linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells
- Department of Genetics, Yale University, United States
- Yale Center for Genome Analysis, Yale University, United States
- Department of Cell and Developmental Biology, University College London, United Kingdom
- Department of Computer Science, Yale University, United States
- Stowers Institute for Medical Research, United States
- Department of Molecular & Integrative Physiology, University of Kansas School of Medicine, United States
- Yale Stem Cell Center, Yale University School of Medicine, United States
- Yale Cancer Center, Yale University School of Medicine, United States
Figures
Figure 1 with 7 supplements
linc-mipep and linc-wrb loss-of-protein-function mutant larvae are behaviorally hyperactive.
(A) Left, schematic of F0 CRISPR knockout behavioral screen. Zebrafish embryos were injected early at the one-cell embryo stage with multiple sgRNAs and Cas9 targeting the ORF of candidate …
Figure 1—figure supplement 1
Expression of micropeptide candidates.
(A) Left, in situ hybridization expression of linc-epb41l4a (libra, ENDSART00000137620) at 2days post-fertilization (dpf). Right, ribosome protected fragments (RPF) at 12hours post-fertilization …
Figure 1—figure supplement 2
Validation of CRISPR targeting in F0 screen.
(A) DNA Sequencing of each target region from a sample pool of 8 individual embryos at 24hpf. Discordance of wild type Sanger sequencing reads (orange traces, Wild type sequence) compared to F0 …
Figure 1—figure supplement 3
Screening for micropeptide loss-of-function effects on zebrafish baseline behavior.
(A) Behavioral fingerprints for independent experimental replicates for libra, linc-cd74, linc-foxp2, and linc-loc100334485 (labeled linc-loc485). Deviation (Z-score, mean ± SEM) of each mutant …
Figure 1—figure supplement 4
Average daytime activity differences between WT and F0 knockouts of candidate micropeptides.
Dot plots of the average daytime activity at 6 dpf between sibling wild-type larvae injected with scrambled guides (WT+scr) and F0 knockouts of candidate micropeptides. Left axis, average activity …
Figure 1—figure supplement 5
linc-mipep and linc-wrb gene expression in early zebrafish development.
(A) Gene location of linc-mipep, currently annotated as si:ch73-1a9.3, on chromosome 10 (Danio rerio, danRer11). linc-mipep contains 6 exons, a 5’UTR and a 3’UTR on the forward strand and is located …
Figure 1—figure supplement 6
Stable linc-mipep and linc-wrb mutant behavioral profiles and sequence verification.
(A) Left, locomotor activity of linc-mipepdel-1.8kb/del-1.8kb (linc-mipep -/-, green); linc-mipepdel-1.8kb/+ (linc-mipep +/-, orange); and wild-type (linc-mipep +/+, blue) sibling larvae over 2 …
Figure 1—figure supplement 7
linc-mipep and linc-wrb loss-of-protein-function mutant larvae are behaviorally hyperactive in a dose-dependent manner.
(A) Left, locomotor activity of wild type (WT, blue) or maternal-zygotic linc-mipep delATG/delATG (MZ linc-mipep delATG, orange) larvae over 24hr. Right, average activity at 6 dpf plotted for …
Figure 2 with 6 supplements
linc-mipep and linc-wrb encode proteins with homology to human HMGN1.
(A) Top, diagram of transgenic linc-mipep overexpression construct. Transgenic lines were established via Tol2-mediated integration of 3.5kb ubiquitin B (ubb) promotor driving the linc-mipep coding …
Figure 2—figure supplement 1
linc-wrb mutant behavioral phenotype can be rescued by transgenic linc-mipep CDS, though not by human Hmgn1 CDS.
(A) Western blot against FLAG or Actin of WT or (Tg(ubb:linc-mipep CDS-FLAG-HA-T2A-mCherry) transgenic incross) embryos at 6 hpf. (B) Locomotor activity of linc-wrb heterozygous mutants (+/-) or …
Figure 2—figure supplement 2
Antibody staining confirmation of proteins encoded by linc-mipep and linc-wrb.
(A) The amino acid sequence for the protein encoded by linc-mipep, with the custom antibody designed to detect the underlined sequence in magenta. Arrows indicate the location of mutations in the …
Figure 2—figure supplement 3
linc-mipep and linc-wrb encode proteins with homology to human HMGN1.
