{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T02:51:55Z","timestamp":1792291915262,"version":"4.4.0"},"reference-count":111,"publisher":"Elsevier BV","issue":"12","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T00:00:00Z","timestamp":1758672000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012436","name":"Chinese Academy of Sciences Qingdao Institute of BioEnergy and Bioprocess Technology","doi-asserted-by":"publisher","award":["I201908"],"award-info":[{"award-number":["I201908"]}],"id":[{"id":"10.13039\/501100012436","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012436","name":"Chinese Academy of Sciences Qingdao Institute of BioEnergy and Bioprocess Technology","doi-asserted-by":"publisher","award":["ZDRW-ZS-2016-3"],"award-info":[{"award-number":["ZDRW-ZS-2016-3"]}],"id":[{"id":"10.13039\/501100012436","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012436","name":"Chinese Academy of Sciences Qingdao Institute of BioEnergy and Bioprocess Technology","doi-asserted-by":"publisher","award":["KSZD-EW-Z-017"],"award-info":[{"award-number":["KSZD-EW-Z-017"]}],"id":[{"id":"10.13039\/501100012436","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"publisher","award":["ZR2022QC020"],"award-info":[{"award-number":["ZR2022QC020"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFA0909700"],"award-info":[{"award-number":["2021YFA0909700"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370097"],"award-info":[{"award-number":["32370097"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31900071"],"award-info":[{"award-number":["31900071"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31741005"],"award-info":[{"award-number":["31741005"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200448"],"award-info":[{"award-number":["32200448"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People&apos;s Republic of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Plant Communications"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1016\/j.xplc.2025.101534","type":"journal-article","created":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T19:47:57Z","timestamp":1758829677000},"page":"101534","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"title":["Multi-dimensional epigenomic dynamics converge on H3K4-mediated regulation of low-CO2 adaptation in Nannochloropsis oceanica"],"prefix":"10.1016","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2459-8724","authenticated-orcid":false,"given":"Yanhai","family":"Gong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qintao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianhong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nana","family":"Lv","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuefeng","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Xin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luyang","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0548-8477","authenticated-orcid":false,"given":"Jian","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xplc.2025.101534_bib1","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.jphotobiol.2011.08.004","article-title":"The role of the PsbU subunit in the light sensitivity of PSII in the cyanobacterium Synechococcus 7942","volume":"105","author":"Abasova","year":"2011","journal-title":"J. Photochem. Photobiol., B"},{"key":"10.1016\/j.xplc.2025.101534_bib99","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1038\/nbt.3865","article-title":"Lipid production in Nannochloropsis gaditana is doubled by decreasing expression of a single transcriptional regulator","volume":"35","author":"Ajjawi","year":"2017","journal-title":"Nat. Biotechnol"},{"key":"10.1016\/j.xplc.2025.101534_bib2","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/s13059-015-0767-1","article-title":"HiCPlotter integrates genomic data with interaction matrices","volume":"16","author":"Akdemir","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib3","doi-asserted-by":"crossref","first-page":"2687","DOI":"10.1038\/s41467-023-38183-4","article-title":"Widening the landscape of transcriptional regulation of green algal photoprotection","volume":"14","author":"Arend","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xplc.2025.101534_bib4","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1101\/gr.160374.113","article-title":"Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Res."},{"key":"10.1016\/j.xplc.2025.101534_bib5","doi-asserted-by":"crossref","DOI":"10.1016\/j.algal.2020.101999","article-title":"Epigenetic mechanisms leading to genetic flexibility during abiotic stress responses in microalgae: A review","volume":"50","author":"Bacova","year":"2020","journal-title":"Algal Res."