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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

In vivo multiomic Perturb-seq with enhanced nuclear gRNA capture.

Xinhe Zheng^1,2, Jiwen Li^1,2, Kwanho Kim³

¹Howard Hughes Medical Institute, Chevy Chase, MD, USA.

Biorxiv : the Preprint Server for Biology

|March 27, 2026

Summary

Researchers developed a new CRISPR screening method for efficient analysis of gene perturbations in the brain. This technique improves the study of neurodevelopmental disorders by analyzing both gene activity and epigenetic changes in single cells.

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Area of Science:

Genomics and Molecular Biology
Neuroscience
Epigenetics

Background:

* In vivo CRISPR screening enables studying gene function in complex biological systems.
* Current methods struggle with efficient recovery of guide RNAs (gRNAs) from cell nuclei for multiomic analysis.
* This limitation hinders high-resolution mapping of transcriptomic and epigenomic changes induced by perturbations.

Purpose of the Study:

* To develop an improved in vivo CRISPR screening platform for high-fidelity, high-recovery gRNA assignment.
* To enable scalable, perturbation-resolved single-nucleus multiomics.
* To investigate cell-type-specific transcriptomic and epigenomic phenotypes of neurodevelopmental disorder risk genes.

Main Methods:

* Developed 'in vivo multiomic Perturb-seq', a novel platform combining nuclear transcript anchoring with gRNA-specific capture and amplification.
* Applied the platform to the developing cortex to study neurodevelopmental disorder risk genes.
* Performed single-nucleus multiomic profiling to capture transcriptomic and epigenomic data.

Main Results:

* Achieved high-fidelity and high-recovery gRNA assignment from nuclei.
* Enabled scalable single-nucleus multiomics with precise perturbation resolution.
* Identified cell-type-specific transcriptomic and epigenomic perturbation phenotypes associated with neurodevelopmental disorder risk genes.

Conclusions:

* The developed platform overcomes previous limitations in in vivo CRISPR screening.
* It facilitates comprehensive analysis of gene perturbations at single-cell resolution in the brain.
* This advancement aids in understanding the molecular mechanisms underlying neurodevelopmental disorders.