(A) Multiple sequence alignment of cDNA sequences of human Hmgn1 (hHmgn1), linc-mipep, and linc-wrb. Asterisks, nucleotide conservation across all three CDS. (B) Transcripts for linc-mipep (top), lin…
Figure 2—figure supplement 4
Amino acid sequence alignment for identified HMGN1 sequences across species.
Clustal Omega multiple sequence alignment of the identified or proposed HMGN (ancestral) or HMGN1 sequences across species as indicated. Full sequences of an extended species list are presented in Su…
Figure 2—figure supplement 5
Syntenic analysis of linc-mipep and linc-wrb.
(A) Amphioxus (lancelet) region at the putative syntenic region to human HMGN1 locus, indicated by WRB and BRWD3-like flanking an APEX1-like gene (putative evolutionary location of vertebrate HMGN). …
Figure 2—figure supplement 6
Relationships between genes encoded by linc-mipep and linc-wrb across fish species.
Expanded gene tree of si:ch73-281n10.2 from Ensembl (GRCz11), showing fully expanded tree of identified related genes across fish species. ‘linc-wrb’ is denoted in orange, and ‘linc-mipep’ is …
Figure 3 with 3 supplements
linc-mipep mutants have dysregulation of NMDA receptor-mediated signaling and immediate early gene induction.
(A) Left, hierarchical clustering of the linc-mipep del-1.8kb (schematic of mutation at top) behavioral fingerprints (right), compared with the fingerprints of wild-type zebrafish larvae exposed to …
Figure 3—figure supplement 1
Correlating small molecules from hierarchical clustering of linc-mipep or linc-wrb mutant fingerprints with those of wild-type zebrafish larvae exposed to 550 psychoactive agents.
(A) Hierarchical clustering of the linc-mipep del-1.8kb behavioral fingerprints compared with the fingerprints of wild-type zebrafish larvae exposed to 550 psychoactive agents from 4 to 6 dpf (Rihel …
Figure 3—figure supplement 2
linc-mipep and linc-wrb mutants are sensitized to glucocorticoid receptor agonists.
(A) Locomotor average activity of wild-type larvae treated with DMSO (WT, blue) or with 10μM glucocorticoid receptor agonist Flumethasone (magenta), and linc-mipep del-1.8kb/del-1.8kb larvae treated …
Figure 3—figure supplement 3
Chromatin accessibility of wild type and linc-mipep; linc-wrb mutant brains.
(A) Biplots showing correlations between the wild type brain Omni-ATAC replicates (n=9 brains each, N=3), collected at Zeitgeber Time (ZT) 4. The zebrafish genome was divided into 5Kb windows, and …
Figure 4 with 9 supplements
Evolutionarily newer vertebrate cell types are more susceptible to loss of linc-mipep and linc-wrb proteins.
(A) UMAP representation of WNN analyses of wild type (n=6,942 nuclei) and linc-mipep del-1.8kb/del-1.8kb (n=7740 nuclei) mutant brains at 6 dpf. Identified cell types as labeled. (B) PHATE plot of …
Figure 4—figure supplement 1
Single cell Multiome analyses in wild type and linc-mipep mutant brain nuclei.
(A) UMAP representation of WNN analyses (transcriptomic and chromatin accessibility) of merged wild type (n=6,942 nuclei) and linc-mipep del-1.8kb/del-1.8kb (n=7740 nuclei) mutant brains at 6 dpf, …
Figure 4—figure supplement 2
linc-mipep and linc-wrb expression by cluster in wild type or linc-mipep mutant brain cells.
Expression levels of linc-mipep (si:ch73-1a9.3, left column) or linc-wrb (si:ch73-281n10.2, right column) in either wild type or linc-mipep brain cells. Wild type, WT, blue. linc-mipep, MUT, red. …
Figure 4—figure supplement 3
Single-cell Multiome analyses reveal cell states altered in linc-mipep brain cells.
(A) PHATE plot of integrated diffusion analysis of 6 dpf wild type and linc-mipep del-1.8kb/del-1.8kb mutant brain nuclei, color-coded by broad identified cell type (from Supplementary file 6).(B) …
Figure 4—figure supplement 4
Linc-mipep and Linc-wrb protein expression in cerebellar region of olig2:GFP brains.
(A) Dorsal view confocal images (comparable single Z planes) from Tg(olig2:GFP) brains at 5 dpf, zoomed in on the cerebellum in wild type (top) or linc-mipep;linc-wrb double heterozygous mutant …
Figure 4—figure supplement 5
Accessibility for transcription factor motifs most affected in linc-mipep brain cells.
