1
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Lv S, Wang J, Chen X, Liao X. STPoseNet: A real-time spatiotemporal network model for robust mouse pose estimation. iScience 2024; 27:109772. [PMID: 38711440 PMCID: PMC11070338 DOI: 10.1016/j.isci.2024.109772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/15/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Animal behavior analysis plays a crucial role in contemporary neuroscience research. However, the performance of the frame-by-frame approach may degrade in scenarios with occlusions or motion blur. In this study, we propose a spatiotemporal network model based on YOLOv8 to enhance the accuracy of key-point detection in mouse behavioral experimental videos. This model integrates a time-domain tracking strategy comprising two components: the first part utilizes key-point detection results from the previous frame to detect potential target locations in the subsequent frame; the second part employs Kalman filtering to analyze key-point changes prior to detection, allowing for the estimation of missing key-points. In the comparison of pose estimation results between our approach, YOLOv8, DeepLabCut and SLEAP on videos of three mouse behavioral experiments, our approach demonstrated significantly superior performance. This suggests that our method offers a new and effective means of accurately tracking and estimating pose in mice through spatiotemporal processing.
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Affiliation(s)
- Songyan Lv
- Guangxi Key Laboratory of Special Biomedicine & Advanced Institute for Brain and Intelligence, School of Medicine, Guangxi University, Nanning 530004, China
| | - Jincheng Wang
- Guangxi Key Laboratory of Special Biomedicine & Advanced Institute for Brain and Intelligence, School of Medicine, Guangxi University, Nanning 530004, China
| | - Xiaowei Chen
- Guangxi Key Laboratory of Special Biomedicine & Advanced Institute for Brain and Intelligence, School of Medicine, Guangxi University, Nanning 530004, China
| | - Xiang Liao
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing 400030, China
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2
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Zaytseva O, Mitchell NC, Muckle D, Delandre C, Nie Z, Werner JK, Lis JT, Eyras E, Hannan RD, Levens DL, Marshall OJ, Quinn LM. Psi promotes Drosophila wing growth via direct transcriptional activation of cell cycle targets and repression of growth inhibitors. Development 2023; 150:286725. [PMID: 36692218 PMCID: PMC10110491 DOI: 10.1242/dev.201563] [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: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/25/2023]
Abstract
The first characterised FUSE Binding Protein family member, FUBP1, binds single-stranded DNA to activate MYC transcription. Psi, the sole FUBP protein in Drosophila, binds RNA to regulate P-element and mRNA splicing. Our previous work revealed pro-growth functions for Psi, which depend, in part, on transcriptional activation of Myc. Genome-wide functions for FUBP family proteins in transcriptional control remain obscure. Here, through the first genome-wide binding and expression profiles obtained for a FUBP family protein, we demonstrate that, in addition to being required to activate Myc to promote cell growth, Psi also directly binds and activates stg to couple growth and cell division. Thus, Psi knockdown results in reduced cell division in the wing imaginal disc. In addition to activating these pro-proliferative targets, Psi directly represses transcription of the growth inhibitor tolkin (tok, a metallopeptidase implicated in TGFβ signalling). We further demonstrate tok overexpression inhibits proliferation, while tok loss of function increases mitosis alone and suppresses impaired cell division caused by Psi knockdown. Thus, Psi orchestrates growth through concurrent transcriptional activation of the pro-proliferative genes Myc and stg, in combination with repression of the growth inhibitor tok.
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Affiliation(s)
- Olga Zaytseva
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Naomi C Mitchell
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Damien Muckle
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Zuqin Nie
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - John T Lis
- Cornell University, Ithaca, NY 14850, USA
| | - Eduardo Eyras
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Ross D Hannan
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | | | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Leonie M Quinn
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
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3
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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4
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Zhang X, Yang D, Yang X, Zhang X, Zhang Y, Huang Y, Zhang S, Liu Z. U1 small nuclear ribonucleoprotein is essential for early larval development in silkworm, Bombyx mori. INSECT SCIENCE 2022; 29:379-387. [PMID: 34231971 DOI: 10.1111/1744-7917.12946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
U1 small nuclear ribonucleoproteins (U1 snRNP) associates with 5' splice sites in the form of ribonucleoprotein particles and is highly conserved among species. The physiological functions of U1 snRNP in a lepidopteran model insect Bombyx mori is mostly unknown. Here, we showed that U1 snRNP plays an important role in the development of silkworm. Knockout of U1 snRNP in silkworm showed either delayed or stationary 1st instar larva development compared with the wild-type group. U1 snRNP deletion mutants exhibited abnormal cellular phenotypes with enlarged cell nucleus, scant cytoplasm and enlarged nuclei. RNA-seq analysis revealed that genes involved in metabolic pathway, biosynthesis of secondary metabolites and steroid hormone biosynthesis were significantly affected by U1 snRNP depletion. Taken together, our study suggests that U1 snRNP homeostasis plays an important role in silkworm development.
