{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T22:45:36Z","timestamp":1776465936333,"version":"3.51.2"},"reference-count":100,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T00:00:00Z","timestamp":1770854400000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T00:00:00Z","timestamp":1769904000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000053","name":"National Eye Institute","doi-asserted-by":"publisher","award":["R01EY033734"],"award-info":[{"award-number":["R01EY033734"]}],"id":[{"id":"10.13039\/100000053","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Aging Cell"],"published-print":{"date-parts":[[2026,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Alterations in biological rhythms are a common feature of aging, and disruption of circadian rhythms can exacerbate age\u2010associated pathologies. The retina is critical for detecting light for both vision and for transmitting time\u2010of\u2010day information to the brain, synchronizing rhythms throughout the body. Disruption of circadian rhythms by manipulating the molecular clock leads to premature retinal degeneration in flies and mice, and gene expression rhythms are altered in models of age\u2010associated ocular disease. Despite this, it is unknown how or why the gene expression rhythms of the retina change with age. Here, we show that ~70% of the\n                    <jats:italic>Drosophila<\/jats:italic>\n                    transcriptome is rhythmically expressed throughout the diurnal cycle, with ~40% of genes showing altered rhythms with age. These transcriptome\u2010wide changes in aging photoreceptors are accompanied by shifts in the rhythmic patterns of RNA Polymerase II (Pol II) occupancy, histone H3 lysine 4 (H3K4) methylation, and chromatin accessibility, without major changes in the occupancy of the circadian clock transcription factors Clock (Clk) and Cycle (Cyc). Instead, aging decreases genome\u2010wide levels of several different histone methyl marks including H3K4 methylation, whose relative levels across the day correlate with the phase of rhythmic gene expression. Moreover, reduction of H3K4me3 by the knockdown of the three methyltransferases in young photoreceptors results in massive changes to rhythmic gene expression under diurnal light conditions. We conclude that there are broad epigenetic shifts in the aging retina that correlate with and may contribute to widespread alterations in rhythmic gene expression.\n                  <\/jats:p>","DOI":"10.1111\/acel.70396","type":"journal-article","created":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T12:22:30Z","timestamp":1770898950000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Broad Epigenetic Shifts in the Aging\n                    <i>Drosophila<\/i>\n                    Retina Contribute to Its Altered Diurnal Rhythmic Transcriptome"],"prefix":"10.1111","volume":"25","author":[{"given":"Sarah E.","family":"McGovern","sequence":"first","affiliation":[{"name":"Department of Biochemistry Purdue University  West Lafayette Indiana USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaoya","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Biochemistry Purdue University  West Lafayette Indiana USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Makayla N.","family":"Marlin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry Purdue University  West Lafayette Indiana USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophia A.","family":"Pruitt","sequence":"additional","affiliation":[{"name":"Department of Biochemistry Purdue University  West Lafayette Indiana USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5933-9952","authenticated-orcid":false,"given":"Vikki M.","family":"Weake","sequence":"additional","affiliation":[{"name":"Department of Biochemistry Purdue University  West Lafayette Indiana USA"},{"name":"Purdue Center for Cancer Research Purdue University  West Lafayette Indiana USA"},{"name":"Purdue Institute for Integrative Neuroscience Purdue University  West Lafayette Indiana USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2026,2,12]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.178079.111"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22922-6"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1808137115"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2023.102929"},{"key":"e_1_2_11_7_1","article-title":"From Reads to Genes to Pathways: Differential Expression Analysis of RNA\u2010Seq Experiments Using Rsubread and the edgeR Quasi\u2010Likelihood Pipeline","volume":"5","author":"Chen Y.","year":"2016","journal-title":"F1000Res"},{"key":"e_1_2_11_8_1","article-title":"edgeR 4.0: Powerful Differential Analysis of Sequencing Data With Expanded Functionality and Improved Support for Small Counts and Larger Datasets","volume":"53","author":"Chen Y.","year":"2024","journal-title":"bioRxiv"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-018-0031-9"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4396"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107525"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.280.5369.1599"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2746"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1196766"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030039"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-48"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.3389\/freae.2023.1187980"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF02215177"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1152\/jn.01066.2007"},{"key":"e_1_2_11_21_1","first-page":"245","article-title":"ggplot2: Elegant Graphics for Data Analysis","volume":"174","author":"Hadley W.","year":"2016","journal-title":"Journal of the Royal Statistical Society. Series A, Statistics in Society"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u20104939\u20103578\u20109_16"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2021.100127"},{"key":"e_1_2_11_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-4304-3"},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01761"},{"key":"e_1_2_11_26_1","first-page":"1","article-title":"Dietary Restriction and the Transcription Factor Clock Delay Eye Aging to Extend Lifespan in Drosophila melanogaster","volume":"13","author":"Hodge B. A.","year":"2022","journal-title":"Nature Communications 2022 13:1"},{"key":"e_1_2_11_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2025.07.010"},{"key":"e_1_2_11_28_1","doi-asserted-by":"publisher","DOI":"10.1172\/JCI90328"},{"key":"e_1_2_11_29_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010021"},{"key":"e_1_2_11_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyab079"},{"key":"e_1_2_11_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-32273-5"},{"key":"e_1_2_11_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1961"},{"key":"e_1_2_11_33_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0201-4"},{"key":"e_1_2_11_34_1","first-page":"349","article-title":"Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals","volume":"338","author":"Koike