(A) Accessibility for select transcription factor motifs, ordered by related family members, that are significantly more accessible per WNN cluster (as described in Figure 4d) in either wild type or …
Figure 4—figure supplement 6
Sample omni-ATAC peaks.
(A) Wild type 5 dpf brains (blue) or linc-mipep; linc-wrb mutant 5 dpf brains (pink) chromatin accessibility tracks, at chr9:32,748,367–32,750,069 (DanRer11) downstream olig2. (B) Wild type 5 dpf …
Figure 4—figure supplement 7
dot plot for relevant genes differentially expressed in clusters of interest.
Expression levels of genes of interest that significantly change expression in wild type or linc-mipep mutant granule cell (8), OPC (35), or Purkinje cell (38) clusters, shown for all clusters. Wild …
Figure 4—figure supplement 8
Violin plots for NMDA receptor subunits differentially expressed in OPCs.
(A) Violin plots of grin1a expression levels from WNN analysis clusters (identities in Figure 4—figure supplement 1C) of wild type brain nuclei at 6 dpf, in wild type (WT, yellow) or linc-mipep …
Figure 4—figure supplement 9
Violin plots for genes differentially expressed in OPCs that are also enriched in granule cells.
(A) Violin plots of erbb4b expression levels from WNN analysis clusters (identities in Figure 4—figure supplement 1C) of wild type brain nuclei at 6 dpf, in wild type (WT, yellow) or linc-mipep …
Author response image 1
Tables
Appendix 1—key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Danio rerio) | si:ch73-1a9.3, linc-mipep (also called lnc-rps25) - now hmgn1b | Ensembl | ENSDARG00000103919 | |
| Gene (Danio rerio) | si:ch73-281n10.2, linc-wrb - now hmgn1a | Ensembl | ENSDARG00000097102 | |
| Gene (Homo sapiens) | Hmgn1 | Ensembl | ENSG00000205581 | |
| Genetic reagent (Danio rerio) | linc-mipepdel1.78kb | This paper | Mutant line | ya126, available from Giraldez Lab; submitted through ZIRC |
| Genetic reagent (Danio rerio) | linc-mipepATG-del6 | This paper | Mutant line | ya127, available from Giraldez Lab; submitted through ZIRC |
| Genetic reagent (Danio rerio) | linc-mipepdel8 | This paper | Mutant line | ya128, available from Giraldez Lab; submitted through ZIRC |
| Genetic reagent (Danio rerio) | linc-mipep3’UTR-del74 | This paper | Mutant line | ya129, available from Giraldez Lab; submitted through ZIRC |
| Genetic reagent (Danio rerio) | linc-wrbdel11 | This paper | Mutant line | ya130, available from Giraldez Lab; submitted through ZIRC |
| Genetic reagent(Danio rerio) | Tg(olig2:egfp)vu12 | Shin et al., 2003 | transgenic line | Previously published line |
| Genetic reagent(Danio rerio) | Tg(ubb:linc-mipep-FLAG-HA-T2A-mCherry) | This paper | Transgenic line | ya145, available from Giraldez lab; submitted through ZIRC |
| Genetic reagent(Danio rerio) | Tg(ubb:human-Hmgn1-FLAG-HA-T2A-mCherry) | This paper | Transgenic line | ya151, available from Giraldez Lab; submitted through ZIRC |
| Antibody | rabbit polyclonal anti-Linc-wrb | This paper | Custom antibody | custom antibody, (1:100–200) for antibody staining; works with ProK or acetone permeabilization. |
| Antibody | Rabbit polyclonal anti-Linc-mipep | This paper | Custom antibody | custom antibody, (1:100–200)for antibody staining; works with ProK or acetone permeabilization. |
| Antibody | mouse monoclonal anti-FLAG | Sigma | Cat #:F3165 | Western blot (1:2000) |
| Antibody | rabbit polyclonal Actin | Sigma | Cat #: A5060 | Western blot (1:2000) |
| Antibody | rabbit polyclonal anti-RNA Polymerase II antibody | Abcam | Cat #: ab817 | ChIP-seq (4µg) |
| Recombinant DNA reagent | ubb:linc-mipep-FLAG-HA-T2A-mCherry | This paper | Plasmid | Available from Giraldez Lab |
| Recombinant DNA reagent | ubb:humanHmgn1-FLAG-HA-T2A-mCherry | This paper | Plasmid | Available from Giraldez Lab |
| Peptide, recombinant protein | EnGen Spy Cas9 NLS (Cas9 protein) | New England Biolabs | Cat #: M0646T | |
