Multipotent progenitors instruct ontogeny of the superior colliculus.
The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.
Pubmed ID: 38096816 RIS Download
Research resources used in this publication
- Illumina NovaSeq 6000 Sequencing System (RRID:SCR_016387) (instrument resource)
- Sutter P-1000 Next Generation Micropipette Puller (RRID:SCR_021042) (instrument resource)
- Olympus BX51WI Fixed Stage Upright Microscope (RRID:SCR_023069) (instrument resource)
- Sony Biotechnology SH800S Cell Sorter (RRID:SCR_018066) (instrument resource)
- Zeiss Axio Imager 2 (RRID:SCR_018876) (instrument resource)
- Olympus cellSens Software (RRID:SCR_014551) (software resource)
- STAR (RRID:SCR_004463) (software resource)
- scVelo (RRID:SCR_018168) (software resource)
- Velocyto (RRID:SCR_018167) (software resource)
- scater (RRID:SCR_015954) (software resource)
- SeuratWrappers (RRID:SCR_022555) (software resource)
- Monocle3 (RRID:SCR_018685) (software resource)
- Seurat (RRID:SCR_016341) (software resource)
- R Project for Statistical Computing (RRID:SCR_001905) (software resource)
- Cell Ranger (RRID:SCR_017344) (software resource)
- Fiji (RRID:SCR_002285) (software resource)
- GraphPad Prism (RRID:SCR_002798) (software resource)
- ZEISS ZEN Microscopy Software (RRID:SCR_013672) (software resource)
- B6;129P2-Mapttm2Arbr/J (RRID:IMSR_JAX:021162) (organism)
- B6;129S-Sox2tm1(cre/ERT2)Hoch/J (RRID:IMSR_JAX:017593) (organism)
- C;129S4-Ptentm1Hwu/J (RRID:IMSR_JAX:004597) (organism)
- B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato.-EGFP)Luo/J (RRID:IMSR_JAX:007676) (organism)
-
CD1;B6N-MADM-TGtm1(Chr19)Biat; Igs40
-
CD1;B6N-MADM-GTtm1(Chr19)Biat; Igs40
- STOCK Igs2tm2(ACTB-tdTomato.-EGFP)Luo/J (RRID:IMSR_JAX:013751) (organism)
- STOCK Igs2tm1(ACTB-EGFP.-tdTomato)Luo/J (RRID:IMSR_JAX:013749) (organism)
Additional research tools detected in this publication
None foundAntibodies used in this publication
- Anti-NeuN (RRID:AB_2298772)
- Anti-Doublecortin antibody (RRID:AB_732011)
- Rabbit Anti-RFP / DsRed Polyclonal Antibody, Unconjugated (RRID:AB_591279)
- RRID NOT VALID - THIS IS NOT AN ANTIBODY: DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride) (RRID:AB_2629482)
- Donkey Anti-Mouse IgG (H+L) Polyclonal Antibody, Alexa Fluor ?? 647 Conjugated (RRID:AB_162542)
- Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 647 (RRID:AB_2535864)
- Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 568 (RRID:AB_2534104)
- Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 647 (RRID:AB_2536183)
- Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 568 (RRID:AB_2534017)
- Alexa Fluor 488 AffiniPure Donkey Anti-Chicken IgY (IgG) (H+L) (RRID:AB_2340375)
- Sox9 (D8G8H) Rabbit mAb #82630 (RRID:AB_2665492)
- ANTI-OLIG-2 (RRID:AB_570666)
- Ki67 antibody - Proliferation Marker (RRID:AB_443209)
- Chicken Anti-beta Galactosidase Polyclonal Antibody, Unconjugated (RRID:AB_307210)
- anti-tdTomato (RRID:AB_2722750)
- Anti-Green Fluorescent Protein Antibody (RRID:AB_10000240)
Associated grants
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This is a list of tools and resources that we have found mentioned in this publication.
