Striking circadian neuron diversity and cycling of Drosophila alternative splicing
- University of California, Berkeley, United States
- Howard Hughes Medical Institute, Brandeis University, United States
- Brandeis University, United States
Figures
Figure 1 with 2 supplements
Many novel alternatively spliced junctions were identified in isolated Drosophila neurons.
Alternatively spliced junctions (AS junctions) were identified in RNA-seq libraries generated from isolated Drosophila neurons (DN1s, LNds, LNvs, and dopaminergic (TH)) as well as from a separately …
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Figure 1—source data 1
AS junctions identified in DN1, LNd, LNv, TH neurons and heads.
- https://doi.org/10.7554/eLife.35618.006
Figure 1—figure supplement 1
Many AS junctions with varying lengths were identified in isolated neuron subtypes.
Alternatively spliced junctions (AS junctions) were identified in RNA-seq libraries generated from isolated Drosophila neurons (DN1s, LNds, LNvs, and dopaminergic (TH)) as well as from a separately …
Figure 1—figure supplement 2
Transcripts with neuron subgroup specific novel ALT junctions reflect critical neuronal functions.
Gene ontology analyses of those transcripts that present neuron subgroup-specific novel ALT junctions that are not found in whole head samples for (A) LNv neurons, (B) LNd neurons, (C) DN1 neurons …
Figure 2
Cry and CG10483 transcripts show neuron subtype-specific alternative splicing that is absent in the heterogeneous head sample.
Neuron subtype-specific novel alternative splicing of cry and CG10483 are shown. RNA-seq data tracks derived from the neuronal samples are shown, with arcs representing splice junctions and the …
Figure 3 with 3 supplements
Identification of differentially spliced AS events in circadian neurons compared to non-circadian, TH neurons.
(A) AS events that were differentially spliced in the circadian neurons (DN1, LNd and LNv) compared to the dopaminergic neurons (TH) were identified using JUM, respectively. The number and type of …
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Figure 3—source data 1
Differentially spliced AS events in DN1 neurons versus the non-circadian TH neurons.
- https://doi.org/10.7554/eLife.35618.012
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Figure 3—source data 2
Differentially spliced AS events in LNd neurons versus the non-circadian TH neurons.
- https://doi.org/10.7554/eLife.35618.013
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Figure 3—source data 3
Differentially spliced AS events in LNv neurons versus the non-circadian TH neurons.
- https://doi.org/10.7554/eLife.35618.014
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Figure 3—source data 4
Differentially spliced AS events in DN1 neurons versus LNd neurons.
- https://doi.org/10.7554/eLife.35618.015
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Figure 3—source data 5
Differentially spliced AS events in LNd neurons versus LNv neurons.
- https://doi.org/10.7554/eLife.35618.016
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Figure 3—source data 6
Differentially spliced AS events in DN1 neurons versus LNv neurons.
- https://doi.org/10.7554/eLife.35618.017
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Figure 3—source data 7
Differentially expressed gene transcripts in DN1 neurons versus the non-circadian TH neurons.
- https://doi.org/10.7554/eLife.35618.018
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Figure 3—source data 8
Differentially expressed gene transcripts in LNd neurons versus the non-circadian TH neurons.
- https://doi.org/10.7554/eLife.35618.019
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Figure 3—source data 9
Differentially expressed gene transcripts in LNv neurons versus the non-circadian TH neurons.
- https://doi.org/10.7554/eLife.35618.020
Figure 3—figure supplement 1
Overlap of differentially spliced AS events in circadian neurons compared to non-circadian, TH neurons in each conventionally recognized splicing pattern category.
Venn graphs showing the overlap of differentially alternatively spliced AS events among the three circadian neuron subtypes versus TH neurons, in each splicing pattern category. Most of the …
Figure 3—figure supplement 2
Identification of differentially spliced AS events among the circadian neuron subpopulations.
AS events that were differentially spliced in each of the circadian neuron subpopulations compared to another (DN1 vs. LNd, LNd vs. LNv and DN1 vs. LNv) were identified using JUM, respectively. The …
Figure 3—figure supplement 3
Functional comparison of differentially spliced cassette exons and non-differentially spliced cassette exons in circadian versus non-circadian TH neurons.
