The Prop1-like homeobox gene unc-42 specifies the identity of synaptically connected neurons
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, United States
- Department of Statistics, Zuckerman Institute, Columbia University, United States
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, United States
- Department of Biological Sciences, University at Buffalo, The State University of New York, United States
Figures
Figure 1 with 2 supplements
unc-42 is expressed in synaptically connected neurons of a nociceptive reflex circuit.
(A) unc-42 reporters used in this study. (B) unc-42 CRISPR-engineered reporter (ot986) expression over the course of development. The unc-42 fosmid reporter shows the same expression in the adult (Re…
Figure 1—figure supplement 1
unc-42 expression quantification.
(A) Quantification of the number of neurons observed at each embryonic stage in the unc-42 CRISPR reporter (ot986). Each circle represents one animal. Red lines indicate the median. (B) …
Figure 1—figure supplement 2
unc-42 expression does not follow lineage history.
unc-42 expression is superimposed on the embryonic lineage of C. elegans (Sulston et al., 1983), with each line indicating one cell.
Figure 2
Motion and posture defects in unc-42 mutants.
Individual motion and posture features were compared between wild type, unc-42(e419), and unc-42(e419) rescue (unc-42(e419); otEx7280[unc-42fosmid]) using the WormTracker. Each circle represents the …
Figure 3
unc-42 affects neurotransmitter identity.
(A) The expression of the unc-17/VAChT fosmid reporter in RMF and RMH neurons is mildly affected in unc-42 and lim-4 single mutants, but enhanced in unc-42; lim-4 double mutants. (B, C) The …
Figure 4
unc-42 affects ionotropic glutamate receptor expression.
(A) The expression of a nmr-1 transgene reporter is lost in the AVD neurons in unc-42 mutants. n = 8 wild type and 69 unc-42(e419) animals. (B) A glr-2 reporter transgene shows expression defects in …
Figure 5
unc-42 affects ionotropic acetylcholine and tyramine receptor expression.
(A) In the absence of unc-42, the RIV, SAAD, SAAV, SMDD, and SMDV neurons do not show acr-2 transgene reporter expression. n = 30 wild type and 20 unc-42(e419) animals. (B) An acr-15 reporter …
Figure 6
unc-42 affects peptidergic communication .
(A) A flp-26 reporter transgene shows expression defects in the AVH neurons in the absence of unc-42. n = 22 wild type and 26 unc-42(e419) animals. (B) A flp-22 reporter transgene shows expression de…
Figure 7 with 3 supplements
Behavioral defects of unc-42 target genes.
(A, B) Behavioral phenotypic summaries of the individual motion and posture features identified in Figure 2 for neuropeptide and neuropeptide receptor mutants (A) and for putative cell/cell …
Figure 7—figure supplement 1
Loss of neuropeptide, neuropeptide receptors, and putative cell/cell recognition molecules affects locomotion.
In each panel (A-R), the individual motion and posture features identified in Figure 2 were compared between wild type and neuropeptide, neuropeptide receptor, cell/cell recognition molecule, and …
Figure 7—figure supplement 2
Effects of unc-42 on sra-11 expression.
In the absence of unc-42, the AVB neurons fail to express a sra-11 reporter. n = 28 wild type and 36 unc-42(e419) animals. p-values shown by Fisher’s exact test.
Figure 7—figure supplement 3
Effects of unc-42 loss on ASH differentiation.
In the absence of unc-42, the ASH fails to express reporter transgenes for (A) srh-15 (n = 16 wild type and 20 unc-42(e419) animals), (B) osm-10 (n = 10 wild type and 12 unc-42(e419) animals), and (C…
Figure 8 with 3 supplements
unc-42 does not affect generation of relative soma position of neurons but partially affects axon extension of some neuron classes.
(A) A rab-3 pan-neuronal reporter transgene does not show defects in neuron generation and relative soma position in the absence of unc-42. See also Figure 8—figure supplement 1. (B) In the absence …
Figure 8—figure supplement 1
unc-42 does not control cell soma position.
(A, V) In the absence of unc-42, the NeuroPAL reporter transgene does not show defects in neuron generation and relative soma position at the L1 and L4 larval stages. (B–U, W–OO) Quantification of …
Figure 8—figure supplement 2
Rescue of unc-42 in the command interneurons does not restore axon anatomy, and loss of unc-42 does not affect axon anatomy in all neurons.
(A) ASI, AIY, ADE, and IL2 neurons do not show nerve ring axon outgrowth defects in unc-42 mutants. p-values shown by Fisher’s exact test. n > 20 for wild type and unc-42(e419) animals. (B) …
Figure 8—figure supplement 3
Putative cell/cell recognition molecules and the unc-6 netrin guidance cue do not affect presynaptic specializations.
(A) The number and position of presynaptic specializations of the AIB neurons is not affected in the absence of unc-6 or ncam-1 (transgene otIs681). (B) In rig-6 mutants, the number and position of …
Figure 9
unc-42 affects synaptic connectivity.