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Affiliation(s)
- Xiaoqian Zhang
- College Forestry, Shangdong Agriculture University, Shangdong Province, Taian, China
| | - Dehong Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xu Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xinran Zhang
- College Forestry, Shangdong Agriculture University, Shangdong Province, Taian, China
| | - Yong Zhang
- Soochow University, Suzhou, Jiangsu Province, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Shengxiang Zhang
- College Forestry, Shangdong Agriculture University, Shangdong Province, Taian, China
| | - Zulian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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5
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Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Zaytseva O, Mitchell NC, Guo L, Marshall OJ, Parsons LM, Hannan RD, Levens DL, Quinn LM. Transcriptional repression of Myc underlies the tumour suppressor function of AGO1 in Drosophila. Development 2020; 147:147/11/dev190231. [PMID: 32527935 PMCID: PMC7295588 DOI: 10.1242/dev.190231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/27/2020] [Indexed: 12/29/2022]
Abstract
Here, we report novel tumour suppressor activity for the Drosophila Argonaute family RNA-binding protein AGO1, a component of the miRNA-dependent RNA-induced silencing complex (RISC). The mechanism for growth inhibition does not, however, involve canonical roles as part of the RISC; rather, AGO1 controls cell and tissue growth by functioning as a direct transcriptional repressor of the master regulator of growth, Myc. AGO1 depletion in wing imaginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion and cell growth in a manner dependent on Myc abundance. Moreover, increased Myc promoter activity and elevated Myc mRNA in AGO1-depleted animals requires RNA polymerase II transcription. Further support for transcriptional AGO1 functions is provided by physical interaction with the RNA polymerase II transcriptional machinery (chromatin remodelling factors and Mediator Complex), punctate nuclear localisation in euchromatic regions and overlap with Polycomb Group transcriptional silencing loci. Moreover, significant AGO1 enrichment is observed on the Myc promoter and AGO1 interacts with the Myc transcriptional activator Psi. Together, our data show that Drosophila AGO1 functions outside of the RISC to repress Myc transcription and inhibit developmental cell and tissue growth. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: In the Drosophila wing, the Argonaute family protein AGO1 acts independently of the miRNA-silencing pathway to restrict tissue growth by directly repressing transcription of the master growth regulator Myc.
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Affiliation(s)
- Olga Zaytseva
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Naomi C Mitchell
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Linna Guo
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | | | | | - Ross D Hannan
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - David L Levens
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Leonie M Quinn
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
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7
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Xu J, Liu W, Yang D, Chen S, Chen K, Liu Z, Yang X, Meng J, Zhu G, Dong S, Zhang Y, Zhan S, Wang G, Huang Y. Regulation of olfactory-based sex behaviors in the silkworm by genes in the sex-determination cascade. PLoS Genet 2020; 16:e1008622. [PMID: 32520935 PMCID: PMC7307793 DOI: 10.1371/journal.pgen.1008622] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/22/2020] [Accepted: 05/04/2020] [Indexed: 11/28/2022] Open
Abstract
Insect courtship and mating depend on integration of olfactory, visual, and tactile cues. Compared to other insects, Bombyx mori, the domesticated silkworm, has relatively simple sexual behaviors as it cannot fly. Here by using CRISPR/Cas9 and electrophysiological techniques we found that courtship and mating behaviors are regulated in male silk moths by mutating genes in the sex determination cascade belonging to two conserved pathways. Loss of Bmdsx gene expression significantly reduced the peripheral perception of the major pheromone component bombykol by reducing expression of the product of the BmOR1 gene which completely blocked courtship in adult males. Interestingly, we found that mating behavior was regulated independently by another sexual differentiation gene, Bmfru. Loss of Bmfru completely blocked mating, but males displayed normal courtship behavior. Lack of Bmfru expression significantly reduced the perception of the minor pheromone component bombykal due to the down regulation of BmOR3 expression; further, functional analysis revealed that loss of the product of BmOR3 played a key role in terminating male mating behavior. Our results suggest that Bmdsx and Bmfru are at the base of the two primary pathways that regulate olfactory-based sexual behavior. The fundamental