},{"key":"10.1016\/j.xplc.2025.101534_bib6","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/j.tplants.2010.03.006","article-title":"Photorespiration: players, partners and origin","volume":"15","author":"Bauwe","year":"2010","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.xplc.2025.101534_bib7","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.ymeth.2012.05.001","article-title":"Hi-C: a comprehensive technique to capture the conformation of genomes","volume":"58","author":"Belton","year":"2012","journal-title":"Methods"},{"key":"10.1016\/j.xplc.2025.101534_bib8","article-title":"Role of chromatin architecture in plant stress responses: An update","volume":"11","author":"Bhadouriya","year":"2020","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.xplc.2025.101534_bib108","doi-asserted-by":"crossref","first-page":"11459","DOI":"10.1073\/pnas.2002068117","article-title":"Histone H3K9 methylation promotes formation of genome compartments in Caenorhabditis elegans via chromosome compaction and perinuclear anchoring","volume":"117","author":"Bian","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xplc.2025.101534_bib9","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13059-020-02216-8","article-title":"Histone modifications during the life cycle of the brown alga Ectocarpus","volume":"22","author":"Bourdareau","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib10","doi-asserted-by":"crossref","first-page":"1860","DOI":"10.1105\/tpc.111.093435","article-title":"Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii","volume":"24","author":"Brueggeman","year":"2012","journal-title":"Plant Cell"},{"key":"10.1016\/j.xplc.2025.101534_bib11","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41586-022-04662-9","article-title":"Alternative photosynthesis pathways drive the algal CO2-concentrating mechanism","volume":"605","author":"Burlacot","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.xplc.2025.101534_bib12","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1016\/j.tplants.2023.03.018","article-title":"Energy crosstalk between photosynthesis and the algal CO2-concentrating mechanisms","volume":"28","author":"Burlacot","year":"2023","journal-title":"Trends Plant Sci."},{"key":"10.1016\/j.xplc.2025.101534_bib101","doi-asserted-by":"crossref","first-page":"6486","DOI":"10.1073\/pnas.0711310105","article-title":"The MUT9p kinase phosphorylates histone H3 threonine 3 and is necessary for heritable epigenetic silencing in Chlamydomonas","volume":"105","author":"Casas-Mollano","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xplc.2025.101534_bib13","first-page":"e114","article-title":"DMRcaller: a versatile R\/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts","volume":"46","author":"Catoni","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xplc.2025.101534_bib111","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1016\/j.molp.2017.05.001","article-title":"Genome-wide nucleosome occupancy and organization modulates the plasticity of gene transcriptional status in maize","volume":"10","author":"Chen","year":"2017","journal-title":"Mol. Plant"},{"key":"10.1016\/j.xplc.2025.101534_bib14","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1101\/gr.142067.112","article-title":"DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing","volume":"23","author":"Chen","year":"2013","journal-title":"Genome Res."},{"key":"10.1016\/j.xplc.2025.101534_bib15","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/cr.2012.15","article-title":"Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization","volume":"22","author":"Chepelev","year":"2012","journal-title":"Cell Res."},{"key":"10.1016\/j.xplc.2025.101534_bib16","doi-asserted-by":"crossref","first-page":"6049","DOI":"10.1038\/s41467-021-26325-5","article-title":"Augmented CO2 tolerance by expressing a single H+-pump enables microalgal valorization of industrial flue gas","volume":"12","author":"Choi","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xplc.2025.101534_bib17","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1016\/j.molp.2017.09.007","article-title":"H2A.Z represses gene expression by modulating promoter nucleosome structure and enhancer histone modifications in Arabidopsis","volume":"10","author":"Dai","year":"2017","journal-title":"Mol. Plant"},{"key":"10.1016\/j.xplc.2025.101534_bib18","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xplc.2025.101534_bib19","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1126\/science.1185198","article-title":"The growing human footprint on coastal and open-ocean biogeochemistry","volume":"328","author":"Doney","year":"2010","journal-title":"Science"},{"key":"10.1016\/j.xplc.2025.101534_bib20","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst."