{"doi":"10.1093/plphys/kiad652","title":"Genetic dissection of <i>cis</i>-regulatory control of <i>ZmWUSCHEL1</i> expression by type B RESPONSE REGULATORS","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Mutations in cis-regulatory regions play an important role in the domestication and improvement of crops by altering gene expression. However, assessing the in vivo impact of cis-regulatory elements (CREs) on transcriptional regulation and phenotypic outcomes remains challenging. Previously, we showed that the dominant Barren inflorescence3 (Bif3) mutant of maize (Zea mays) contains a duplicated copy of the homeobox transcription factor gene ZmWUSCHEL1 (ZmWUS1), named ZmWUS1-B. ZmWUS1-B is controlled by a spontaneously generated novel promoter region that dramatically increases its expression and alters patterning and development of young ears. Overexpression of ZmWUS1-B is caused by a unique enhancer region containing multimerized binding sites for type B RESPONSE REGULATORs (RRs), key transcription factors in cytokinin signaling. To better understand how the enhancer increases the expression of ZmWUS1 in vivo, we specifically targeted the ZmWUS1-B enhancer region by CRISPR-Cas9-mediated editing. A series of deletion events with different numbers of type B RR DNA binding motifs (AGATAT) enabled us to determine how the number of AGATAT motifs impacts in vivo expression of ZmWUS1-B and consequently ear development. In combination with dual-luciferase assays in maize protoplasts, our analysis reveals that AGATAT motifs have an additive effect on ZmWUS1-B expression, while the distance separating AGATAT motifs does not appear to have a meaningful impact, indicating that the enhancer activity derives from the sum of individual CREs. These results also suggest that in maize inflorescence development, there is a threshold of buffering capacity for ZmWUS1 overexpression.</jats:p>","journal":"Plant Physiology","year":2024,"id":640012,"datarank":0.37273599746820013,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.0,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":11,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1663232,"name":"Liz Cortes","orcid":"0000-0002-2881-9216","position":1,"is_corresponding":false},{"id":906864,"name":"Andrea Gallavotti","orcid":"0000-0002-1901-2971","position":2,"is_corresponding":false},{"id":1368281,"name":"Zongliang Chen","orcid":"0000-0003-1469-3699","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Genetic dissection of <i>cis</i>-regulatory control of <i>ZmWUSCHEL1</i> expression by type B RESPONSE REGULATORS","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Mutations in cis-regulatory regions play an important role in the domestication and improvement of crops by altering gene expression. However, assessing the in vivo impact of cis-regulatory elements (CREs) on transcriptional regulation and phenotypic outcomes remains challenging. Previously, we showed that the dominant Barren inflorescence3 (Bif3) mutant of maize (Zea mays) contains a duplicated copy of the homeobox transcription factor gene ZmWUSCHEL1 (ZmWUS1), named ZmWUS1-B. ZmWUS1-B is controlled by a spontaneously generated novel promoter region that dramatically increases its expression and alters patterning and development of young ears. Overexpression of ZmWUS1-B is caused by a unique enhancer region containing multimerized binding sites for type B RESPONSE REGULATORs (RRs), key transcription factors in cytokinin signaling. To better understand how the enhancer increases the expression of ZmWUS1 in vivo, we specifically targeted the ZmWUS1-B enhancer region by CRISPR-Cas9-mediated editing. A series of deletion events with different numbers of type B RR DNA binding motifs (AGATAT) enabled us to determine how the number of AGATAT motifs impacts in vivo expression of ZmWUS1-B and consequently ear development. In combination with dual-luciferase assays in maize protoplasts, our analysis reveals that AGATAT motifs have an additive effect on ZmWUS1-B expression, while the distance separating AGATAT motifs does not appear to have a meaningful impact, indicating that the enhancer activity derives from the sum of individual CREs. These results also suggest that in maize inflorescence development, there is a threshold of buffering capacity for ZmWUS1 overexpression.</jats:p>","is_dataset_classified":null,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"38060616","pmcid":"PMC10980522","openalex_id":"https://openalex.org/W4389426703","authors":[],"funders":[{"funder_name":"National Science Foundation","grant_id":"IOS#2026561","title":null},{"funder_name":"National Science Foundation","grant_id":"IOS#1916804","title":null},{"funder_name":"National Science Foundation","grant_id":"1916804","title":"TRTech-PGR:  MAPPING AND FUNCTIONAL CHARACTERIZATION OF CIS-REGULATORY MODULE VARIATION IN PLANTS"},{"funder_name":"National Science Foundation","grant_id":"2026561","title":"Collaborative Research: Mechanisms and Manipulation of Maize Meristem Size"},{"funder_name":"Rutgers University","grant_id":"","title":null}],"total_grants":5,"fwci":3.1463,"citation_percentile":0.91307704,"influential_citations":0,"citation_trend":[{"year":2024,"count":5},{"year":2025,"count":4},{"year":2026,"count":2}],"oa_status":"hybrid","license":"cc-by-nc-nd","oa_locations":[{"url":"https://academic.oup.com/plphys/advance-article-pdf/doi/10.1093/plphys/kiad652/54092460/kiad652.pdf","host_type":"journal"},{"url":"https://academic.oup.com/plphys/advance-article-pdf/doi/10.1093/plphys/kiad652/54092460/kiad652.pdf","host_type":"publisher"},{"url":"https://academic.oup.com/plphys/advance-article-pdf/doi/10.1093/plphys/kiad652/54641925/kiad652.pdf","host_type":"publisher"},{"url":"https://academic.oup.com/plphys/article-pdf/194/4/2240/57121569/kiad652.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/plphys/kiad652","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/38060616","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10980522","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC10980522","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC10980522?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/plphys/kiad652","host_type":""}],"fields_of_study":["Plant Molecular Biology Research","Chromosomal and Genetic Variations","Plant Virus Research Studies","0301 basic medicine","03 medical and health sciences"],"mesh_terms":["Binding Sites","DNA-Binding Proteins","Enhancer Elements, Genetic","Regulatory Sequences, Nucleic Acid","Transcription Factors"],"keywords":["Enhancer","Biology","Transcription factor","Genetics","Regulatory sequence","Gene","Gene expression","Homeobox","Regulation of gene expression","Mutant","Cell biology","Research Report","DNA-Binding Proteins","Binding Sites","Enhancer Elements, Genetic","Regulatory Sequences, Nucleic Acid","Transcription Factors"],"sdg_mappings":[{"sdg_number":2,"sdg_label":"2. 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