Keywords: Pallium, Cortico-Spinal Tract, Neocortex, Corticogenesis, Phgdh, Serine, 

Books to read:

Neocortical Neurogenesis in Development and Evolution

2024

Molecular mechanisms of corpus callosum development: a four-step journey

A critical period of translational control during brain development at codon resolution

Protein translation rate determines neocortical neuron fate

Fate-Restricted Neural Progenitors in the Mammalian Cerebral Cortex

Conserved and divergent gene regulatory programs of the mammalian neocortex

Transcriptomic cytoarchitecture reveals principles of human neocortex organization

mRNA-Decapping Associated DcpS Enzyme Controls Critical Steps of Neuronal Development. 

Making sense of mRNA landscapes: Translation control in neurodevelopment.

A role for the serotonin 2A receptor in the expansion and functioning of human transmodal cortex

Development and Evolution of Thalamocortical Connectivity.

Neocortical neurogenesis in development and evolution-Human-specific features

Development and evolution of the primate neocortex from a progenitor cell perspective

Dynamic subtype- and context-specific subcellular RNA regulation in growth cones of developing neurons of the cerebral cortex

Patterning the cerebral cortex into distinct functional domains during development 

Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors

High-resolution 3D ultrastructural analysis of developing mouse neocortex reveals long slender processes of endothelial cells that enter neural cells

Patterning the cerebral cortex into distinct functional domains during development

Activity-dependent feedback regulation of thalamocortical axon development by Lhx2 in cortical layer 4 neurons

Layer 6b controls brain state via apical dendrites and the higher-order thalamocortical system

Mapping recurrent mosaic copy number variation in human neurons

Developmental Mouse Brain Common Coordinate Framework

Metabotropic signaling within somatostatin interneurons controls transient thalamocortical inputs during development

Cortical somatostatin interneuron subtypes form cell-type-specific circuits

Single-cell delineation of lineage and genetic identity in the mouse brain

Layer 1 neocortex: Gating and integrating multidimensional signals

Functional Implications of the Prosomeric Brain Model. 

Integrated platform for multiscale molecular imaging and phenotyping of the human brain 

SCIENCE; VOL. 384, NO. 6701

Messenger RNA transport on lysosomal vesicles maintains axonal mitochondrial homeostasis and prevents axonal degeneration 

Unsupervised restoration of a complex learned behavior after large-scale neuronal perturbation

The subcommissural organ regulates brain development via secreted peptides

Closed-loop recruitment of striatal interneurons prevents compulsive-like grooming behaviors

Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex

BRN1/2 Function in Neocortical Size Determination and Microcephaly

Pan-cellular organelles and suborganelles-from common functions to cellular diversity?

A global gene regulatory program and its region-specific regulator partition neurons into commissural and ipsilateral projection types

How Do Cortical Excitatory Neurons Terminate Their Migration at the Right Place? Critical Roles of Environmental Elements

Semaphorin 6A–Plexin A2/A4 Interactions with Radial Glia Regulate Migration Termination of Superficial Layer Cortical Neurons

Gene regulatory landscape of cerebral cortex folding

Specific contribution of Reelin expressed by Cajal-Retzius cells or GABAergic interneurons to cortical lamination

Evolution of genetic mechanisms regulating cortical neurogenesis

A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution

Ultrastructural Axon–Myelin UnitAlterations in Multiple Sclerosis Correlatewith Inflammation

Large-scale automatic reconstruction of neuronal processes from electron microscopy images

Massively parallel characterization of regulatory elements in the developing human cortex

Single-cell multi-cohort dissection of the schizophrenia transcriptome

Perivascular neurons instruct 3D vascular lattice formation via neurovascular contact

A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

A Meta-Atlas of the Developing Human Cortex Identifies Modules Driving Cell Subtype Specification

An integrative, multiscale view on neural theories of consciousness

A thalamocortical substrate for integrated information via critical synchronous bursting

Abnormal higher-order network interactions in Parkinson's disease visual hallucinations

The Role of Neurod Genes in Brain Development, Function, and Disease

Tracing related...

