{"doi":"10.1016/j.jbc.2022.101674","title":"Identification of cis-regulatory modules for adeno-associated virus-based cell-type-specific targeting in the retina and brain","abstract":"Adeno-associated viruses (AAVs) targeting specific cell types are powerful tools for studying distinct cell types in the central nervous system (CNS). Cis-regulatory modules (CRMs), e.g., enhancers, are highly cell-type-specific and can be integrated into AAVs to render cell type specificity. Chromatin accessibility has been commonly used to nominate CRMs, which have then been incorporated into AAVs and tested for cell type specificity in the CNS. However, chromatin accessibility data alone cannot accurately annotate active CRMs, as many chromatin-accessible CRMs are not active and fail to drive gene expression in vivo. Using available large-scale datasets on chromatin accessibility, such as those published by the ENCODE project, here we explored strategies to increase efficiency in identifying active CRMs for AAV-based cell-type-specific labeling and manipulation. We found that prescreening of chromatin-accessible putative CRMs based on the density of cell-type-specific transcription factor binding sites (TFBSs) can significantly increase efficiency in identifying active CRMs. In addition, generation of synthetic CRMs by stitching chromatin-accessible regions flanking cell-type-specific genes can render cell type specificity in many cases. Using these straightforward strategies, we generated AAVs that can target the extensively studied interneuron and glial cell types in the retina and brain. Both strategies utilize available genomic datasets and can be employed to generate AAVs targeting specific cell types in CNS without conducting comprehensive screening and sequencing experiments, making a step forward in cell-type-specific research. Adeno-associated viruses (AAVs) targeting specific cell types are powerful tools for studying distinct cell types in the central nervous system (CNS). Cis-regulatory modules (CRMs), e.g., enhancers, are highly cell-type-specific and can be integrated into AAVs to render cell type specificity. Chromatin accessibility has been commonly used to nominate CRMs, which have then been incorporated into AAVs and tested for cell type specificity in the CNS. However, chromatin accessibility data alone cannot accurately annotate active CRMs, as many chromatin-accessible CRMs are not active and fail to drive gene expression in vivo. Using available large-scale datasets on chromatin accessibility, such as those published by the ENCODE project, here we explored strategies to increase efficiency in identifying active CRMs for AAV-based cell-type-specific labeling and manipulation. We found that prescreening of chromatin-accessible putative CRMs based on the density of cell-type-specific transcription factor binding sites (TFBSs) can significantly increase efficiency in identifying active CRMs. In addition, generation of synthetic CRMs by stitching chromatin-accessible regions flanking cell-type-specific genes can render cell type specificity in many cases. Using these straightforward strategies, we generated AAVs that can target the extensively studied interneuron and glial cell types in the retina and brain. Both strategies utilize available genomic datasets and can be employed to generate AAVs targeting specific cell types in CNS without conducting comprehensive screening and sequencing experiments, making a step forward in cell-type-specific research. Molecular tools that allow for cell-type-specific labeling and manipulation in the central nervous system (CNS) are important for understanding how this complex tissue works and responds to disease. Adeno-associated viruses (AAVs), which can provide safe and long-lasting expression, offer a powerful way to target CNS cells in a rapid, cost-effective, and efficient manner (1Samulski R.J. Muzyczka N. AAV-mediated gene therapy for research and therapeutic purposes.Annu. Rev. Virol. 2014; 1: 427-451Crossref PubMed Scopus (248) Google Scholar, 2Bennett J. Wellman J. Marshall K.A. McCague S. Ashtari M. DiStefano-Pappas J. Elci O.U. Chung D.C. Sun J. Wright J.F. Cr","journal":"Journal of Biological Chemistry","year":2022,"id":280601,"datarank":0.3453877639491069,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.0,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9529,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":819145,"name":"Yue Sun","orcid":"0000-0002-5681-130X","position":1,"is_corresponding":false},{"id":464213,"name":"Candace S. Y. Chan","orcid":"0000-0001-9667-7996","position":2,"is_corresponding":false},{"id":464859,"name":"Man-Ru Wu","orcid":null,"position":3,"is_corresponding":false},{"id":844083,"name":"Lei Gu","orcid":"0000-0001-5119-3517","position":4,"is_corresponding":false},{"id":464215,"name":"Alexander E. Davis","orcid":"0000-0002-6897-0965","position":5,"is_corresponding":false},{"id":955085,"name":"Baokun Gu","orcid":"0009-0003-8672-9395","position":6,"is_corresponding":false},{"id":955500,"name":"Wenlin Zhang","orcid":null,"position":7,"is_corresponding":false},{"id":95978,"name":"Bogdan Tanasă","orcid":"0000-0002-3797-8171","position":8,"is_corresponding":false},{"id":955086,"name":"Lei Zhong","orcid":"0000-0002-5035-7919","position":9,"is_corresponding":false},{"id":411995,"name":"Mark M. Emerson","orcid":"0000-0002-1914-5782","position":10,"is_corresponding":false},{"id":479645,"name":"Lu Chen","orcid":"0000-0002-8097-2699","position":11,"is_corresponding":false},{"id":248055,"name":"Jun Ding","orcid":"0000-0003-0690-1312","position":12,"is_corresponding":false},{"id":395781,"name":"Sui Wang","orcid":"0000-0003-1563-9117","position":13,"is_corresponding":false},{"id":464217,"name":"Cheng‐Hui Lin","orcid":"0000-0002-1479-9533","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:29:03.247347Z","pmid":"35148987","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}