1
|
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.
Collapse
|
2
|
Hayden AN, Brandel KL, Merlau PR, Vijayakumar P, Leptich EJ, Pietryk EW, Gaytan ES, Ni CW, Chao HT, Rosenfeld JA, Arey RN. Behavioral screening of conserved RNA-binding proteins reveals CEY-1/YBX RNA-binding protein dysfunction leads to impairments in memory and cognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574402. [PMID: 38260399 PMCID: PMC10802296 DOI: 10.1101/2024.01.05.574402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
RNA-binding proteins (RBPs) regulate translation and plasticity which are required for memory. RBP dysfunction has been linked to a range of neurological disorders where cognitive impairments are a key symptom. However, of the 2,000 RBPs in the human genome, many are uncharacterized with regards to neurological phenotypes. To address this, we used the model organism C. elegans to assess the role of 20 conserved RBPs in memory. We identified eight previously uncharacterized memory regulators, three of which are in the C. elegans Y-Box (CEY) RBP family. Of these, we determined that cey-1 is the closest ortholog to the mammalian Y-Box (YBX) RBPs. We found that CEY-1 is both necessary in the nervous system for memory ability and sufficient to increase memory. Leveraging human datasets, we found both copy number variation losses and single nucleotide variants in YBX1 and YBX3 in individuals with neurological symptoms. We identified one predicted deleterious YBX3 variant of unknown significance, p.Asn127Tyr, in two individuals with neurological symptoms. Introducing this variant into endogenous cey-1 locus caused memory deficits in the worm. We further generated two humanized worm lines expressing human YBX3 or YBX1 at the cey-1 locus to test evolutionary conservation of YBXs in memory and the potential functional significance of the p.Asn127Tyr variant. Both YBX1/3 can functionally replace cey-1, and introduction of p.Asn127Tyr into the humanized YBX3 locus caused memory deficits. Our study highlights the worm as a model to reveal memory regulators and identifies YBX dysfunction as a potential new source of rare neurological disease.
Collapse
Affiliation(s)
- Ashley N Hayden
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Katie L Brandel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Paul R Merlau
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | | | - Emily J Leptich
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Edward W Pietryk
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
| | - Elizabeth S Gaytan
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Postbaccalaureate Research Education Program, Baylor College of Medicine, Houston, TX, 77030
| | - Connie W Ni
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Neuroscience, Rice University, Houston, TX 77005
| | - Hsiao-Tuan Chao
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Baylor Genetics Laboratories, Houston, TX 77021
| | - Rachel N Arey
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
| |
Collapse
|