{"doi":"10.1101/2024.01.05.574340","title":"Investigating the <i>cis-</i> Regulatory Basis of C <sub>3</sub> and C <sub>4</sub> Photosynthesis in Grasses at Single-Cell Resolution","abstract":"Abstract While considerable knowledge exists about the enzymes pivotal for C 4 photosynthesis, much less is known about the cis- regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C 4 enzymes for five different grass species. This study spans four C 4 species, covering three distinct photosynthetic subtypes: Zea mays and Sorghum bicolor (NADP-ME), Panicum miliaceum (NAD-ME), Urochloa fusca (PEPCK), along with the C 3 outgroup Oryza sativa . We studied the cis- regulatory landscape of enzymes essential across all C 4 species and those unique to C 4 subtypes, measuring cell-type-specific biases for C 4 enzymes using chromatin accessibility data. Integrating these data with phylogenetics revealed diverse co-option of gene family members between species, showcasing the various paths of C 4 evolution. Besides promoter proximal ACRs, we found that, on average, C 4 genes have two to three distal cell-type-specific ACRs, highlighting the complexity and divergent nature of C 4 evolution. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution of cis -regulation at these C 4 loci. This study illuminates the dynamic and complex nature of CRE evolution in C 4 photosynthesis, particularly highlighting the intricate cis- regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C 3 crop performance under changing climatic conditions.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":484989,"datarank":0.29188652235829704,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.0,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9468,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1212277,"name":"Xiaoyu Tu","orcid":"0000-0002-0082-8989","position":1,"is_corresponding":false},{"id":1212855,"name":"Daiquan Jiang","orcid":null,"position":2,"is_corresponding":false},{"id":1064763,"name":"Haidong Yan","orcid":"0000-0002-9903-2672","position":3,"is_corresponding":false},{"id":699191,"name":"Xuan Zhang","orcid":"0000-0002-6635-371X","position":4,"is_corresponding":false},{"id":351488,"name":"Alexandre P. Marand","orcid":"0000-0001-9100-8320","position":5,"is_corresponding":false},{"id":497214,"name":"Silin Zhong","orcid":"0000-0002-0198-7383","position":6,"is_corresponding":false},{"id":258660,"name":"Robert J. Schmitz","orcid":"0000-0001-7538-6663","position":7,"is_corresponding":false},{"id":911067,"name":"John Pablo Mendieta","orcid":"0000-0002-7858-7302","position":0,"is_corresponding":true}],"reference_count":85,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:07:47.633574Z","pmid":"38405933","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":[]}