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Wolfe Z, Liska D, Norris A. Deep Transcriptomics Reveals Cell-Specific Isoforms of Pan-Neuronal Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594572. [PMID: 38826410 PMCID: PMC11142100 DOI: 10.1101/2024.05.16.594572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Profiling gene expression in single neurons using single-cell RNA-Seq is a powerful method for understanding the molecular diversity of the nervous system. Profiling alternative splicing in single neurons using these methods is more challenging, however, due to low capture efficiency and sensitivity. As a result, we know much less about splicing patterns and regulation across neurons than we do about gene expression. Here we leverage unique attributes of the C. elegans nervous system to investigate deep cell-specific transcriptomes complete with biological replicates generated by the CeNGEN consortium, enabling high-confidence assessment of splicing across neuron types even for lowly-expressed genes. Global splicing maps reveal several striking observations, including pan-neuronal genes that harbor cell-specific splice variants, abundant differential intron retention across neuron types, and a single neuron highly enriched for upstream alternative 3' splice sites. We develop an algorithm to identify unique cell-specific expression patterns and use it to discover both cell-specific isoforms and potential regulatory RNA binding proteins that establish these isoforms. Genetic interrogation of these RNA binding proteins in vivo identifies three distinct regulatory factors employed to establish unique splicing patterns in a single neuron. Finally, we develop a user-friendly platform for spatial transcriptomic visualization of these splicing patterns with single-neuron resolution.
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Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [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: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
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Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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Sanfeliu-Cerdán N, Català-Castro F, Mateos B, Garcia-Cabau C, Ribera M, Ruider I, Porta-de-la-Riva M, Canals-Calderón A, Wieser S, Salvatella X, Krieg M. A MEC-2/stomatin condensate liquid-to-solid phase transition controls neuronal mechanotransduction during touch sensing. Nat Cell Biol 2023; 25:1590-1599. [PMID: 37857834 PMCID: PMC10635833 DOI: 10.1038/s41556-023-01247-0] [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: 07/22/2022] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
A growing body of work suggests that the material properties of biomolecular condensates ensuing from liquid-liquid phase separation change with time. How this aging process is controlled and whether the condensates with distinct material properties can have different biological functions is currently unknown. Using Caenorhabditis elegans as a model, we show that MEC-2/stomatin undergoes a rigidity phase transition from fluid-like to solid-like condensates that facilitate transport and mechanotransduction, respectively. This switch is triggered by the interaction between the SH3 domain of UNC-89 (titin/obscurin) and MEC-2. We suggest that this rigidity phase transition has a physiological role in frequency-dependent force transmission in mechanosensitive neurons during body wall touch. Our data demonstrate a function for the liquid and solid phases of MEC-2/stomatin condensates in facilitating transport or mechanotransduction, and a previously unidentified role for titin homologues in neurons.
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Affiliation(s)
- Neus Sanfeliu-Cerdán
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Frederic Català-Castro
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Borja Mateos
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Ribera
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Iris Ruider
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Montserrat Porta-de-la-Riva
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Adrià Canals-Calderón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stefan Wieser
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Michael Krieg
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain.
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Taylor M, Marx O, Norris A. TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation. Nucleic Acids Res 2023; 51:9610-9628. [PMID: 37587694 PMCID: PMC10570059 DOI: 10.1093/nar/gkad665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/20/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
Gene expression is a multistep process and crosstalk among regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant gene expression coordination, we performed a systematic reverse-genetic interaction screen in C. elegans, combining RNA binding protein (RBP) and transcription factor (TF) mutants to generate over 100 RBP;TF double mutants. We identified many unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1, and the homeodomain TF ceh-14. Losing any one of these genes alone has no effect on the health of the organism. However, fust-1;ceh-14 and tdp-1;ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-Seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. A skipped exon in the polyglutamine-repeat protein pqn-41 is aberrantly included in tdp-1 mutants, and genetically forcing this exon to be skipped in tdp-1;ceh-14 double mutants rescues their fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility and a shared molecular role in exon inhibition.
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Affiliation(s)
- Morgan Taylor
- Southern Methodist University, Dallas, TX 75205, USA
| | - Olivia Marx
- Southern Methodist University, Dallas, TX 75205, USA
| | - Adam Norris
- Southern Methodist University, Dallas, TX 75205, USA
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Liska D, Wolfe Z, Norris A. VISTA: visualizing the spatial transcriptome of the C.elegans nervous system. BIOINFORMATICS ADVANCES 2023; 3:vbad127. [PMID: 37810458 PMCID: PMC10560093 DOI: 10.1093/bioadv/vbad127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/07/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023]
Abstract
Summary Profiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode worm Caenorhabditis elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm's invariant cell lineage and a series of recently generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a "spatial heatmap" in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated from in vivo reporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future. Availability and implementation VISTA is freely available at the following URL: https://public.tableau.com/app/profile/smu.oit.data.insights/viz/VISTA_16814210566130/VISTA.