},{"key":"10.1016\/j.xplc.2025.101534_bib21","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1038\/nprot.2017.124","article-title":"Chromatin-state discovery and genome annotation with ChromHMM","volume":"12","author":"Ernst","year":"2017","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xplc.2025.101534_bib22","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1111\/nph.16125","article-title":"Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants","volume":"225","author":"Fan","year":"2020","journal-title":"New Phytol."},{"key":"10.1016\/j.xplc.2025.101534_bib23","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1105\/tpc.112.097949","article-title":"Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5\/CCM1","volume":"24","author":"Fang","year":"2012","journal-title":"Plant Cell"},{"key":"10.1016\/j.xplc.2025.101534_bib24","doi-asserted-by":"crossref","first-page":"8689","DOI":"10.1073\/pnas.1002720107","article-title":"Conservation and divergence of methylation patterning in plants and animals","volume":"107","author":"Feng","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xplc.2025.101534_bib25","doi-asserted-by":"crossref","first-page":"241","DOI":"10.3390\/plants12020241","article-title":"DNA methylation in algae and its impact on abiotic stress responses","volume":"12","author":"Ferrari","year":"2023","journal-title":"Plants"},{"key":"10.1016\/j.xplc.2025.101534_bib26","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/j.cell.2015.04.010","article-title":"N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas","volume":"161","author":"Fu","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.xplc.2025.101534_bib27","doi-asserted-by":"crossref","DOI":"10.1038\/srep38228","article-title":"MicroRNAs modulate adaption to multiple abiotic stresses in Chlamydomonas reinhardtii","volume":"6","author":"Gao","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.xplc.2025.101534_bib28","doi-asserted-by":"crossref","first-page":"4537","DOI":"10.1073\/pnas.1700139114","article-title":"The carbonic anhydrase CAH1 is an essential component of the carbon-concentrating mechanism in Nannochloropsis oceanica","volume":"114","author":"Gee","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xplc.2025.101534_bib29","doi-asserted-by":"crossref","first-page":"2828","DOI":"10.1038\/s41467-019-10773-1","article-title":"The repressive role of Arabidopsis H2A.Z in transcriptional regulation depends on AtBMI1 activity","volume":"10","author":"G\u00f3mez-Zambrano","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xplc.2025.101534_bib30","doi-asserted-by":"crossref","first-page":"1736","DOI":"10.1111\/tpj.15025","article-title":"The NanDeSyn database for Nannochloropsis systems and synthetic biology","volume":"104","author":"Gong","year":"2020","journal-title":"Plant J."},{"key":"10.1016\/j.xplc.2025.101534_bib31","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xplc.2025.101534_bib32","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41586-020-2151-x","article-title":"Landscape of cohesin-mediated chromatin loops in the human genome","volume":"583","author":"Grubert","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.xplc.2025.101534_bib33","doi-asserted-by":"crossref","first-page":"18557","DOI":"10.1073\/pnas.1010478107","article-title":"SET DOMAIN GROUP2 is the major histone H3 lysine 4 trimethyltransferase in Arabidopsis","volume":"107","author":"Guo","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xplc.2025.101534_bib34","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.cbpa.2016.09.014","article-title":"Photorespiration and the potential to improve photosynthesis","volume":"35","author":"Hagemann","year":"2016","journal-title":"Curr. Opin. Chem. Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib35","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.ceb.2022.01.003","article-title":"Molecular architecture of enhancer\u2013promoter interaction","volume":"74","author":"Hamamoto","year":"2022","journal-title":"Curr. Opin. Cell Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib36","doi-asserted-by":"crossref","first-page":"14288","DOI":"10.1073\/pnas.0606291103","article-title":"Global temperature change","volume":"103","author":"Hansen","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xplc.2025.101534_bib37","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1016\/j.tibs.2020.05.001","article-title":"Chaperone machineries of Rubisco - The most abundant enzyme","volume":"45","author":"Hayer-Hartl","year":"2020","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.xplc.2025.101534_bib106","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1038\/cr.2011.23","article-title":"Regulation and function of DNA methylation in plants and