ArticleeLife2022
Machine learning sequence prioritization for cell type-specific enhancer design.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
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- Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.Nature communications · 2025Article
- Combining Machine Learning and Multiplexed,bioRxiv : the preprint server for biology · 2025Article
- Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.bioRxiv : the preprint server for biology · 2025Article
- AnFrontiers in genetics · 2025Article
- Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition.Cell reports · 2024Article
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- Spatial, transcriptomic and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition.bioRxiv : the preprint server for biology · 2024Article
- MultipleXed Population Selection and Enrichment single nucleus RNA sequencing (XPoSE-seq) enables sample identity retention during transcriptional profiling of rare populations.bioRxiv : the preprint server for biology · 2023Article
- Machine-guided design of synthetic cell type-specificbioRxiv : the preprint server for biology · 2023Article
- The nature and neurobiology of fear and anxiety: State of the science and opportunities for accelerating discovery.Neuroscience and biobehavioral reviews · 2023Review
- OnTarget: in silico design of MiniPromoters for targeted delivery of expression.Nucleic acids research · 2023Article
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- Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system.Current research in neurobiology · 2023Review
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Corrections and comments
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Authors and funding
18 authors at 2 institutions in 2 countries.
Funding
Abstract
Recent discoveries of extreme cellular diversity in the brain warrant rapid development of technologies to access specific cell populations within heterogeneous tissue. Available approaches for engineering-targeted technologies for new neuron subtypes are low yield, involving intensive transgenic strain or virus screening. Here, we present Specific Nuclear-Anchored Independent Labeling (SNAIL), an improved virus-based strategy for cell labeling and nuclear isolation from heterogeneous tissue. SNAIL works by leveraging machine learning and other computational approaches to identify DNA sequence features that confer cell type-specific gene activation and then make a probe that drives an affinity purification-compatible reporter gene. As a proof of concept, we designed and validated two novel SNAIL probes that target parvalbumin-expressing (PV+) neurons. Nuclear isolation using SNAIL in wild-type mice is sufficient to capture characteristic open chromatin features of PV+ neurons in the cortex, striatum, and external globus pallidus. The SNAIL framework also has high utility for multispecies cell probe engineering; expression from a mouse PV+ SNAIL enhancer sequence was enriched in PV+ neurons of the macaque cortex. Expansion of this technology has broad applications in cell type-specific observation, manipulation, and therapeutics across species and disease models.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.