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Affiliation(s)
- David Liska
- Office of Information Technology, Southern Methodist University, Dallas, TX 75205, United States
| | - Zachery Wolfe
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75205, United States
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75205, United States
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Bergwell M, Smith A, Smith E, Dierlam C, Duran R, Haastrup E, Napier-Jameson R, Seidel R, Potter W, Norris A, Iyer J. A primary microcephaly-associated sas-6 mutation perturbs centrosome duplication, dendrite morphogenesis, and ciliogenesis in Caenorhabditis elegans. Genetics 2023; 224:iyad105. [PMID: 37279547 PMCID: PMC10411591 DOI: 10.1093/genetics/iyad105] [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: 05/01/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023] Open
Abstract
The human SASS6(I62T) missense mutation has been linked with the incidence of primary microcephaly in a Pakistani family, although the mechanisms by which this mutation causes disease remain unclear. The SASS6(I62T) mutation corresponds to SAS-6(L69T) in Caenorhabditis elegans. Given that SAS-6 is highly conserved, we modeled this mutation in C. elegans and examined the sas-6(L69T) effect on centrosome duplication, ciliogenesis, and dendrite morphogenesis. Our studies revealed that all the above processes are perturbed by the sas-6(L69T) mutation. Specifically, C. elegans carrying the sas-6(L69T) mutation exhibit an increased failure of centrosome duplication in a sensitized genetic background. Further, worms carrying this mutation also display shortened phasmid cilia, an abnormal phasmid cilia morphology, shorter phasmid dendrites, and chemotaxis defects. Our data show that the centrosome duplication defects caused by this mutation are only uncovered in a sensitized genetic background, indicating that these defects are mild. However, the ciliogenesis and dendritic defects caused by this mutation are evident in an otherwise wild-type background, indicating that they are stronger defects. Thus, our studies shed light on the novel mechanisms by which the sas-6(L69T) mutation could contribute to the incidence of primary microcephaly in humans.
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Affiliation(s)
- Mary Bergwell
- Oklahoma Medical Research Foundation, Cell Cycle & Cancer Biology Research Program, Oklahoma City, OK 73104, USA
| | - Amy Smith
- Pfizer Inc., Pharmaceutical R&D – Drug Product Design & Development, Chesterfield, MO 63017, USA
| | - Ellie Smith
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Carter Dierlam
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Ramon Duran
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Erin Haastrup
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | | | - Rory Seidel
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - William Potter
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Adam Norris
- Southern Methodist University, Department of Biological Sciences, Dallas, TX 75275, USA
| | - Jyoti Iyer
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
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Liska D, Wolfe Z, Norris A. VISTA: Visualizing the Spatial Transcriptome of the C. elegans Nervous System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538711. [PMID: 37163055 PMCID: PMC10168398 DOI: 10.1101/2023.04.28.538711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Profiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode worm C. elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm's invariant cell lineage and a series of recently-generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a "spatial heatmap" in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated from in vivo reporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation, and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future.
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Affiliation(s)
- David Liska
- Office of Information Technology, Southern Methodist University. Dallas, TX USA
| | - Zachery Wolfe
- Department of Biological Sciences, Southern Methodist University. Dallas, TX USA
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University. Dallas, TX USA
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Liang X, Taylor M, Napier-Jameson R, Calovich-Benne C, Norris A. A Conserved Role for Stomatin Domain Genes in Olfactory Behavior. eNeuro 2023; 10:ENEURO.0457-22.2023. [PMID: 36858824 PMCID: PMC10035767 DOI: 10.1523/eneuro.0457-22.2023] [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: 11/08/2022] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
The highly-conserved stomatin domain has been identified in genes throughout all classes of life. In animals, different stomatin domain-encoding genes have been implicated in the function of the kidney, red blood cells, and specific neuron types, although the underlying mechanisms remain unresolved. In one well-studied example of stomatin domain gene function, the Caenorhabditis elegans gene mec-2 and its mouse homolog Stoml3 are required for the function of mechanosensory neurons, where they modulate the activity of mechanosensory ion channels on the plasma membrane. Here, we identify an additional shared function for mec-2 and Stoml3 in a very different sensory context, that of olfaction. In worms, we find that a subset of stomatin domain genes are expressed in olfactory neurons, but only mec-2 is strongly required for olfactory behavior. mec-2 acts cell-autonomously and multiple alternatively-spliced isoforms of mec-2 can be substituted for each other. We generate a Stoml3 knock-out (KO) mouse and demonstrate that, like its worm homolog mec-2, it is required for olfactory behavior. In mice, Stoml3 is not required for odor detection, but is required for odor discrimination. Therefore, in addition to their shared roles in mechanosensory behavior, mec-2 and Stoml3 also have a shared role in olfactory behavior.
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Affiliation(s)
- Xiaoyu Liang
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275
| | - Morgan Taylor
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275
| | | | - Canyon Calovich-Benne
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275
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