insect sexual behaviors, courtship and mating, result from successful integration of olfactory, vision, tactile and other complex innate behaviors. In the widely used insect model, Drosophila melanogaster, the sex determination cascade genes fruitless and doublesex are involved in the regulation of courtship and mating behaviors; however, little is known about the function of these sexual differentiation genes in regulating sex behaviors of Lepidoptera. Here we combine genetics and electrophysiology to investigate regulation pathway of sexual behaviors in the model lepidopteran insect, the domesticated silk moth, Bombyx mori. Our results support the presence of two genetic pathways in B. mori, named Bmdsx-BmOR1-bombykol and Bmfru-BmOR3-bombykal, which control distinct aspects of male sexual behavior that are modulated by olfaction. This is the first comprehensive report about the role of sex differentiation genes in the male sexual behavior in the silk moth.
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Affiliation(s)
- Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dehong Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Shuqing Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Kai Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zulian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xu Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jing Meng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guanheng Zhu
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Shuanglin Dong
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Shuai Zhan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (GW); (YH)
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (GW); (YH)
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8
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Foley LE, Ling J, Joshi R, Evantal N, Kadener S, Emery P. Drosophila PSI controls circadian period and the phase of circadian behavior under temperature cycle via tim splicing. eLife 2019; 8:50063. [PMID: 31702555 PMCID: PMC6890465 DOI: 10.7554/elife.50063] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/07/2019] [Indexed: 12/30/2022] Open
Abstract
The Drosophila circadian pacemaker consists of transcriptional feedback loops subjected to post-transcriptional and post-translational regulation. While post-translational regulatory mechanisms have been studied in detail, much less is known about circadian post-transcriptional control. Thus, we targeted 364 RNA binding and RNA associated proteins with RNA interference. Among the 43 hits we identified was the alternative splicing regulator P-element somatic inhibitor (PSI). PSI regulates the thermosensitive alternative splicing of timeless (tim), promoting splicing events favored at warm temperature over those increased at cold temperature. Psi downregulation shortens the period of circadian rhythms and advances the phase of circadian behavior under temperature cycle. Interestingly, both phenotypes were suppressed in flies that could produce TIM proteins only from a transgene that cannot form the thermosensitive splicing isoforms. Therefore, we conclude that PSI regulates the period of Drosophila circadian rhythms and circadian behavior phase during temperature cycling through its modulation of the tim splicing pattern.
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Affiliation(s)
- Lauren E Foley
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Jinli Ling
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | - Radhika Joshi
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
| | | | - Sebastian Kadener
- Hebrew University of Jerusalem, Jerusalem, Israel.,Brandeis University, Waltham, United States
| | - Patrick Emery
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, United States
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9
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Datta SR, Anderson DJ, Branson K, Perona P, Leifer A. Computational Neuroethology: A Call to Action. Neuron 2019; 104:11-24. [PMID: 31600508 PMCID: PMC6981239 DOI: 10.1016/j.neuron.2019.09.038] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/16/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
The brain is worthy of study because it is in charge of behavior. A flurry of recent technical advances in measuring and quantifying naturalistic behaviors provide an important opportunity for advancing brain science. However, the problem of understanding unrestrained behavior in the context of neural recordings and manipulations remains unsolved, and developing approaches to addressing this challenge is critical. Here we discuss considerations in computational neuroethology-the science of quantifying naturalistic behaviors for understanding the brain-and propose strategies to evaluate progress. We point to open questions that require resolution and call upon the broader systems neuroscience community to further develop and leverage measures of naturalistic, unrestrained behavior, which will enable us to more effectively probe the richness and complexity of the brain.
