{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T20:34:52Z","timestamp":1778272492627,"version":"3.51.4"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["5R01GM047475-24"],"award-info":[{"award-number":["5R01GM047475-24"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"US Department of Agriculture Agricultural Research Service Current Research Information System","award":["2030-21000-051-00D"],"award-info":[{"award-number":["2030-21000-051-00D"]}]},{"name":"US Department of Agriculture NIFA-AFRI postdoctoral fellowship","award":["2017-67012-26105"],"award-info":[{"award-number":["2017-67012-26105"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The phytochrome (phy)-PHYTOCHROME-INTERACTING FACTOR (PIF) sensory module perceives and transduces light signals to direct target genes (DTGs), which then drive the adaptational responses in plant growth and development appropriate to the prevailing environment. These signals include the first exposure of etiolated seedlings to sunlight upon emergence from subterranean darkness and the change in color of the light that is filtered through, or reflected from, neighboring vegetation (\u201cshade\u201d). Previously, we identified three broad categories of rapidly signal-responsive genes: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. Here, we investigate the potential role of epigenetic chromatin modifications in regulating these contrasting patterns of phy-PIF module-induced expression of DTGs in Arabidopsis (Arabidopsis thaliana). Using RNA-seq and ChIP-seq to determine time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, we show that, whereas the initial dark-to-light transition triggers a rapid, apparently temporally coincident decline of both parameters, the light-to-shade transition induces similarly rapid increases in transcript levels that precede increases in H3K4me3 levels. Together with other recent findings, these data raise the possibility that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade\/light switching that is intrinsic to vegetational canopies under natural sunlight conditions.<\/jats:p>","DOI":"10.1093\/plphys\/kiac282","type":"journal-article","created":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T08:11:50Z","timestamp":1654675910000},"page":"1915-1926","source":"Crossref","is-referenced-by-count":6,"title":["Shade triggers posttranscriptional PHYTOCHROME-INTERACTING FACTOR-dependent increases in H3K4 trimethylation"],"prefix":"10.1093","volume":"190","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7863-9889","authenticated-orcid":false,"given":"Robert H","family":"Calderon","sequence":"first","affiliation":[{"name":"Department of Plant and Microbial Biology, University of California , Berkeley, California, 94720, USA"},{"name":"Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture , Albany, California, 94710, USA"},{"name":"Department of Plant Physiology, Ume\u00e5 Plant Science Centre, Ume\u00e5 University , Ume\u00e5, 901 87, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jutta","family":"Dalton","sequence":"additional","affiliation":[{"name":"Department of Plant and Microbial Biology, University of California , Berkeley, California, 94720, USA"},{"name":"Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture , Albany, California, 94710, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4495-3447","authenticated-orcid":false,"given":"Yu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Plant and Microbial Biology, University of California , Berkeley, California, 94720, USA"},{"name":"Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture , Albany, California, 94710, USA"},{"name":"US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, California, 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6064-3460","authenticated-orcid":false,"given":"Peter H","family":"Quail","sequence":"additional","affiliation":[{"name":"Department of Plant and Microbial Biology, University of California , Berkeley, California, 94720, USA"},{"name":"Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture , Albany, California, 94710, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,6,8]]},"reference":[{"key":"2022102807571557200_kiac282-B1","doi-asserted-by":"crossref","first-page":"2232","DOI":"10.1073\/pnas.0711675105","article-title":"Mechanistic duality of transcription factor function in phytochrome 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