animals","volume":"21","author":"He","year":"2011","journal-title":"Cell Res"},{"key":"10.1016\/j.xplc.2025.101534_bib107","doi-asserted-by":"crossref","first-page":"104699","DOI":"10.1016\/j.envexpbot.2021.104699","article-title":"H3K4me2, H4K5ac and DNA methylation function in short- and long-term heat stress responses through affecting the expression of the stress-related genes in G. hirsutum","volume":"194","author":"He","year":"2022","journal-title":"Environ. Exp. Bot"},{"key":"10.1016\/j.xplc.2025.101534_bib92","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1104\/pp.113.216721","article-title":"A common histone modification code on C4 genes in maize and its conservation in sorghum and Setaria italica","volume":"162","author":"Heimann","year":"2013","journal-title":"Plant Physiol"},{"key":"10.1016\/j.xplc.2025.101534_bib38","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.xplc.2025.101534_bib39","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1038\/nclimate2683","article-title":"Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression","volume":"5","author":"Hennon","year":"2015","journal-title":"Nat. Clim. Change"},{"key":"10.1016\/j.xplc.2025.101534_bib96","doi-asserted-by":"crossref","first-page":"4745","DOI":"10.1128\/MCB.01181-13","article-title":"The MLL3\/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers","volume":"33","author":"Hu","year":"2013","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib40","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1186\/s13068-017-0868-z","article-title":"Transcriptome and key genes expression related to carbon fixation pathways in Chlorella PY-ZU1 cells and their growth under high concentrations of CO2","volume":"10","author":"Huang","year":"2017","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/j.xplc.2025.101534_bib109","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1111\/nph.17062","article-title":"Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana","volume":"229","author":"Jabre","year":"2021","journal-title":"New Phytol"},{"key":"10.1016\/j.xplc.2025.101534_bib41","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1186\/s13068-015-0386-9","article-title":"Effects of overexpression of a bHLH transcription factor on biomass and lipid production in Nannochloropsis salina","volume":"8","author":"Kang","year":"2015","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/j.xplc.2025.101534_bib42","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/s13068-023-02358-4","article-title":"Transcriptional insights into Chlorella sp. ABC-001: a comparative study of carbon fixation and lipid synthesis under different CO2 conditions","volume":"16","author":"Koh","year":"2023","journal-title":"Biotechnol. Biofuels Bioprod."},{"key":"10.1016\/j.xplc.2025.101534_bib105","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13068-019-1462-3","article-title":"Heterologous synthesis of chlorophyll b in Nannochloropsis salina enhances growth and lipid production by increasing photosynthetic efficiency","volume":"12","author":"Koh","year":"2019","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/j.xplc.2025.101534_bib102","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2007.02.005","article-title":"Chromatin modifications and their function","volume":"128","author":"Kouzarides","year":"2007","journal-title":"Cell"},{"key":"10.1016\/j.xplc.2025.101534_bib43","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","article-title":"Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications","volume":"27","author":"Krueger","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xplc.2025.101534_bib44","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1101\/gr.136184.111","article-title":"ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia","volume":"22","author":"Landt","year":"2012","journal-title":"Genome Res."},{"key":"10.1016\/j.xplc.2025.101534_bib45","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xplc.2025.101534_bib46","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xplc.2025.101534_bib47","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1104\/pp.15.01827","article-title":"Two bHLH transcription factors, bHLH34 and bHLH104, regulate iron homeostasis in Arabidopsis thaliana","volume":"170","author":"Li","year":"2016","journal-title":"Plant Physiol."},{"key":"10.1016\/j.xplc.2025.101534_bib48","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xplc.2025.101534_bib49","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"10.1016\/j.xplc.2025.101534_bib97","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1101\/gr.115519.110","article-title":"Broad chromosomal domains of histone modification patterns in C. elegans","volume":"21","author":"Liu","year":"2011","journal-title":"Genome Res"},{"key":"10.1016\/j.xplc.2025.101534_bib50","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1007\/s00248-023-02322-7","article-title":"Epigenetic regulation in response to CO2 fluctuation in marine microalga Nannochloropsis oceanica","volume":"87","author":"Liu","year":"2023","journal-title":"Microb. Ecol."