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Affiliation(s)
| | - David J Anderson
- Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA, 91125, USA; Tianqiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kristin Branson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Pietro Perona
- Division of Engineering & Applied Sciences 136-93, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew Leifer
- Department of Physics, Princeton University, Princeton, NJ 08544, USA; Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
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10
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Pereira TD, Aldarondo DE, Willmore L, Kislin M, Wang SSH, Murthy M, Shaevitz JW. Fast animal pose estimation using deep neural networks. Nat Methods 2018; 16:117-125. [PMID: 30573820 DOI: 10.1038/s41592-018-0234-5] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023]
Abstract
The need for automated and efficient systems for tracking full animal pose has increased with the complexity of behavioral data and analyses. Here we introduce LEAP (LEAP estimates animal pose), a deep-learning-based method for predicting the positions of animal body parts. This framework consists of a graphical interface for labeling of body parts and training the network. LEAP offers fast prediction on new data, and training with as few as 100 frames results in 95% of peak performance. We validated LEAP using videos of freely behaving fruit flies and tracked 32 distinct points to describe the pose of the head, body, wings and legs, with an error rate of <3% of body length. We recapitulated reported findings on insect gait dynamics and demonstrated LEAP's applicability for unsupervised behavioral classification. Finally, we extended the method to more challenging imaging situations and videos of freely moving mice.
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Affiliation(s)
- Talmo D Pereira
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Diego E Aldarondo
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.,Program in Neuroscience, Harvard University, Cambridge, MA, USA
| | - Lindsay Willmore
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Mikhail Kislin
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Samuel S-H Wang
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Joshua W Shaevitz
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA. .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA. .,Department of Physics, Princeton University, Princeton, NJ, USA.
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11
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Stegeman R, Hall H, Escobedo SE, Chang HC, Weake VM. Proper splicing contributes to visual function in the aging Drosophila eye. Aging Cell 2018; 17:e12817. [PMID: 30003673 PMCID: PMC6156539 DOI: 10.1111/acel.12817] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Changes in splicing patterns are a characteristic of the aging transcriptome; however, it is unclear whether these age-related changes in splicing facilitate the progressive functional decline that defines aging. In Drosophila, visual behavior declines with age and correlates with altered gene expression in photoreceptors, including downregulation of genes encoding splicing factors. Here, we characterized the significance of these age-regulated splicing-associated genes in both splicing and visual function. To do this, we identified differential splicing events in either the entire eye or photoreceptors of young and old flies. Intriguingly, aging photoreceptors show differential splicing of a large number of visual function genes. In addition, as shown previously for aging photoreceptors, aging eyes showed increased accumulation of circular RNAs, which result from noncanonical splicing events. To test whether proper splicing was necessary for visual behavior, we knocked down age-regulated splicing factors in photoreceptors in young flies and examined phototaxis. Notably, many of the age-regulated splicing factors tested were necessary for proper visual behavior. In addition, knockdown of individual splicing factors resulted in changes in both alternative splicing at age-spliced genes and increased accumulation of circular RNAs. Together, these data suggest that cumulative decreases in splicing factor expression could contribute to the differential splicing, circular RNA accumulation, and defective visual behavior observed in aging photoreceptors.
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Affiliation(s)
- Rachel Stegeman
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
- Present address:
University of Minnesota Medical SchoolMinneapolisMinnesota
| | - Hana Hall
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
| | | | - Henry C. Chang
- Department of Biological SciencesPurdue UniversityWest LafayetteIndiana
| | - Vikki M. Weake
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
- Purdue University Center for Cancer ResearchPurdue UniversityWest LafayetteIndiana
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12
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Signor S, Nuzhdin S. Dynamic changes in gene expression and alternative splicing mediate the response to acute alcohol exposure in Drosophila melanogaster. Heredity (Edinb) 2018; 121:342-360. [PMID: 30143789 PMCID: PMC6133934 DOI: 10.1038/s41437-018-0136-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/21/2018] [Accepted: 07/19/2018] [Indexed: 12/18/2022] Open
Abstract
Environmental changes typically cause rapid gene expression responses in the exposed organisms, including changes in the representation of gene isoforms with different functions or properties. Identifying the genes that respond to environmental change, including in genotype-specific ways, is an important step in treating the undesirable physiological effects of stress, such as exposure to toxins or ethanol. Ethanol is a unique environmental stress in that chronic exposure results in permanent physiological changes and the development of alcohol use disorders. Drosophila is a classic model for deciphering the mechanisms of the response to alcohol exposure, as it meets the criteria for the development of alcohol use disorders, and has similar physiological underpinnings with vertebrates. Because many studies on the response to ethanol have relied on a priori candidate genes, broad surveys of gene expression and splicing are required and have been investigated here. Further, we expose Drosophila to ethanol in an environment that is genetically, socially, and ecologically relevant. Both expression and splicing differences, inasmuch as they can be decomposed, contribute to the response to ethanol in Drosophila melanogaster. However, we find that while D. melanogaster responds to ethanol, there is very little genetic variation in how it responds to ethanol. In addition, the response to alcohol over time is dynamic, suggesting that incorporating time into studies on the response to the environment is important.