| Sequence-based reagent | gBlocks | Integrated DNA Technologies (IDT) | Gene blocks | Sequences in materials section |
| Sequence-based reagent | All synthetic guide RNAs | Synthego | See Supplementary file 1 | |
| Sequence-based reagent | primers for genotyping and qPCR probes | Sigma | see Supplementary file 1, and materials section | |
| Sequence-based reagent | primers for RNA in situ hybridization probes | Sigma | see Supplementary file 1 | |
| Commercial assay or kit | Neurobasal Medium | Thermo Fisher Scientific | Cat #: 21103049 | |
| Commercial assay or kit | B-27 Supplement (50X), serum free | Thermo Fisher Scientific | Cat #: 17504044 | |
| Commercial assay or kit | Monarch RNA Cleanup Kit | New England Biolabs | Cat #: T2040L | |
| Commercial assay or kit | DIG RNA Labeling Mix | Roche | Cat #: 11277073910 | |
| Commercial assay or kit | NBT/BCIP Stock Solution | Roche | Cat #: 11681451001 | |
| Commercial assay or kit | EZ-Tn5 Transposase | Lucigen | Cat #: TNP92110 | |
| Commercial assay or kit | Anti-Digoxigenin-AP, Fab fragments | Roche | Cat #: 11093274910 | |
| Commercial assay or kit | NEBNext High-Fidelity 2X PCR Master Mix | New England Biolabs | Cat #: M0541 | |
| Commercial assay or kit | Agencourt AMPureXP beads | Beckman Coulter Genomics | Cat #: A63881 | |
| Commercial assay or kit | Flowmi Cell Strainers, porosity 70μm | Bel-Art SP Scienceware | Cat #: H13680-0070 | |
| Commercial assay or kit | Flowmi Cell Strainers, porosity 40μm | Bel-Art SP Scienceware | Cat #: H13680-0040 | |
| Commercial assay or kit | Trizol Reagent | Trizol Reagent | Cat #: 15596–018 | |
| Commercial assay or kit | Nuclei Buffer* (20X) | 10x Genomics | Cat #: 2000153/2000207 | |
| Commercial assay or kit | Nonidet P40 (NP40) Substitute | Sigma-Aldrich | Cat #: 74385 | |
| Commercial assay or kit | NuPAGE 4 to 12%, Bis-Tris, 1.0–1.5mm, Mini Protein Gels | Thermo Fisher Scientific | Cat #: NP0322BOX | |
| Commercial assay or kit | NuPAGE MOPS SDS Running Buffer | Thermo Fisher Scientific | Cat #: NP0001 | |
| Commercial assay or kit | 10X Phosphate-Buffered Saline (PBS), pH 7.4 | American Bio | Cat #: AB11072-01000 | |
| Commercial assay or kit | Amplitaq DNA Polymerase | Applied Biosystems | Cat #: N8080153 | |
| Commercial assay or kit | SuperScript III Reverse Transcriptase | Invitrogen | Cat #: 18080044 | |
| Commercial assay or kit | SuperScript III Reverse Transcriptase | Invitrogen | Cat #: 18080044 | |
| Commercial assay or kit | MinElute Kit | Qiagen | Cat #: 28004 | |
| Commercial assay or kit | Chromium Single Cell Multiome ATAC + Gene Expression | 10x Genomics | 10x Genomics | |
| Chemical compound, drug | Trizma Hydrochloride Solution, pH 7.4 | Sigma-Aldrich | Cat #: T2194 | |
| Chemical compound, drug | Sodium Chloride Solution, 5M | Sigma-Aldrich | Cat #: 59,222C | |
| Chemical compound, drug | Magnesium Chloride Solution, 1M | Sigma-Aldrich | Cat #: M1028 | |
| Chemical compound, drug | L-701,324 | Tocris Bioscience | Cat #: 0907 | dissolved in DMSO |
| Chemical compound, drug | Flumethasone | Selleck Chem | Cat #: S4088 | dissolved in DMSO |
| Chemical compound, drug | Tricaine-S Topical Anesthetics | Pentair Aquatic Eco-Systems | Cat #: TRS1 | |
| Chemical compound, drug | Triton X –100 | Sigma-Aldrich | Cat #: T9284 | |
| Chemical compound, drug | Tween-20 | Sigma-Aldrich | Cat #: P1379 | |
| Chemical compound, drug | Digitonin (5%) | Thermo Fisher Scientific | Cat #: BN2006 | |
| Chemical compound, drug | DAPI | Thermo Fisher Scientific | Cat #: D1306 | |
| Chemical compound, drug | 16% Paraformaldehyde aqueous solution | Electron Microscopy Sciences | Electron Microscopy Sciences | |
| Chemical compound, drug | cOmplete, EDTA-free Protease Inhibitor Cocktail | Roche | ||
| Chemical compound, drug | T7 RNA Polymerase | Roche | Cat #: RPOLT7-RO | |