Distinct populations of cortical pyramidal neurons mediate drug reward and aversion

Combinatorial quantification of distinct neural projections from retrograde tracing

Diverse and asymmetric patterns of single-neuron projectome in regulating interhemispheric connectivity

Anterograde transneuronal tracing and genetic control with engineered yellow fever vaccine YFV-17D

Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons

Fezf2 expression in layer 5 projection neurons of mature mouse motor cortex

Decomposing cortical activity through neuronal tracing connectome-eigenmodes in marmosets

Somatosensory cortex and central amygdala regulate neuropathic pain-mediated peripheral immune response via vagal projections to the spleen

BAcTrace, a tool for retrograde tracing of neuronal circuits in Drosophila

Optimization of whole-brain rabies virus tracing technology for small cell populations

Pulse labeling and long-term tracing of newborn neurons in the adult subgranular zone

Ventral striatal islands of Calleja neurons control grooming in mice

Single cell tracing of Pomc neurons reveals recruitment of ‘Ghost’ subtypes with atypical identity in a mouse model of obesity

Behavior/Physiology

The cellular coding of temperature in the mammalian cortex

Expression Pattern & Corticogenesis...

[Land mark papers on marker genes & signaling pathways of cortical layers]

Formation of the Mouse Internal Capsule and Cerebral Peduncle: A Pioneering Role for Striatonigral Axons as Revealed in Isl1 Conditional Mutants

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

Tle4 controls both developmental acquisition and early post-natal maturation of corticothalamic projection neuron identity

Evolutionary conservation and cell type specificity of nuclear compartments in the brain

Cellular anatomy of the mouse primary motor cortex

Prox1 expression patterns in the developing and adult murine brain

COUP-TFI regulates the balance of cortical patterning between frontal/motor and sensory areas

Lhx2 specifies regional fate in Emx1 lineage of telencephalic progenitors generating cerebral cortex

Geniculocortical input drives genetic distinctions between primary and higher-order visual areas

Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits

Sema7A and Sema4D Heterodimerization is Essential for Membrane Targeting and Neocortical Wiring 

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain 

DNA methylation atlas of the mouse brain at single-cell resolution 

Cell-cycle control and cortical development

From trans to cis: transcriptional regulatory networks in neocortical development

Novel functions of LHX2 and PAX6 in the developing telencephalon revealed upon combined loss of both genes

Cux2 expression regulated by Lhx2 in the upper layer neurons of the developing cortex

Mechanisms that regulate the number of neurons during mouse neocortical development

Cell-cycle-independent transitions in temporal identity of mammalian neural progenitor cells

Specific contribution of neurons from the Dbx1 lineage to the piriform cortex 

Flow cytometric analysis of neural stem cells in the developing and adult mouse brain

Cell Division Modes and Cleavage Planes of Neural Progenitors during Mammalian Cortical Development

Control of asymmetric cell division of mammalian neural progenitors. 

Rack1 is essential for corticogenesis by preventing p21-dependent senescence in neural stem cells

Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size

Downregulation of ribosome biogenesis during early forebrain development 

Subcellular mRNA localization and local translation of Arhgap11a in radial glial progenitors regulates cortical development

The exon junction complex component EIF4A3 is essential for mouse and human cortical progenitor mitosis and neurogenesis

Founder cells shape brain evolution

WNT protein-independent constitutive nuclear localization of beta-catenin protein and its low degradation rate in thalamic neurons

Zic Deficiency in the Cortical Marginal Zone and Meninges Results in Cortical Lamination Defects Resembling Those in Type II Lissencephaly

LMO4 functions as a co-activator of neurogenin 2 in the developing cortex

Cdk5-mediated phosphorylation of RapGEF2 controls neuronal migration in the developing cerebral cortex

Satb2 Regulates the Differentiation of Both Callosal and Subcerebral Projection Neurons in the Developing Cerebral Cortex

 Patterning and plasticity of the cerebral cortex. 

Area patterning of the Mammalian cortex. 

Cell-Autonomous beta-Catenin Signaling Regulates Cortical Precursor Proliferation. 

 Cortical neurons arise in symmetric and asymmetric division zones and migrate through specific phases 

 Neurons derived from radial glial cells establish radial units in neocortex 

Foxg1 confines Cajal-Retzius neuronogenesis and hippocampal morphogenesis to the dorsomedial pallium 

Fezl is required for the birth and specification of corticospinal motor neurons. 

Fezl regulates the differentiation and axon targeting of layer 5 subcortical projection neurons in cerebral cortex. 

Neuronal production and precursor proliferation defects in the neocortex of mice with loss of function in the canonical Wnt signaling pathway

 Persistent expression of stabilized beta-catenin delays maturation of radial glial cells into intermediate progenitors. 