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Affiliation(s)
- Sarah Signor
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
| | - Sergey Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
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13
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JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns. Proc Natl Acad Sci U S A 2018; 115:E8181-E8190. [PMID: 30104386 DOI: 10.1073/pnas.1806018115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-sequencing data rely on preannotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the junction usage model (JUM) that uses a bottom-up approach to identify, analyze, and quantitate global AS profiles without any prior transcriptome annotations. JUM accurately reports global AS changes in terms of the five conventional AS patterns and an additional "composite" category composed of inseparable combinations of conventional patterns. JUM stringently classifies the difficult and disease-relevant pattern of intron retention (IR), reducing the false positive rate of IR detection commonly seen in other annotation-based methods to near-negligible rates. When analyzing AS in RNA samples derived from Drosophila heads, human tumors, and human cell lines bearing cancer-associated splicing factor mutations, JUM consistently identified approximately twice the number of novel AS events missed by other methods. Computational simulations showed JUM exhibits a 1.2 to 4.8 times higher true positive rate at a fixed cutoff of 5% false discovery rate. In summary, JUM provides a framework and improved method that removes the necessity for transcriptome annotations and enables the detection, analysis, and quantification of AS patterns in complex metazoan transcriptomes with superior accuracy.
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Lee YJ, Wang Q, Rio DC. Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5. Genes Dev 2018; 32:1060-1074. [PMID: 30042133 PMCID: PMC6075143 DOI: 10.1101/gad.316034.118] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/29/2018] [Indexed: 01/12/2023]
Abstract
Alternative premessenger RNA (pre-mRNA) splicing is a post-transcriptional mechanism for controlling gene expression. Splicing patterns are determined by both RNA-binding proteins and nuclear pre-mRNA structure. Here, we analyzed pre-mRNA splicing patterns, RNA-binding sites, and RNA structures near these binding sites coordinately controlled by two splicing factors: the heterogeneous nuclear ribonucleoprotein hnRNPA1 and the RNA helicase DDX5. We identified thousands of alternative pre-mRNA splicing events controlled by these factors by RNA sequencing (RNA-seq) following RNAi. Enhanced cross-linking and immunoprecipitation (eCLIP) on nuclear extracts was used to identify protein-RNA-binding sites for both proteins in the nuclear transcriptome. We found a significant overlap between hnRNPA1 and DDX5 splicing targets and that they share many closely linked binding sites as determined by eCLIP analysis. In vivo SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemical RNA structure probing data were used to model RNA structures near several exons controlled and bound by both proteins. Both sequence motifs and in vivo UV cross-linking sites for hnRNPA1 and DDX5 were used to map binding sites in their RNA targets, and often these sites flanked regions of higher chemical reactivity, suggesting an organized nature of nuclear pre-mRNPs. This work provides a first glimpse into the possible RNA structures surrounding pre-mRNA splicing factor-binding sites.
