{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T15:24:17Z","timestamp":1783178657168,"version":"3.54.6"},"reference-count":67,"publisher":"American Association for the Advancement of Science (AAAS)","license":[{"start":{"date-parts":[[2023,11,29]],"date-time":"2023-11-29T00:00:00Z","timestamp":1701216000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,11,29]],"date-time":"2023-11-29T00:00:00Z","timestamp":1701216000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,11,24]],"date-time":"2023-11-24T00:00:00Z","timestamp":1700784000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["csbj.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Comput Struct Biotechnol J"],"published-print":{"date-parts":[[2024,12]]},"abstract":"<jats:p>\n                    The long noncoding RNAs (lncRNAs) are involved in numerous fundamental biological processes, including circadian regulation. Although recent studies have revealed insights into the functions of lncRNAs, how the lncRNAs regulate circadian rhythms still requires a deeper investigation. In this study, we generate two datasets of RNA-seq profiles of the mouse (\n                    <jats:italic toggle=\"yes\">Mus musculus<\/jats:italic>\n                    ) testis under light-dark (LD) cycle. The first dataset included 18,613 unannotated transcripts measured at 12 time points, each with duplicate samples, under LD conditions; while the second dataset included 21,414 unannotated transcripts measured at six time points, each with three replicates, under desynchronized and control conditions. We identified 5964 testicular lncRNAs in each dataset by BLASTing these transcripts against the known mouse lncRNAs from the NONCODE database. MetaCycle analyses were performed to identify 519, 475, and 494 rhythmically expressed mouse testicular lncRNAs in the 12-time-point dataset, the six-time-point control dataset, and the six-time-point desynchronized dataset, respectively. A comparison of the expression profiles of the lncRNAs under desynchronized and control conditions revealed that 427 rhythmically expressed lncRNAs from the control condition became arrhythmic under the desynchronized condition, suggesting a possible loss of rhythmicity. In contrast, 446 arrhythmic lncRNAs from the control condition became rhythmic under the desynchronized condition, suggesting a possible gain of rhythmicity. Interestingly, 48 lncRNAs were rhythmically expressed under both desynchronized and control conditions. These oscillating lncRNAs were divided into morning lncRNAs, evening lncRNAs, and night lncRNAs based on their time-course expression patterns. We interrogated the promoter regions of these rhythmically expressed mouse testicular lncRNAs to predict their possible regulation by the E-box, D-box, or RORE promoter motifs. GO and KEGG analyses were performed to identify the possible biological functions of these rhythmically expressed mouse testicular lncRNAs. Further, we conducted conservation analyses of the rhythmically expressed mouse testicular lncRNAs with lncRNAs from humans, rats, and zebrafish, and uncovered three mouse testicular lncRNAs conserved across these four species. Finally, we computationally predicted the conserved lncRNA-encoded peptides and their 3D structures from each of the four species. Taken together, our study revealed thousands of rhythmically expressed lncRNAs in the mouse testis, setting the stage for further computational and experimental validations.\n                  <\/jats:p>","DOI":"10.1016\/j.csbj.2023.11.046","type":"journal-article","created":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T23:09:45Z","timestamp":1701212985000},"page":"330-346","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"title":["Thousands of oscillating LncRNAs in the mouse testis"],"prefix":"10.34133","volume":"23","author":[{"given":"Shital Kumar","family":"Mishra","sequence":"first","affiliation":[{"name":"Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China"},{"name":"School of Biology &amp; Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taole","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China"},{"name":"School of Biology &amp; Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China"},{"name":"School of Biology &amp; Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","published-online":{"date-parts":[[2023,11,29]]},"reference":[{"issue":"12","key":"e_1_4_2_2_2","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/S0968-0004(00)01695-9","article-title":"Life\u2019s 24-hour clock: molecular control of circadian rhythms in animal cells","volume":"25","author":"Young M.W.","year":"2000","unstructured":"YoungM.W.Life\u2019s 24-hour clock: molecular control of circadian rhythms in animal cellsTrends Biochem Sci2512200060160611116186","journal-title":"Trends Biochem Sci"},{"key":"e_1_4_2_3_2","doi-asserted-by":"crossref","unstructured":"Breed M.D. Conceptual Breakthroughs in Ethology and Animal Behavior Chapter 5 - 1729 Biological Clocks 2017 Academic Press 15 16","DOI":"10.1016\/B978-0-12-809265-1.00005-8"},{"key":"e_1_4_2_4_2","doi-asserted-by":"crossref","first-page":"8819","DOI":"10.1073\/pnas.96.16.8819","article-title":"Biological clocks","volume":"96","author":"Norio Ishida M.K.","year":"1999","unstructured":"Norio IshidaM.K.AlladaR.A.V.I.Biological clocksPNAS9619998819882010430850","journal-title":"PNAS"},{"key":"e_1_4_2_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41575-020-00401-5"},{"key":"e_1_4_2_6_2","doi-asserted-by":"crossref","DOI":"10.1021\/bi5007354","article-title":"Circadian clock, cancer, and chemotherapy","author":"Sancar Aziz","year":"2015","unstructured":"Sancar Aziz Lindsey-Boltz Laura A. 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