(A) Cross-species conservation comparison. Average PhastCon scores across 27 insect species for the set of differentially spliced cassette exons (AS) and non-differentially spliced cassette exons …
Figure 4
N-syb and Shab undergo differential splicing in circadian neurons compared to non-circadian, TH neurons.
(A) In LNvs, the Neuronal synaptobrevin (N-syb) transcript is enriched for the isoform that includes an exon present in variant J. The alternatively spliced exon is marked by ‘*’. Use of this exon …
Figure 5
Differentially alternatively spliced transcripts in LNvs and DN1s compared to non-circadian neurons reflect specific neuronal functions.
(A) Gene ontology analysis of those transcripts that undergo differential alternative splicing in DN1s reveals enrichments in potassium ion transport, calmodulin-dependent protein kinases, and …
Figure 6 with 3 supplements
Identification of cycling alternative splicing in Drosophila circadian neurons.
To identify cycling time-of-day changes in alternative splicing, the frequency at which each sub-AS-junction is utilized in every profiled AS structure was examined across six timepoints taken at …
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Figure 6—source data 1
Cycling AS events in DN1, LNd, LNv and TH neurons.
- https://doi.org/10.7554/eLife.35618.027
Figure 6—figure supplement 1
Predominant inclusion of exon a of the Sgg transcript in LNv and DN1 neurons.
The frequency of inclusion of exon b of the Sgg transcript in LNv (blue) and DN1 (red) neurons is shown. Low levels of exon b inclusion are found throughout the day. The x-axis shows Zeitgeber time …
Figure 6—figure supplement 2
Identification of slo transcripts that exhibit cycling alternative splicing in Drosophila circadian neurons.
(A) Slowpoke (Slo) undergoes cycling alternative splicing in DN1 neurons. Sashimi plots highlight RNA-seq signals within the region of Slo that where exons 2a (marked by ‘*’) and exon 2b (marked by …
Figure 6—figure supplement 3
Transcripts with neuron subgroup-specific cycling AS structures reflect crucial neuronal functions.
Gene ontology analyses of those transcripts that have neuron subgroup-specific cycling AS structures for (A) LNv neurons, (B) LNd neurons, (C) DN1 neurons, respectively.
Figure 7 with 1 supplement
Cycling alternative splicing and mRNA expression in Drosophila circadian neurons.
(A) The phase distribution of cycling AS structures in DN1 neurons is plotted as a histogram (blue) with the phase distribution of all cycling transcripts in DN1 neurons overlaid (orange). In DN1s, …
Figure 7—figure supplement 1
Phase distribution of cycling AS structures in LNvs and LNds.
The phase distribution of cycling AS structures in LNv and LNd neurons is plotted as a histogram (blue) with the phase distribution of all cycling transcripts overlaid (orange). In LNvs, cycling …
Tables
Key resources table
Additional files
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Supplementary file 1
The distribution of splice site type (including reverse strand) in the AS junctions detected in each neuron group/sample.
The distribution of splice site type in the AS junctions (including reverse strand) detected in each neuron group/sample that are within a gene.
- https://doi.org/10.7554/eLife.35618.030
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Supplementary file 2
Gene ontology analyses of those transcripts that present neuron subgroup specific novel ALT junctions that are not found in whole head samples for each neuron subpopulation.
- https://doi.org/10.7554/eLife.35618.031
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Supplementary file 3
Gene ontology analyses of those transcripts that present neuron subgroup specific cycling AS structures.
- https://doi.org/10.7554/eLife.35618.032
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Supplementary file 4
Mapping statistics of the neuronal RNA-seq data to the Drosophila genome (dm3).
- https://doi.org/10.7554/eLife.35618.033
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Supplementary file 5
Commands for STAR mapping.
- https://doi.org/10.7554/eLife.35618.034
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Transparent reporting form
- https://doi.org/10.7554/eLife.35618.035
