, Feng ZT, Kung HF. Microarray Profile of Brain Aging-Related Genes in the Frontal Cortex of SAMP8. J Mol Neurosci 2009; 41:12-6. [DOI: 10.1007/s12031-009-9215-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 06/30/2009] [Indexed: 12/23/2022]
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Pantelidou M, Zographos SE, Lederer CW, Kyriakides T, Pfaffl MW, Santama N. Differential expression of molecular motors in the motor cortex of sporadic ALS. Neurobiol Dis 2007; 26:577-89. [PMID: 17418584 DOI: 10.1016/j.nbd.2007.02.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 01/31/2007] [Accepted: 02/04/2007] [Indexed: 12/13/2022] Open
Abstract
The molecular mechanisms underlying the selective neurodegeneration of motor neurons in amyotrophic lateral sclerosis (ALS) are inadequately understood. Recent breakthroughs have implicated impaired axonal transport, mediated by molecular motors, as a key element for disease onset and progression. The current work identifies the expression of 15 kinesin-like motors in healthy human motor cortex, including three novel isoforms. Our comprehensive quantitative mRNA analysis in control and sporadic ALS (SALS) motor cortex specimens detects SALS-specific down-regulation of KIF1Bbeta and novel KIF3Abeta, two isoforms we show to be enriched in the brain, and also of SOD1, a key enzyme linked to familial ALS. This is accompanied by a marked reduction of KIF3Abeta protein levels. In the motor cortex KIF3Abeta localizes in cholinergic neurons, including upper motor neurons. No mutations causing splicing defects or altering protein-coding sequences were identified in the genes of the three proteins. The present study implicates two motor proteins as possible candidates in SALS pathology.
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Affiliation(s)
- Maria Pantelidou
- Department of Biological Sciences, University of Cyprus and Cyprus Institute of Neurology and Genetics, P.O. Box 20537, 1678 Nicosia, Cyprus
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Phelps MA, Foraker AB, Swaan PW. Cytoskeletal motors and cargo in membrane trafficking: opportunities for high specificity in drug intervention. Drug Discov Today 2003; 8:494-502. [PMID: 12818519 DOI: 10.1016/s1359-6446(03)02707-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane trafficking comprises the directed transport of vesicle and/or organelle cargos to specific locations throughout the cell, and is primarily driven by molecular motors tracking along microtubules and microfilaments. The mechanisms by which specific motor complexes attach to their respective vesicular cargo is of great interest, and is only now starting to be unraveled. The proteins identified as links between the molecular motors and the vesicular cargo are viable drug targets and represent opportunities to regulate small groups of related proteins or even single proteins, such as receptors and transporters, at the cytosolic trafficking level. Ultimately, continued development in this area will lead to greater success in directing endocytosed drugs to the desired intracellular targets, such as the cell nucleus or the basolateral membrane.
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Affiliation(s)
- Mitch A Phelps
- Biophysics Program, The Ohio State University, Columbus, OH 43210-1291, USA
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