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Affiliation(s)
- Yeon J Lee
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
- Center for RNA Systems Biology, University of California at Berkeley, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, California 94720, USA
| | - Qingqing Wang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
- Center for RNA Systems Biology, University of California at Berkeley, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, California 94720, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
- Center for RNA Systems Biology, University of California at Berkeley, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, California 94720, USA
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Wang Q, Abruzzi KC, Rosbash M, Rio DC. Striking circadian neuron diversity and cycling of Drosophila alternative splicing. eLife 2018; 7:35618. [PMID: 29863472 PMCID: PMC6025963 DOI: 10.7554/elife.35618] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/31/2018] [Indexed: 11/13/2022] Open
Abstract
Although alternative pre-mRNA splicing (AS) significantly diversifies the neuronal proteome, the extent of AS is still unknown due in part to the large number of diverse cell types in the brain. To address this complexity issue, we used an annotation-free computational method to analyze and compare the AS profiles between small specific groups of Drosophila circadian neurons. The method, the Junction Usage Model (JUM), allows the comprehensive profiling of both known and novel AS events from specific RNA-seq libraries. The results show that many diverse and novel pre-mRNA isoforms are preferentially expressed in one class of clock neuron and also absent from the more standard Drosophila head RNA preparation. These AS events are enriched in potassium channels important for neuronal firing, and there are also cycling isoforms with no detectable underlying transcriptional oscillations. The results suggest massive AS regulation in the brain that is also likely important for circadian regulation.
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Affiliation(s)
- Qingqing Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Center for RNA Systems Biology (CRSB), University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States
| | - Katharine C Abruzzi
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavior Genomics, Brandeis University, Waltham, United States
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavior Genomics, Brandeis University, Waltham, United States
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Center for RNA Systems Biology (CRSB), University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States
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piRNA-mediated regulation of transposon alternative splicing in the soma and germ line. Nature 2017; 552:268-272. [PMID: 29211718 PMCID: PMC5933846 DOI: 10.1038/nature25018] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated1. The piwi-interacting small RNAs (piRNAs) pathway is critically important for transposable element regulation, by inducing transcriptional silencing or post-transcriptional decay of mRNAs2. Here, we show that piRNAs and piRNA biogenesis components regulate pre-mRNA splicing of P transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in germ cells. Unexpectedly, we show that the piRNA pathway components do not act to reduce P-element transposon transcript levels during P-M hybrid dysgenesis, a syndrome that affects germline development in Drosophila3,4. Instead, splicing regulation is mechanistically achieved in concert with piRNA-mediated changes to repressive chromatin states, and relies on the function of the Piwi-piRNA complex proteins Asterix/Gtsf15–7 and Panoramix/Silencio8,9, as well as Heterochromatin Protein 1a (Su(var)205/HP1a). Furthermore, we show that this machinery, together with the piRNA Flamenco cluster10, not only controls the accumulation of Gypsy retrotransposon transcripts11 but also regulates splicing of Gypsy mRNAs in cultured ovarian somatic cells, a process required for the production of infectious particles that can lead to heritable transposition events12,13. Our findings identify splicing regulation as a new role and essential function for the Piwi pathway in protecting the genome against transposon mobility, and provide a model system for studying the role of chromatin structure in modulating alternative splicing during development.
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Rhythmic Behavior Is Controlled by the SRm160 Splicing Factor in Drosophila melanogaster. Genetics 2017; 207:593-607. [PMID: 28801530 DOI: 10.1534/genetics.117.300139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
Circadian clocks organize the metabolism, physiology, and behavior of organisms throughout the day-night cycle by controlling daily rhythms in gene expression at the transcriptional and post-transcriptional levels. While many transcription factors underlying circadian oscillations are known, the splicing factors that modulate these rhythms remain largely unexplored. A genome-wide assessment of the alterations of gene expression in a null mutant of the alternative splicing regulator SR-related matrix protein of 160 kDa (SRm160) revealed the extent to which alternative splicing impacts on behavior-related genes. We show that SRm160 affects gene expression in pacemaker neurons of the Drosophila brain to ensure proper oscillations of the molecular clock. A reduced level of SRm160 in adult pacemaker neurons impairs circadian rhythms in locomotor behavior, and this phenotype is caused, at least in part, by a marked reduction in period (per) levels. Moreover, rhythmic accumulation of the neuropeptide PIGMENT DISPERSING FACTOR in the dorsal projections of these neurons is abolished after SRm160 depletion. The lack of rhythmicity in SRm160-downregulated flies is reversed by a fully spliced per construct, but not by an extra copy of the endogenous locus, showing that SRm160 positively regulates per levels in a splicing-dependent manner. Our findings highlight the significant effect of alternative splicing on the nervous system and particularly on brain function in an in vivo model.