 Inactivation of the beta-catenin gene by Wnt1-Cre-mediated deletion results in dramatic brain malformation and failure of craniofacial development 

A network of genetic repression and derepression specifies projection fates in the developing neocortex 

Sonic Hedgehog Expression in Corticofugal Projection Neurons Directs Cortical Microcircuit Formation  

The Rho GTPase Rac1 is Required for Proliferation and Survival of Progenitors in the Developing Forebrain 

Laminar and Columnar Development of Barrel Cortex Relies on Thalamocortical Neurotransmission

Single-cell analysis of the postnatal dorsal V-SVZ revealsa role for Bmpr1a signaling in silencing pallial germinalactivity

Vision-dependent specification of cell types and function in the developing cortex

Heterogeneous fates of simultaneously-born neurons in the cortical ventricular zone

Temporal controls over cortical projection neuron fate diversity

Temporal controls over inter-areal cortical projection neuron fate diversity

An Early Cortical Progenitor-Specific Mechanism Regulates Thalamocortical Innervation

Temporal plasticity of apical progenitors in the developing mouse neocortex

A Translaminar Genetic Logic for the Circuit Identity of Intracortically Projecting Neurons

Multiple parallel cell lineages in the developing mammalian cerebral cortex

Centrosomal microtubule nucleation regulates radial migration of projection neurons independently of polarization in the developing brain

Ribosome inactivation regulates translation elongation in neurons

Cell Type-Specific Transcriptional Control of Gsk3β in the Developing Mammalian Neocortex

Cortical progenitor biology: key features mediating proliferation versus differentiation

Changes in Wnt-Dependent Neuronal Morphology Underlie the Anatomical Diversification of Neocortical Homologs in Amniotes

A complex epigenome-splicing crosstalk governs epithelial-to-mesenchymal transition in metastasis and brain development

Plasticity in cell migration modes across development, physiology, and disease

Disruption of NEUROD2 causes a neurodevelopmental syndrome with autistic features via cell-autonomous defects in forebrain glutamatergic neurons

Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex 

Of mice and monkeys: Somatosensory processing in two prominent animal models

LHX2 Interacts with the NuRD Complex and Regulates Cortical Neuron Subtype Determinants Fezf2 and Sox11

Laminar dynamics of deep projection neurons and mode of subplate formation are hallmarks of histogenetic subdivisions of the human cingulate cortex before onset of arealization

Early Regional Patterning in the Human Prefrontal Cortex Revealed by Laminar Dynamics of Deep Projection Neuron Markers

.

Thalamocortical axons regulate neurogenesis and laminar fates in the early sensory cortex

Heterogeneous nuclear ribonucleoprotein U (HNRNPU) safeguards the developing mouse cortex

ERK signaling expands mammalian cortical radial glial cells and extends the neurogenic period 

Non-canonical role for Lpar1-EGFP subplate neurons in early postnatal mouse somatosensory cortex

Maintenance of neural stem cell positional identity by mixed-lineage leukemia 1

Astrocytes & Glia 

Oligodendrocyte precursor cells engulf synapses during circuit remodeling in mice

PAX6 can substitute for LHX2 and override NFIA-induced astrogliogenesis in developing hippocampus in vivo

Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals

 Switching modes in corticogenesis: mechanisms of neuronal subtype transitions and integration in the cerebral cortex 

Asymmetric inheritance of radial glial fibers by cortical neurons

Radial Glial Cells: New Views on Old Questions

Developmental emergence of cortical neurogliaform cell diversity

A human-specific enhancer fine-tunes radial glia potency and corticogenesis

Distributed Motor Control of Limb Movements in Rat Motor and Somatosensory Cortex: The Sensorimotor Amalgam Revisited 

Human & Primate Brain...

PRDM16 co-operates with LHX2 to shape the human brain

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions

Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders

Phylogenetic differences in the morphology and shape of the central sulcus in great apes and humans: implications for the evolution of motor functions 

CSMD1 regulates brain complement activity and circuit development

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. 

Pruning hypothesis comes of age

Radial Glial Cells: New Views on Old Questions

Brain Plasticity in Humans and Model Systems: Advances, Challenges, and Future Directions

Increased number of excitatory synapsis and decreased number of inhibitory synapsis in the prefrontal cortex in autism

Glycine is a transmitter in the human and chimpanzee cochlear nuclei

Hippocampus

Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2

Techniques

HiC

1. Cite-Seq

2. HiC

3. ATAC-Seq

4. SC-RNA

5. Multiome

MERFISH, Spatial 

Rat movements reflect internal decision dynamics in an evidence accumulation task

Tractography gone wild: probabilistic fibre tracking using the wild bootstrap with diffusion tensor MRI.

