In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system

  1. Lori Glenwinkel
  2. Seth R Taylor
  3. Kasper Langebeck-Jensen
  4. Laura Pereira
  5. Molly B Reilly
  6. Manasa Basavaraju
  7. Ibnul Rafi
  8. Eviatar Yemini
  9. Roger Pocock
  10. Nenad Sestan
  11. Marc Hammarlund
  12. David M Miller III
  13. Oliver Hobert  Is a corresponding author
  1. Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, United States
  2. Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, United States
  3. Biotech Research and Innovation Centre, University of Copenhagen, Denmark
  4. Department of Neurobiology, Yale University School of Medicine, United States
  5. Department of Genetics, Yale University School of Medicine, United States
  6. Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Australia
8 figures and 5 additional files

Figures

Background.

(A) Possible models for regulation of terminal gene batteries. (B) Four examples of terminal selectors (>20 markers tested >1 binding site mutated). All genes shown are direct targets of the …

Data sources overview.

(A) Top: Differentially expressed genes per single cell profile (Taylor et al., 2021). Bottom: Reporter count per neuron class from the Brain Atlas collection (a compendium of reporter expression …

Figure 2—source data 1

DNA binding motif logos.

Images were downloaded from cisbp.ccbr.utoronto.ca/. See motif source information in Supplementary file 1A.

https://cdn.elifesciences.org/articles/64906/elife-64906-fig2-data1-v1.pdf
Figure 3 with 3 supplements
TargetOrtho2 development.

(A) Ortholog schematic for eight nematode genomes included in TargetOrtho2. Fifty motif features used by TargetOrtho2’s classifier to rank candidate transcription factor (TF) target genes are shown …

Figure 3—figure supplement 1
TargetOrtho2 development cross-validation results.

(A) Prediction of transcription factor (TF) target genes with supervised learning. Diagram of cross-validation scheme for choosing the best classifier for target gene prediction from experimentally …

Figure 3—figure supplement 2
Four bona fide terminal selectors are enriched for phylogenetically conserved transcription factor (TF) binding sites (Brain Atlas data).

Motif matches in neuron class reporter genes. UNC-3 motif (OH2011) from Kratsios et al., 2011, ASE motif (OH2007) from Etchberger et al., 2007, AIY motif (OH2004) from Wenick and Hobert, 2004, ADL …

Figure 3—figure supplement 3
Comparison of in vivo and in vitro derived transcription factor (TF) DNA binding motifs.

(A) Data from single cell differential gene expression profiles. (B) Data from Brain Atlas.

Figure 4 with 4 supplements
Terminal selectors with published genetic loss-of-function data.

(A) Transcription factors (TFs) with previously described effects on select identity features are predicted to broadly control neuron type-specific gene batteries. TFs and target neuron …

Figure 4—figure supplement 1
Proportion of predicted coordinated regulators versus number of markers tested.

(A) Single cell RNA-seq differential gene expression data. (B) Brain Atlas reporter data.

Figure 4—figure supplement 2
Comparison of in vivo and in vitro derived TF DNA binding motifs.

(A) Data from single cell differential gene expression profiles. (B) Data from Brain Atlas.

Figure 4—figure supplement 3
Four bona fide terminal selectors are enriched for phylogenetically conserved TF binding sites (Brain Atlas data).

Motif matches in neuron class reporter genes. UNC-3 motif (OH2011) from Kratsios et al., 2011, ASE motif (OH2007) from Etchberger et al., 2007, AIY motif (OH2004) from Wenick and Hobert, 2004 ADL …

Figure 4—figure supplement 4
Motif presence in published, TF-dependent reporter genes.
Experimental validation of putative terminal selectors.

(A) Genetic loss-of-function mutant analysis for three transcription factors (TFs) with little previous evidence of direct regulation. ODR-7 is required for expression of ins-1 and pgp-2 reporters …

Figure 6 with 1 supplement
Motif signatures in the nervous system from single cell data.

(A) Overview of all transcription factor (TF) motif signatures in differentially expressed neuron class genes across the nervous system. Most neuron classes have a candidate ‘coordinated regulator’ …

Figure 6—figure supplement 1
Motif presence in published, transcription factor (TF)-dependent reporter genes.
Terminal selector combinations inferred from motif co-occurences.

(A) Co-motif signatures from pairwise cofactor analysis. (1) ‘co-occuring coordinated signatures’ (orange) in which not only is each TF individually characterized as a ‘coordinated regulator’ (Figure…

Figure 7—source data 1

Chord diagrams that shows predicted terminal selector combinations (with joined enrichment of binding sites in terminal gene batteries) for all neuron classes.

https://cdn.elifesciences.org/articles/64906/elife-64906-fig7-data1-v1.pdf
Comparison of Brain Atlas reporter-based motif analysis and single cell RNA-sequencing derived results.

(A) The proportion of motifs per transcription factor (TF) per neuron class is significantly correlated between the two datasets. (B) Motif signature model assignments per TF per neuron class are …

Additional files

Supplementary file 1

Data sources.

(A) Motif information. Log-odd PSSM in MEME format for non-CISBP source motifs can be found at the end of (A). (B) Single cell differentially expressed genes as binary expression matrix. (C) Brain Atlas binary expression matrix.

https://cdn.elifesciences.org/articles/64906/elife-64906-supp1-v1.xlsx
Supplementary file 2

Motif analysis results from single cell differential expression data.

(A) Results from transcription factor (TF) with genetic loss-of-function data including results that were further validated in vivo. (B) Results for four, well-characterized terminal selectors. (C) Nervous system-wide motif analysis results from single cell differential gene expression data. (D) Cofactor results from motif analysis of single cell differential gene expression data. (E) All predicted coordinated regulators (candidate terminal selectors) by neuron class. (F) Candidate target neuron class gene batteries by coordinated regulatory TF. (G) All co-occuring coordinated signatures (candidate terminal selector co-regulators).

https://cdn.elifesciences.org/articles/64906/elife-64906-supp2-v1.xlsx
Supplementary file 3

Motif analysis stats from Brain Atlas reporter data.

(A) Brain Atlas single factor motif analysis results. (B) Cofactor results. (C) Agreement of top two regulators between datasets.

https://cdn.elifesciences.org/articles/64906/elife-64906-supp3-v1.xlsx
Supplementary file 4

Strain information.

https://cdn.elifesciences.org/articles/64906/elife-64906-supp4-v1.xlsx
Transparent reporting form
https://cdn.elifesciences.org/articles/64906/elife-64906-transrepform-v1.docx

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