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Zaytseva O, Quinn LM. Controlling the Master: Chromatin Dynamics at the MYC Promoter Integrate Developmental Signaling. Genes (Basel) 2017; 8:genes8040118. [PMID: 28398229 PMCID: PMC5406865 DOI: 10.3390/genes8040118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/15/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023] Open
Abstract
The transcription factor and cell growth regulator MYC is potently oncogenic and estimated to contribute to most cancers. Decades of attempts to therapeutically target MYC directly have not resulted in feasible clinical applications, and efforts have moved toward indirectly targeting MYC expression, function and/or activity to treat MYC-driven cancer. A multitude of developmental and growth signaling pathways converge on the MYC promoter to modulate transcription through their downstream effectors. Critically, even small increases in MYC abundance (<2 fold) are sufficient to drive overproliferation; however, the details of how oncogenic/growth signaling networks regulate MYC at the level of transcription remain nebulous even during normal development. It is therefore essential to first decipher mechanisms of growth signal-stimulated MYC transcription using in vivo models, with intact signaling environments, to determine exactly how these networks are dysregulated in human cancer. This in turn will provide new modalities and approaches to treat MYC-driven malignancy. Drosophila genetic studies have shed much light on how complex networks signal to transcription factors and enhancers to orchestrate Drosophila MYC (dMYC) transcription, and thus growth and patterning of complex multicellular tissue and organs. This review will discuss the many pathways implicated in patterning MYC transcription during development and the molecular events at the MYC promoter that link signaling to expression. Attention will also be drawn to parallels between mammalian and fly regulation of MYC at the level of transcription.
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Affiliation(s)
- Olga Zaytseva
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
- School of Biomedical Sciences, University of Melbourne, Parkville 3010, Australia.
| | - Leonie M Quinn
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
- School of Biomedical Sciences, University of Melbourne, Parkville 3010, Australia.
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Abstract
Drosophila genetic studies demonstrate that cell and tissue growth regulation is a primary developmental function of P-element somatic inhibitor (Psi), the sole ortholog of FUBP family RNA/DNA-binding proteins. Psi achieves growth control through interaction with Mediator, observations that should put to rest controversy surrounding Pol II transcriptional functions for these KH domain proteins.
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Affiliation(s)
- Leonie M Quinn
- a Department of Cancer Biology and Therapeutics , The John Curtin School of Medical Research, The Australian National University , Canberra , ACT , Australia
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20
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Peng G, Ji P, Zhao F. A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. Genome Biol 2016; 17:232. [PMID: 27855707 PMCID: PMC5114782 DOI: 10.1186/s13059-016-1094-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/31/2016] [Indexed: 11/10/2022] Open
Abstract
Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions. We present inGAP-CDG, which can construct full-length and non-redundant coding sequences from unassembled transcriptomes by using a codon-based de Bruijn graph to simplify the assembly process and a machine learning-based approach to filter false positives. Compared with other methods, inGAP-CDG exhibits a significant increase in predicted coding sequence length and robustness to sequencing errors and varied read length.
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Affiliation(s)
- Gongxin Peng
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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Lee H, Choi HW, Zhang C, Park ZY, Kim YJ. A Pair of Oviduct-Born Pickpocket Neurons Important for Egg-Laying in Drosophila melanogaster. Mol Cells 2016; 39:573-9. [PMID: 27378227 PMCID: PMC4959023 DOI: 10.14348/molcells.2016.0121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 05/25/2016] [Accepted: 05/25/2016] [Indexed: 12/31/2022] Open
Abstract
During copulation, male Drosophila transfers Sex Peptide (SP) to females where it acts on internal sensory neurons expressing pickpocket (ppk). These neurons induce a post-mating response (PMR) that includes elevated egg-laying and refractoriness to re-mating. Exactly how ppk neurons regulate the different aspects of the PMR, however, remains unclear. Here, we identify a small subset of the ppk neurons which requires expression of a pre-mRNA splicing factor CG3542 for egg-laying, but not refractoriness to mating. We identify two CG3542-ppk expressing neurons that innervate the upper oviduct and appear to be responsible for normal egg-laying. Our results suggest specific subsets of the ppk neurons are responsible for each PMR component.
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Affiliation(s)
- Hyunjin Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Hyun Woo Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Chen Zhang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Young-Joon Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
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