LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification
By onThe genetic mechanisms underlying the expansion in size and complexity of the human brain remain poorly understood. Long interspersed nuclear element–1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. Using multiomics profiling, we here demonstrate that L1 promoters are dynamically active in the developing and the adult human brain. L1s generate hundreds of developmentally regulated and cell type–specific transcripts, many that are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived long noncoding RNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPR interference silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.
Localised axotomy of human Cortical Neurons (CNs) from induced pluripotent stem cells (iPSCs)
By onThis protocol describes the process followed to perform localised axotomy of iPSC-derived human cortical axons cultured within fluid-walled dumbbells in 6 cm TCT-treated Petri dishes.
Fabrication of fluid-walled dumbbells and generation of the human corticostriatal pathway
By onThis protocol described the generation of fluid-walled dumbbells for culturing of induced pluripotent stem cell-derived neurons with directional connectivity so as to recapitulate the human corticostriatal connectivity.
Automatic flow in fluid-walled dumbbells driven by Laplace pressure
By onThis protocol describes experiments performed to quantify pressure and volume variations inside fluid-walled dumbbells when a pressure difference is generated between the two chambers.
A role for the subthalamic nucleus in aversive learning
By onThe subthalamic nucleus (STN) is critical for behavioral control; its dysregulation consequently correlates with neurological disorders, including PD. To investigate STN and aversion, affective behavior is addressed using optogenetics in mice.
State-dependent GABAergic regulation of striatal spiny projection neuron excitability: NEURON + Python model of striatal projection neurons
By onThis repository contains a NEURON + Python model of striatal projection neurons (or SPNs) designed to simulate the interaction between GABAergic and glutamatergic synaptic inputs.
Measuring alpha-synuclein concentration in hiPSCs using ELISA
By onThis protocol uses a classical ELISA experimental design with sensitive electrochemical detection to provide a measure of 𝜶-synuclein concentration in the conditioned media of cultured iPSC-derived human cells.
Preparation of tissue for Ribo-Tag/RNAseq analysis
By onThis protocols describes the RiboTag virus vectors injected into mouse brain, tissue dissection, immunoprecipitation and RNA extraction for RNAseq.
Fura-2 a.m. imaging in hiPSCs for measuring intracellular calcium
By onThis protocol outlines Fura-2 imaging of ionomycin response, with and without R568, a CaSR positive modulator, in hiPSCs.
Immunocytochemistry for CASR in iPSc-derived dopaminergic neurons
By onCASR immunocytochemistry protocol to accompany Kilfeather, Khoo et al., 2023: Single cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, ageing and disease
A549 PIP4P1 (TMEM55B) KO (CVCL_D3VW)
By onA549 PIP4P1 (TMEM55B) CRISPR/CAS9 A549 knock-out cell line generated from parental A549 cells (ATCC A549 CCl-185) using CRISPR/Cas9 gene-editing technology. The cell line was verified by immunoblotting analysis and DNA-sequencing analysis. Used in publication: doi: https://doi.org/10.1101/2023.06.07.544051
mRNA purification by translating ribosome affinity purification (TRAP) of DAT-expressing cells (dopaminergic neurons) in mouse ventral midbrain
By onThis protocol describes the capture of eGFP-L10a-tagged ribosomes and mRNA from DAT-expressing cells (dopaminergic neurons) in mouse ventral midbrain.
Section 1: Enzymatic DNA Fragmentation (Manually)
By onThis protocol details manual enzymatic DNA Fragmentation prior to Section 2: NGS library preparation for sequencing.
Section 2: NGS library preparation for sequencing
By onThis protocol details NGS library preparation for sequencing and should be performed after Section 1: Enzymatic DNA Fragmentation (Manually).
Detection of accessible cholesterol in primary cilia using purified His-ALOD4-mNeon in 3T3 Fibroblasts
By onThe protocol described here is based upon previously established methods (Kinnebrew et al., 2019; Johnson and Radhakrishnan, 2021) and has also been used successfully to label cilia in RPE cells.
Section 3: Libraries quality control (QC)
By onThis protocol details quality control of libraries and should be performed after Section 2: NGS library preparation for sequencing.
Regional Mouse Brain Analysis (Modified QUINT)
By onThis is series of protocols that has been adapted from published and unpublished protocols broadly referred to as the QUINT workflow: QuPath visualization/segmentation QuickNII Brain Atlas Registration QMask Hemispheric Separation Visualign Transformation Nutil Data Integration QUINT Workflow Appendix QUINT Workflow for Fluorescence Note that the original QUINT workflow was generated by Yates and colleagues, and all credit for development of these programs goes to that team. References for each software are listed in the protocol.
Whole mount dissection and staining of enteric nervous system
By onThis protocol details whole mount dissection and staining of the enteric nervous system.
KOLF2.1 iPSCs AAVS1-NGN2
By oniPSCs from British Caucasian male, modified with NEUROG2 using CRISPR/Cas9 in AAVS1 locus. Contains mutations in ARID2 (p.Pro197Hisfs*12) and COL3A1 (p.Gly1176Ser). Derived from skin fibroblasts of a 55-59-year-old male.
Gut mucosal cells transfer α-synuclein to the vagus nerve
By onPublished: These findings highlight a potential non-neuronal source of fibrillar α-synuclein protein that might arise in gut mucosal cells. View original preprint.