},{"key":"10.1016\/j.xplc.2025.101534_bib51","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1111\/nph.14596","article-title":"SET DOMAIN GROUP701 encodes a H3K4-methytransferase and regulates multiple key processes of rice plant development","volume":"215","author":"Liu","year":"2017","journal-title":"New Phytol."},{"key":"10.1016\/j.xplc.2025.101534_bib52","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13072-019-0285-6","article-title":"H3K4me2 functions as a repressive epigenetic mark in plants","volume":"12","author":"Liu","year":"2019","journal-title":"Epigenetics Chromatin"},{"key":"10.1016\/j.xplc.2025.101534_bib53","first-page":"2730","article-title":"Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle","volume":"169","author":"Lopez","year":"2015","journal-title":"Plant Physiol."},{"key":"10.1016\/j.xplc.2025.101534_bib54","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib55","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1093\/jexbot\/51.345.659","article-title":"Chlorophyll fluorescence--a practical guide","volume":"51","author":"Maxwell","year":"2000","journal-title":"J. Exp. Bot."},{"key":"10.1016\/j.xplc.2025.101534_bib56","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2017.02100","article-title":"Arabidopsis basic helix-loop-helix 34 (bHLH34) is involved in glucose signaling through binding to a GAGA cis-element","volume":"8","author":"Min","year":"2017","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.xplc.2025.101534_bib57","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/biostatistics\/kxx017","article-title":"A fully Bayesian latent variable model for integrative clustering analysis of multi-type omics data","volume":"19","author":"Mo","year":"2018","journal-title":"Biostatistics"},{"key":"10.1016\/j.xplc.2025.101534_bib58","doi-asserted-by":"crossref","first-page":"129","DOI":"10.3390\/plants12010129","article-title":"CO2 levels modulate carbon utilization, energy levels and inositol polyphosphate profile in Chlorella","volume":"12","author":"Morales-Pineda","year":"2023","journal-title":"Plants"},{"key":"10.1016\/j.xplc.2025.101534_bib59","article-title":"Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae","volume":"1","author":"Ngan","year":"2015","journal-title":"Nat. Plants"},{"key":"10.1016\/j.xplc.2025.101534_bib60","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1186\/s12864-018-4546-8","article-title":"A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data","volume":"19","author":"Oluwadare","year":"2018","journal-title":"BMC Genom."},{"key":"10.1016\/j.xplc.2025.101534_bib61","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/embor.2012.52","article-title":"Enhancers: emerging roles in cell fate specification","volume":"13","author":"Ong","year":"2012","journal-title":"EMBO Rep."},{"key":"10.1016\/j.xplc.2025.101534_bib62","doi-asserted-by":"crossref","first-page":"4198","DOI":"10.1038\/emboj.2011.295","article-title":"H3K4 tri-methylation provides an epigenetic signature of active enhancers","volume":"30","author":"Pekowska","year":"2011","journal-title":"EMBO J."},{"key":"10.1016\/j.xplc.2025.101534_bib63","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/nprot.2016.095","article-title":"Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown","volume":"11","author":"Pertea","year":"2016","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xplc.2025.101534_bib64","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.cell.2008.05.029","article-title":"Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci","volume":"134","author":"Petesch","year":"2008","journal-title":"Cell"},{"key":"10.1016\/j.xplc.2025.101534_bib65","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1021\/acssynbio.7b00362","article-title":"Nontransgenic marker-free gene disruption by an episomal CRISPR system in the oleaginous microalga, Nannochloropsis oceanica CCMP1779","volume":"7","author":"Poliner","year":"2018","journal-title":"ACS Synth. Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib94","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.biosystems.2017.11.005","article-title":"Evidence for the implication of the histone code in building the genome structure","volume":"164","author":"Prakash","year":"2018","journal-title":"Biosystems"},{"key":"10.1016\/j.xplc.2025.101534_bib66","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.pbi.2015.05.011","article-title":"Stress-induced structural changes in plant chromatin","volume":"27","author":"Probst","year":"2015","journal-title":"Curr. Opin. Plant Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib67","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xplc.2025.101534_bib68","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/ncomms1688","article-title":"Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana","volume":"3","author":"Radakovits","year":"2012","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xplc.2025.101534_bib69","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1159\/000351342","article-title":"Cyanobacterial carboxysomes: Microcompartments that facilitate CO2 fixation","volume":"23","author":"Rae","year":"2013","journal-title":"Microb. Physiol."},{"key":"10.1016\/j.xplc.2025.101534_bib70","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xplc.2025.101534_bib98","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/j.molcel.2016.06.018","article-title":"An evolutionary conserved epigenetic mark of polycomb response elements implemented by Trx\/MLL\/COMPASS","volume":"63","author":"Rickels","year":"2016","journal-title":"Mol. Cell."},{"key":"10.1016\/j.xplc.2025.101534_bib71","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xplc.2025.101534_bib72","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1038\/s41467-023-37800-6","article-title":"Light-independent regulation of algal photoprotection by CO2 availability","volume":"14","author":"Ruiz-Sola","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xplc.2025.101534_bib73","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.09343","article-title":"Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements","volume":"4","author":"Secco","year":"2015","journal-title":"eLife"},{"key":"10.1016\/j.xplc.2025.101534_bib74","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","article-title":"HiC-Pro: an optimized and flexible pipeline for Hi-C data processing","volume":"16","author":"Servant","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib100","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/s41586-018-0382-x","article-title":"Creating a functional single-chromosome yeast","volume":"560","author":"Shao","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.xplc.2025.101534_bib93","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s12870-020-02814-5","article-title":"Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple","volume":"21","author":"Shi","year":"2021","journal-title":"BMC Plant Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib75","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1007\/s10529-013-1274-7","article-title":"High-CO2 tolerance in microalgae: possible mechanisms and implications for biotechnology and bioremediation","volume":"35","author":"Solovchenko","year":"2013","journal-title":"Biotechnol. Lett."},{"key":"10.1016\/j.xplc.2025.101534_bib76","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1186\/s12859-018-2288-x","article-title":"HiCcompare: an R-package for joint normalization and comparison of HI-C datasets","volume":"19","author":"Stansfield","year":"2018","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.xplc.2025.101534_bib77","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2012","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.xplc.2025.101534_bib78","first-page":"D1104","article-title":"PlantRegMap: charting functional regulatory maps in plants","volume":"48","author":"Tian","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xplc.2025.101534_bib79","doi-asserted-by":"crossref","first-page":"2091","DOI":"10.1038\/ncomms3091","article-title":"Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum","volume":"4","author":"Veluchamy","year":"2013","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xplc.2025.101534_bib80","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/s13059-015-0671-8","article-title":"An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum","volume":"16","author":"Veluchamy","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib81","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.molcel.2019.08.019","article-title":"Histone modifications regulate chromatin compartmentalization by contributing to a phase separation mechanism","volume":"76","author":"Wang","year":"2019","journal-title":"Mol. Cell"},{"key":"10.1016\/j.xplc.2025.101534_bib82","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1111\/tpj.13307","article-title":"Genome editing of model oleaginous microalgae Nannochloropsis spp. by CRISPR\/Cas9","volume":"88","author":"Wang","year":"2016","journal-title":"Plant J."