N.","year":"2012","journal-title":"Science (1979)"},{"key":"e_1_2_11_35_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1432206"},{"key":"e_1_2_11_36_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.117.300657"},{"key":"e_1_2_11_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14529"},{"key":"e_1_2_11_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.nbd.2020.104832"},{"key":"e_1_2_11_39_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_2_11_40_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003118"},{"key":"e_1_2_11_41_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001442"},{"key":"e_1_2_11_42_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt656"},{"key":"e_1_2_11_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/s44318-024-00267-2"},{"key":"e_1_2_11_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.11.001"},{"key":"e_1_2_11_45_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"e_1_2_11_46_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1474\u20109726.2012.00800.x"},{"key":"e_1_2_11_47_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-75009-5"},{"key":"e_1_2_11_48_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13024-025-00800-9"},{"key":"e_1_2_11_49_1","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"e_1_2_11_50_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks042"},{"key":"e_1_2_11_51_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.46314"},{"key":"e_1_2_11_52_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2013.11.017"},{"key":"e_1_2_11_53_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2024.05.014"},{"key":"e_1_2_11_54_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-024-00802-3"},{"key":"e_1_2_11_55_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms9332"},{"key":"e_1_2_11_56_1","doi-asserted-by":"crossref","unstructured":"Parkhitko A. A. L.Wang E.Filine et\u00a0al.2021.\u201cA Genetic Model of Methionine Restriction Extends Drosophila Health\u2010and Lifespan.\u201d PURDUE UNIVERSITY LIBRARY 118.","DOI":"10.1073\/pnas.2110387118"},{"key":"e_1_2_11_57_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.282277.116"},{"key":"e_1_2_11_58_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-019-0179-2"},{"key":"e_1_2_11_59_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_2_11_60_1","doi-asserted-by":"publisher","DOI":"10.3109\/07420528.2011.635237"},{"key":"e_1_2_11_61_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw257"},{"key":"e_1_2_11_62_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0704-0"},{"key":"e_1_2_11_63_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2931"},{"key":"e_1_2_11_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2021.07.017"},{"key":"e_1_2_11_65_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp616"},{"key":"e_1_2_11_66_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-25950-0_2"},{"key":"e_1_2_11_67_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2010.01.018"},{"key":"e_1_2_11_68_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.07.042"},{"key":"e_1_2_11_69_1","doi-asserted-by":"publisher","DOI":"10.1177\/2633105520903708"},{"key":"e_1_2_11_70_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1523007"},{"key":"e_1_2_11_71_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.00764"},{"key":"e_1_2_11_72_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2018.08.015"},{"key":"e_1_2_11_73_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biochem-051710-134100"},{"key":"e_1_2_11_74_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.07.035"},{"key":"e_1_2_11_75_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.redox.2023.102723"},{"key":"e_1_2_11_76_1","doi-asserted-by":"publisher","DOI":"10.1093\/icb\/icac140"},{"key":"e_1_2_11_77_1","doi-asserted-by":"publisher","DOI":"10.1111\/acel.12817"},{"key":"e_1_2_11_78_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.06.045"},{"key":"e_1_2_11_79_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.01612\u201007"},{"key":"e_1_2_11_80_1","doi-asserted-by":"publisher","DOI":"10.1242\/dev.102392"},{"key":"e_1_2_11_81_1","doi-asserted-by":"publisher","DOI":"10.1002\/bies.20777"},{"key":"e_1_2_11_82_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007156"},{"key":"e_1_2_11_83_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.exer.2021.108751"},{"key":"e_1_2_11_84_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10522-025-10281-4"},{"key":"e_1_2_11_85_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05780-8"},{"issue":"15","key":"e_1_2_11_86_1","first-page":"1","article-title":"Efficient Test and Visualization of Multi\u2010Set Intersections","volume":"5","author":"Wang M.","year":"2015","journal-title":"Scientific Reports"},{"key":"e_1_2_11_87_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2015803118"},{"key":"e_1_2_11_88_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020039"},{"key":"e_1_2_11_89_1","article-title":"clusterProfiler 4.0: A Universal Enrichment Tool for Interpreting Omics Data","volume":"2","author":"Wu T.","year":"2021","journal-title":"Innovation"},{"key":"e_1_2_11_90_1","doi-asserted-by":"publisher","DOI":"10.1111\/acel.13737"},{"key":"e_1_2_11_91_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-024-01020-z"},{"key":"e_1_2_11_92_1","doi-asserted-by":"publisher","DOI":"10.3390\/biology12081107"},{"key":"e_1_2_11_93_1","doi-asserted-by":"publisher","DOI":"10.1167\/iovs.64.13.3"},{"key":"e_1_2_11_94_1","doi-asserted-by":"publisher","DOI":"10.1080\/19420889.2015.1102805"},{"key":"e_1_2_11_95_1","article-title":"Thirteen Years of clusterProfiler","volume":"5","author":"Yu G.","year":"2024","journal-title":"Innovation"},{"key":"e_1_2_11_96_1","doi-asserted-by":"publisher","DOI":"10.1089\/omi.2011.0118"},{"key":"e_1_2_11_97_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1011278"},{"key":"e_1_2_11_98_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2115711119"},{"key":"e_1_2_11_99_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137"},{"key":"e_1_2_11_100_1","doi-asserted-by":"publisher","DOI":"10.1177\/0748730418779526"},{"key":"e_1_2_11_101_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2020.01.009"}],"container-title":["Aging Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/acel.70396","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/acel.70396","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/acel.70396","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T19:58:54Z","timestamp":1772999934000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/acel.70396"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":100,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["10.1111\/acel.70396"],"URL":"https:\/\/doi.org\/10.1111\/acel.70396","archive":["Portico"],"relation":{},"ISSN":["1474-9718","1474-9726"],"issn-type":[{"value":"1474-9718","type":"print"},{"value":"1474-9726","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2]]},"assertion":[{"value":"2025-06-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-22","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-02-12","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70396"}}