{"doi":"10.1101/2022.11.09.515199","title":"Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight","abstract":"Abstract The Advanced Plant Experiment-04 - Epigenetic Expression (APEX04-EpEx) experiment onboard the International Space Station examined the spaceflight-altered cytosine methylation in two genetic lines of Arabidopsis thaliana , wild-type Col-0 and the mutant elp2-5, which is deficient in an epigenetic regulator Elongator Complex Subunit 2 (ELP2). Whole-genome bisulfite sequencing (WGBS) revealed distinct spaceflight associated methylation differences, presenting the need to examine specific space- altered methylation at single molecule resolution to associate specific changes over large regions of spaceflight related genes. Therefore flap-enabled next-generation capture (FENGC), a novel targeted multiplexed DNA capture and enrichment technique allowing cleavage at any specified sites, was applied to survey spaceflight-altered DNA methylation at the single-molecule level. The FENGC capture panel contained 108 targets ranging from 509 to 704 nt within the promoter or gene body regions of gene targets derived from spaceflight whole-genome data sets. In addition to genes with significant changes in expression and average methylation levels between spaceflight and ground control, targets without differentially methylated WGBS but with space- altered distributions of the proportion of methylated cytosines per molecule were further identified. Moreover, trends of co-methylation of different cytosine contexts were exhibited in the same DNA molecules. We further identified significant DNA methylation changes in three previously biological process-unknown genes, and two of them showed enhanced root growth rate in loss-of-function mutants (named as ELP2- regulated Methylation in Orbit 1 and 2 ). FENGC makes multiplexed targeted single- molecule profiling of methylation simple and cost-effective, which provides an additional power to population-based data for methylation analysis and identification of epigenetically modified substrates in plants. This case study has revealed regional spaceflight-altered methylation in selected targets, which were not identified by short- read methods in spaceflight plants. The newly identified EMO1 and EMO2 are root growth regulators, which can be epigenetically involved in plant adaptation to spaceflight.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":313024,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9522,"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":77359,"name":"Alberto Riva","orcid":"0000-0001-9150-8333","position":1,"is_corresponding":false},{"id":258271,"name":"Marie‐Pierre L. Gauthier","orcid":"0009-0002-1936-2231","position":2,"is_corresponding":false},{"id":447551,"name":"Michael P. Kladde","orcid":"0000-0001-7951-9291","position":3,"is_corresponding":false},{"id":1010854,"name":"Robert J. Ferl","orcid":"0000-0003-4178-764X","position":4,"is_corresponding":false},{"id":1010855,"name":"Anna‐Lisa Paul","orcid":"0000-0003-2211-2604","position":5,"is_corresponding":false},{"id":989495,"name":"Mingqi Zhou","orcid":"0000-0002-4605-5467","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:33:40.460845Z","pmid":null,"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":[]}