},{"key":"10.1016\/j.xplc.2025.101534_bib83","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1111\/tpj.12829","article-title":"The CO2 concentrating mechanism and photosynthetic carbon assimilation in limiting CO2: how Chlamydomonas works against the gradient","volume":"82","author":"Wang","year":"2015","journal-title":"Plant J."},{"key":"10.1016\/j.xplc.2025.101534_bib84","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1038\/ng.154","article-title":"Combinatorial patterns of histone acetylations and methylations in the human genome","volume":"40","author":"Wang","year":"2008","journal-title":"Nat. Genet."},{"key":"10.1016\/j.xplc.2025.101534_bib85","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/s13068-019-1506-8","article-title":"Transcriptomic and proteomic responses to very low CO2 suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica","volume":"12","author":"Wei","year":"2019","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/j.xplc.2025.101534_bib86","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1111\/tpj.13411","article-title":"RNAi-based targeted gene knockdown in the model oleaginous microalgae Nannochloropsis oceanica","volume":"89","author":"Wei","year":"2017","journal-title":"Plant J."},{"key":"10.1016\/j.xplc.2025.101534_bib87","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1111\/jpy.12623","article-title":"Optimized methods of chromatin immunoprecipitation for profiling histone modifications in industrial microalgae Nannochloropsis spp","volume":"54","author":"Wei","year":"2018","journal-title":"J. Phycol."},{"key":"10.1016\/j.xplc.2025.101534_bib88","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/nbt.1626","article-title":"Single base\u2013resolution methylome of the silkworm reveals a sparse epigenomic map","volume":"28","author":"Xiang","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xplc.2025.101534_bib103","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1038\/nchembio.2218","article-title":"Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2","volume":"12","author":"Xiong","year":"2016","journal-title":"Nat. Chem. Biol"},{"key":"10.1016\/j.xplc.2025.101534_bib89","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s13072-024-00538-6","article-title":"From compartments to loops: understanding the unique chromatin organization in neuronal cells","volume":"17","author":"Zagirova","year":"2024","journal-title":"Epigenetics Chromatin"},{"key":"10.1016\/j.xplc.2025.101534_bib104","doi-asserted-by":"crossref","first-page":"R62","DOI":"10.1186\/gb-2009-10-6-r62","article-title":"Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana","volume":"10","author":"Zhang","year":"2009","journal-title":"Genome Biol"},{"key":"10.1016\/j.xplc.2025.101534_bib90","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based Analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.xplc.2025.101534_bib110","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1104\/pp.15.00125","article-title":"Genome-wide nucleosome occupancy and positioning and their impact on gene expression and evolution in plants","volume":"168","author":"Zhang","year":"2015","journal-title":"Plant Physiol"},{"key":"10.1016\/j.xplc.2025.101534_bib91","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2024.109570","article-title":"Predicting A\/B compartments from histone modifications using deep learning","volume":"27","author":"Zheng","year":"2024","journal-title":"iScience"},{"key":"10.1016\/j.xplc.2025.101534_bib95","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nrg2905","article-title":"Charting histone modifications and the functional organization of mammalian genomes","volume":"12","author":"Zhou","year":"2011","journal-title":"Nat. Rev. Genet."}],"container-title":["Plant Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2590346225002962?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2590346225002962?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T05:20:11Z","timestamp":1773897611000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2590346225002962"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":111,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["S2590346225002962"],"URL":"https:\/\/doi.org\/10.1016\/j.xplc.2025.101534","relation":{},"ISSN":["2590-3462"],"issn-type":[{"value":"2590-3462","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Multi-dimensional epigenomic dynamics converge on H3K4-mediated regulation of low-CO2 adaptation in Nannochloropsis oceanica","name":"articletitle","label":"Article Title"},{"value":"Plant Communications","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xplc.2025.101534","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Inc. on behalf of CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, and Chinese Society for Plant Biology.","name":"copyright","label":"Copyright"}],"article-number":"101534"}}