Anti-Doublecortin antibody (antibody)
RRID:AB_732011
This polyclonal targets Doublecortin
View all literature mentionsRabbit Anti-RFP / DsRed Polyclonal Antibody, Unconjugated (antibody)
RRID:AB_591279
This polyclonal targets RFP / DsRed
View all literature mentionsRRID NOT VALID - THIS IS NOT AN ANTIBODY: DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride) (antibody)
RRID:AB_2629482
This unknown targets
View all literature mentionsDonkey Anti-Mouse IgG (H+L) Polyclonal Antibody, Alexa Fluor ?? 647 Conjugated (antibody)
RRID:AB_162542
This polyclonal targets Mouse IgG (H+L)
View all literature mentionsDonkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 647 (antibody)
RRID:AB_2535864
This polyclonal secondary targets IgG (H+L)
View all literature mentionsDonkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 568 (antibody)
RRID:AB_2534104
This polyclonal secondary targets IgG (H+L)
View all literature mentionsDonkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 647 (antibody)
RRID:AB_2536183
This polyclonal secondary targets IgG (H+L)
View all literature mentionsDonkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 568 (antibody)
RRID:AB_2534017
This polyclonal secondary targets IgG (H+L)
View all literature mentionsAlexa Fluor 488 AffiniPure Donkey Anti-Chicken IgY (IgG) (H+L) (antibody)
RRID:AB_2340375
This polyclonal targets IgY (IgG) (H+L)
View all literature mentionsSox9 (D8G8H) Rabbit mAb #82630 (antibody)
RRID:AB_2665492
This monoclonal targets Sox9
View all literature mentionsANTI-OLIG-2 (antibody)
RRID:AB_570666
This polyclonal targets Oligodendrocute transcription factor 2
View all literature mentionsKi67 antibody - Proliferation Marker (antibody)
RRID:AB_443209
This polyclonal targets Ki67 antibody - Proliferation Marker
View all literature mentionsChicken Anti-beta Galactosidase Polyclonal Antibody, Unconjugated (antibody)
RRID:AB_307210
This polyclonal targets beta Galactosidase
View all literature mentionsanti-tdTomato (antibody)
RRID:AB_2722750
This polyclonal targets tdTomato
View all literature mentionsAnti-Green Fluorescent Protein Antibody (antibody)
RRID:AB_10000240
This polyclonal targets Green Fluorescent Protein (GFP)
View all literature mentionsIllumina NovaSeq 6000 Sequencing System (instrument resource)
RRID:SCR_016387
System unleashes groundbreaking innovations that leverage our proven technology. Now you can get scalable throughput and flexibility for virtually any sequencing method, genome, and scale of project.
View all literature mentionsSutter P-1000 Next Generation Micropipette Puller (instrument resource)
RRID:SCR_021042
P-1000 include diagnostic testing of all puller components, built in error detection of air pressure loss or filament burnout, easy access to ramp test, measurement of jaw temperature, and access to previous pull results with heat on times for each cycle of program.Help topics are pre-loaded to assist with on-site troubleshooting and built-in glossary includes text, pictures, and diagrams explaining terms used in micropipette fabrication. Rotary dial is offered as alternative to keypad for numerical entry.
View all literature mentionsOlympus BX51WI Fixed Stage Upright Microscope (instrument resource)
RRID:SCR_023069
BX51WI is for all physiological experiments such as patch clamping and intravital microscopy. Fixed stage and vibration free frame design ensures stability throughout experiment. Use of infrared light protects living cells and offers high penetration depths of thick tissue slices, while high NA optics allow magnification changes without moving objective.