| Chemical compound, drug | Glycoblue | Thermo Fisher Scientific | Cat #: AM9516 | |
| Software, algorithm | ZebraLab | ViewPoint Behavior Technology | http://viewpoint.fr/en/p/software/zebralab-zebrafish-behavior-screening | |
| Software, algorithm | MATLAB toolboxes | MathWorks | ||
| Software, algorithm | MATLAB R2018a | MathWorks | http://mathworks.com/products/matlab.html | |
| Software, algorithm | Prism 9 | GraphPad | https://www.graphstats.net/graphpad-prism | |
| Software, algorithm | LabxDB seq | Vejnar and Giraldez, 2020 | Used for managing high-throughput sequencing data | |
| Software, algorithm | LabxPipe | Vejnar, 2023b | available at https://github.com/vejnar/LabxPipe | |
| Software, algorithm | ReadKnead | Vejnar, 2023c | available at https://github.com/vejnar/ReadKnead | |
| Software, algorithm | Bowtie2 | Langmead and Salzberg, 2012 | read mapping | |
| Software, algorithm | BEDTools | Quinlan and Hall, 2010 | genome tracks | |
| Software, algorithm | MACS3 and MACS2 | Zhang et al., 2008 | peak calling | |
| Software, algorithm | DESeq2 | Love et al., 2014 | differential analysis | |
| Software, algorithm | deeptools | Ramírez et al., 2014 | ||
| Software, algorithm | gplots | Galili 2020 | available at https://github.com/talgalili/gplots | |
| Software, algorithm | MEME suite | McLeay and Bailey, 2010 | available at https://meme-suite.org/meme/tools/ame | |
| Software, algorithm | GeneAbacus | Vejnar, 2023c | available at https://github.com/vejnar/geneabacus | |
| Software, algorithm | cellranger-arc pipeline (v1.0.1) | 10x Genomics | ||
| Software, algorithm | Weighted Nearest Neighbor (WNN) | Hao et al., 2021 | ||
| Software, algorithm | Integrated Diffusion | Kuchroo et al., 2021; Kuchroo et al., 2022 | ||
| Software, algorithm | Custom sleep analysis software | Rihel, 2023 | available at https://github.com/JRihel/Sleep-Analysis/tree/Sleep-Analysis-Code |
Additional files
-
Supplementary file 1
Information on sORFs identified within lincRNAs and targeting/genotyping information (3 sheets).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp1-v1.xlsx
-
Supplementary file 2
Protein and proximal 3'UTR BLAST results, and related HMGN1 across species (5 sheets).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp2-v1.xlsx
-
Supplementary file 3
Correlating Drugs to linc-mipep1 heterozygous and homozygous mutants, from hierarchical clustering analysis against>500 FDA-approved small molecues (from Rihel et al., 2010), and concentrations used (1 sheet).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp3-v1.xlsx
-
Supplementary file 4
Bulk omni-ATAC-seq on WT or linc-mipep;linc-wrb mutant brains at 5 dpf (4 sheets).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp4-v1.xlsx
-
Supplementary file 5
Single cell Multiome Analyses of WT or linc-mipep mutant brains (sibling-matched) at 5 dpf (8 sheets).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp5-v1.xlsx
-
Supplementary file 6
Integrated Diffusion/MELD analyses using WNN clusters and conditional clusters (2 sheets).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp6-v1.xlsx
-
Supplementary file 7
RNA Polymerase II ChIP-seq on wild type (WT) or linc-mipep; linc-wrb dissected brains at 5days post-fertilization (dpf) (2 sheets).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp7-v1.xlsx
-
Supplementary file 8
ATAC peak intensity plots for statistically different peaks between wild type and linc-mipep mutant cells.
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp8-v1.pdf
-
Supplementary file 9
Key for raw sequencing data from this study deposited in NCBI BioProject PRJNA945049 (1 sheet).
- https://cdn.elifesciences.org/articles/82249/elife-82249-supp9-v1.xlsx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/82249/elife-82249-mdarchecklist1-v1.pdf