(A) A transverse section of the right ventral ganglion in wild type (N2U, section 142) is compared to the corresponding section in unc-42(e270). The following processes are shown: AINL, AVAL, AVBL, …
Figure 10
unc-42 affects electrical synaptic communication (innexins).
(A) A inx-19 reporter transgene shows expression defects in the ASH, AVA, AVB, AVD, AVE, AVK, and RMDL/R neurons in the absence of unc-42. (B) A inx-18a reporter transgene shows expression defects …
Figure 11
unc-42 affects putative cell/cell recognition molecules (IgSFs) and the unc-6 netrin guidance cue.
(A) In the absence of unc-42, the AVA, AVB, AVD, AVD, and RIV neurons do not show unc-6 fosmid transgene reporter expression. n = 16 wild type and 24 unc-42(e419) animals. (B) A rig-3 reporter …
Figure 12
unc-42 cooperates with cofactors in distinct neuron types on the level of target gene promoters.
(A) Predicted UNC-42 binding sites among orthologs in eight nematode species in unc-42 expressing neuron classes. Text on right: species name, ortholog name. Table: UNC-42 binding site enrichment in …
Figure 13 with 2 supplements
hlh-34, ceh-20/Pbx, and unc-62/Meis are collaborators of unc-42.
(A) The loss-of-function syb2697 allele of hlh-34 is a 410 bp deletion. (B) hlh-34(syb2697) mutant animals show an occasional loss of flp-26::BFP expression in the AVH neuron in a NeuroPAL(otIs696) …
Figure 13—figure supplement 1
ceh-24 affects SMB motor neuron, not SMD motor neuron differentiation.
In the absence of ceh-24, the NeuroPAL reporter transgene is absent from the SMBs, not SMD, as previously reported. A solid circle indicates expression, and a dashed circle indicates absence of …
Figure 13—figure supplement 2
unc-42 controls expression of collaborating transcription factors.
In the absence of unc-42, (A) the unc-3 CRISPR reporter show expression defects in the AVB, AVD, SAAV, and SAAD neurons (n = 24 wild type and 26 unc-42(e419) animals), (B) the cfi-1 transgene …
Figure 14
Overlapping circuit organizers may assemble individual circuits into larger-scale connectomes.
(A) Summary of cofactors for UNC-42. Each colored box indicates where the respective transcription factor is expressed within the set of UNC-42(+) neurons and required, like unc-42, for its proper …
Additional files
-
Supplementary file 1
UNC-42(+) neurons and their function.
- https://cdn.elifesciences.org/articles/64903/elife-64903-supp1-v1.docx
-
Supplementary file 2
Strata placement of UNC-42(+) neurons.
Clustering outputs of Brittin et al., 2021, Moyle et al., 2021 are shown for each neuron. Discordant clustering results of neuronal subclasses are shown for RMD and SIB.
- https://cdn.elifesciences.org/articles/64903/elife-64903-supp2-v1.xlsx
-
Supplementary file 3
Homeobox gene expression correlating with synaptic connectivity.
See Materials and methods for details of this analysis. p-values were calculated using the binomial distribution probability mass function and were adjusted for multiple testing using a false discovery rate correction (see Materials and methods). All genes passing the p<0.05 significance threshold are shown here. Overlap with network differential gene expression analysis shaded in yellow. Red font: genes shown to be involved in neuronal identity regulation (Reilly et al., 2020; Hobert, 2016).
- https://cdn.elifesciences.org/articles/64903/elife-64903-supp3-v1.xlsx
-
Supplementary file 4
List of motion behaviors examined in wild type and unc-42(e419) animals.
Green indicates motion features that are not significantly different, while red indicates motion features that are significantly different (p<0.05) between wild type and unc-42(e419) animals. Motion features were measured for the entire animal, and in the head, tail, and midbody regions. They were measured when the animal was moving forward, backward, or paused. Features were measured accounting for when the data is signed, by absolute data values (‘absolute’), positive data values only (‘positive’), and negative data values only (‘negative’). Motion features are described by the frequency, the time spent, and the distance covered. The animal's velocity is described in two parts: speed and motion direction. Crawling, an undulation of the animal's body used for movement, is described as an amplitude and a frequency. Foraging, a rapid movement of the nose as the animal explores its environment, is described as an amplitude and a speed. An omega turn is when the animal bends sharply such that the head touches the tail in order to reverse direction. An upsilon turn is when the animal bends shallowly in order to reverse direction. Time ratio is defined as the total time spent in a particular behavior divided by the total time. See Yemini et al., 2013 for more detailed feature descriptions.
- https://cdn.elifesciences.org/articles/64903/elife-64903-supp4-v1.xls
-
Supplementary file 5
Strains used in this study.
- https://cdn.elifesciences.org/articles/64903/elife-64903-supp5-v1.docx
-
Supplementary file 6
Methods for neuron identification in electron micrographs of unc-42(e270).
- https://cdn.elifesciences.org/articles/64903/elife-64903-supp6-v1.docx
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/64903/elife-64903-transrepform-v1.docx