View all literature mentionsSony Biotechnology SH800S Cell Sorter (instrument resource)
RRID:SCR_018066
Benchtop cell sorter that sorts wide range of cell sizes for many applications using microfluidic sorting chips. Integrated with comprehensive fluidics controls and advanced automation for set-up, acquisition, sort and analysis. System software supports sorting into tubes and 96- and 384-well plates. Software generates FCS 3.0 and FCS 3.1 files that can be exported to third party analysis tools. For non-clinical research use only. For applications in which cross-contamination is concern, optional e-beam sterilized consumables can be used to replace sample line and sorting chip. Optional class A2 Level II biosafety cabinet provides protection for personnel and products. Biosafety cabinet meets international standards.Optical design offers up to four collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and six fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection.
View all literature mentionsZeiss Axio Imager 2 (instrument resource)
RRID:SCR_018876
Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software.
View all literature mentionsOlympus cellSens Software (software resource)
RRID:SCR_014551
Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.
View all literature mentionsSTAR (software resource)
RRID:SCR_004463
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsscVelo (software resource)
RRID:SCR_018168
Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.
View all literature mentionsVelocyto (software resource)
RRID:SCR_018167
Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R.
View all literature mentionsscater (software resource)
RRID:SCR_015954
Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
View all literature mentionsSeuratWrappers (software resource)
RRID:SCR_022555
Software R package that helps format Seurat objects into objects that can be used for trajectory analysis in other packages such as Monocle
View all literature mentionsMonocle3 (software resource)
RRID:SCR_018685
Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.
View all literature mentionsSeurat (software resource)
RRID:SCR_016341
Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
View all literature mentionsR Project for Statistical Computing (software resource)
RRID:SCR_001905
Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsCell Ranger (software resource)
RRID:SCR_017344
Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.
View all literature mentionsFiji (software resource)
RRID:SCR_002285
Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.
View all literature mentionsGraphPad Prism (software resource)
RRID:SCR_002798
Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsZEISS ZEN Microscopy Software (software resource)
RRID:SCR_013672
User interface software for Carl Zeiss light microscopy imaging systems. ZEN is the universal user interface you will see on every imaging system from ZEISS. After selecting fluorophore, ZEN applies the necessary settings to collect and organize data.
View all literature mentionsB6;129P2-Mapttm2Arbr/J (organism)
RRID:IMSR_JAX:021162
Mus musculus with name B6;129P2-Mapttm2Arbr/J from IMSR.
View all literature mentionsB6;129S-Sox2tm1(cre/ERT2)Hoch/J (organism)
RRID:IMSR_JAX:017593
Mus musculus with name B6;129S-Sox2tm1(cre/ERT2)Hoch/J from IMSR.
View all literature mentionsC;129S4-Ptentm1Hwu/J (organism)
RRID:IMSR_JAX:004597
Mus musculus with name C;129S4-Ptentm1Hwu/J from IMSR.
View all literature mentionsB6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato.-EGFP)Luo/J (organism)
RRID:IMSR_JAX:007676
Mus musculus with name B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato.-EGFP)Luo/J from IMSR.
View all literature mentions
CD1;B6N-MADM-TGtm1(Chr19)Biat; Igs40; MADM-19-TG (organism)
RRID:IMSR_EM:14721
Mus musculus with name CD1;B6N-MADM-TGtm1(Chr19)Biat; Igs40
CD1;B6N-MADM-GTtm1(Chr19)Biat; Igs40; MADM-19-GT (organism)
RRID:IMSR_EM:14720
Mus musculus with name CD1;B6N-MADM-GTtm1(Chr19)Biat; Igs40
STOCK Igs2tm2(ACTB-tdTomato.-EGFP)Luo/J (organism)
RRID:IMSR_JAX:013751
Mus musculus with name STOCK Igs2tm2(ACTB-tdTomato.-EGFP)Luo/J from IMSR.
View all literature mentionsSTOCK Igs2tm1(ACTB-EGFP.-tdTomato)Luo/J (organism)
RRID:IMSR_JAX:013749
Mus musculus with name STOCK Igs2tm1(ACTB-EGFP.-tdTomato)Luo/J from IMSR.
View all literature mentions