Jones DK.

IEEE Trans Med Imaging. 2008 Sep;27(9):1268-74. doi: 10.1109/TMI.2008.922191.

PMID: 18779066

Magnetic voluntary head-fixation in transgenic rats enables lifespan imaging of hippocampal neurons

A cross-species framework for investigating perceptual evidence accumulation

Head Mounted multiphoton:- Advances in cellular resolution microscopy for brain imaging in rats

Spatiotemporal, optogenetic control of gene expression in organoids

SLAM‐Drop‐seq reveals mRNA kinetic rates throughout the cell cycle

In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration

Developing a de novo targeted knock-in method based on in utero electroporation into the mammalian brain

In utero gene therapy rescues microcephaly caused by Pqbp1-hypofunction in neural stem progenitor cells

Transcriptional linkage analysis with in vivo AAV-Perturb-seq.

In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag

Cryo-section Dissection of the Adult Subependymal Zone for Accurate and Deep Quantitative Proteome Analysis

Exploring long-range genome interactions using the WashU Epigenome Browser

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

CST

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH 

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Corticospinal Circuits from the Sensory and Motor Cortices Differentially Regulate Skilled Movements through Distinct Spinal Interneurons 

Axonally transported proteins associated with axon growth in rabbit central and peripheral nervous systems 

Human cerebral cortex development from pluripotent stem cells to functional excitatory synapses 

Phenotypic variation of transcriptomic cell types in mouse motor cortex 

Corticospinal neuron subpopulation-specific developmental genes prospectively indicate mature segmentally specific axon projection targeting 

Crim1 and Kelch-like 14 exert complementary dual-directional developmental control over segmentally specific corticospinal axon projection targeting 

Diversity of layer 5 projection neurons in the mouse motor cortex 

Corticospinal populations broadcast complex motor signals to coordinated spinal and striatal circuits 

DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex 

The Corticospinal System: From Development to Motor Control

Long-Distance Growth and Connectivity of Neural Stem Cells after Severe Spinal Cord Injury 

PTEN deletion enhances the regenerative ability of adult corticospinal neurons 

Descending pathways in motor control 

Development of the corticospinal tract in the mouse spinal cord: A quantitative ultrastructural analysis 

Anatomical Diversity of the Adult Corticospinal Tract Revealed by Single-Cell Transcriptional Profiling 

Dissociation of intact adult mouse cortical projection neurons for single-cell RNA-seq 

Postnatal growth of corticospinal axons in the spinal cord of developing mice 

Distinct descending motor cortex pathways and their roles in movement 

Molecular mechanisms of axon guidance in the developing corticospinal tract 

Comparative cellular analysis of motor cortex in human, marmoset and mouse 

Long-distance axon growth ability of corticospinal neurons is lost in a segmentally-distinct manner

Molecular specification of cortico-brainstem versus corticospinal projection neurons in development  

Cbln1 Directs Axon Targeting by Corticospinal Neurons Specifically toward Thoraco-Lumbar Spinal Cord 

Cellular anatomy of the mouse primary motor cortex 

TBR1 directly represses Fezf2 to control the laminar origin and development of the corticospinal tract

Compensatory Actions of Ldb Adaptor Proteins During Corticospinal Motor Neuron Differentiation 

Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. 

The CB(1) cannabinoid receptor drives corticospinal motor neuron differentiation through the Ctip2/Satb2 transcriptional regulation axis. 

Area-specific temporal control of corticospinal motor neuron differentiation by COUP-TFI 

Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo.

Avian Brain Development & Circuit Formation

Thalamic activity-dependent specification of sensory input neurons in the developing chick entopallium

Homology, neocortex, and the evolution of developmental mechanisms.

2024

In vivo imaging in transgenic songbirds reveals super-diffusive neuron migration in the adult brain 

Note: Above study also performed brain tissue grafting and showed integration of these neurons in the host brains.

2009

Transgenic songbirds offer an opportunity to develop a genetic model for vocal learning

by Benajmin B Scott group at Boston University. In the above study they used a systemically expressing GFP transgenic song bird (this bird was made in 2009 in F. Nottebauhm Lab.) and then performed diI tracing and did simulation migration of neurons in the HVC region responsible for song in Zebra Finch.

Neural Crest Cells

Neural crest origin of sympathetic neurons at the dawn of vertebrates