{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:10:22Z","timestamp":1760137822545,"version":"build-2065373602"},"reference-count":43,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T00:00:00Z","timestamp":1648598400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ram\u00f3n Areces Fundation","award":["CIVP19S7917"],"award-info":[{"award-number":["CIVP19S7917"]}]},{"name":"Autonomous Community of Madrid, Spain","award":["B2017\/BMD-3778; LINFOMAS-CM"],"award-info":[{"award-number":["B2017\/BMD-3778; LINFOMAS-CM"]}]},{"name":"Spanish Ministry of Science, Innovation and Universities","award":["RTI2018-093330-B-I00; MCIU\/FEDER, EU"],"award-info":[{"award-number":["RTI2018-093330-B-I00; MCIU\/FEDER, EU"]}]},{"DOI":"10.13039\/501100002704","name":"Asociaci\u00f3n Espa\u00f1ola Contra el C\u00e1ncer","doi-asserted-by":"publisher","award":["AECC, 2018; PROYE18054PIRI"],"award-info":[{"award-number":["AECC, 2018; PROYE18054PIRI"]}],"id":[{"id":"10.13039\/501100002704","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Ministry of Science, Innovation and Universities Juan de la Cierva Grant","award":["IJCI-2016-29155"],"award-info":[{"award-number":["IJCI-2016-29155"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["ncRNA"],"abstract":"<jats:p>Circular RNAs (circRNAs) are suggested to play a discriminative role between some stages of thymocyte differentiation. However, differential aspects of the stage of mature single-positive thymocytes remain to be explored. The purpose of this study is to investigate the differential expression pattern of circRNAs in three different development stages of human thymocytes, including mature single-positive cells, and perform predictions in silico regarding the ability of specific circRNAs when controlling the expression of genes involved in thymocyte differentiation. We isolate human thymocytes at three different stages of intrathymic differentiation and determine the expression of circRNAs and mRNA by RNASeq. We show that the differential expression pattern of 50 specific circRNAs serves to discriminate between the three human thymocyte populations. Interestingly, the downregulation of RAG2, a gene involved in T-cell differentiation in the thymus, could be simultaneously controlled by the downregulation of two circRNASs (hsa_circ_0031584 and hsa_circ_0019079) through the hypothetical liberation of hsa-miR-609. Our study provides, for the first time, significant insights into the usefulness of circRNAs in discriminating between different stages of thymocyte differentiation and provides new potential circRNA\u2013miRNA\u2013mRNA networks capable of controlling the expression of genes involved in T-cell differentiation in the thymus.<\/jats:p>","DOI":"10.3390\/ncrna8020026","type":"journal-article","created":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T21:28:39Z","timestamp":1648675719000},"page":"26","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Patterns of Differentially Expressed circRNAs in Human Thymocytes"],"prefix":"10.3390","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6369-2444","authenticated-orcid":false,"given":"Pilar","family":"L\u00f3pez-Nieva","sequence":"first","affiliation":[{"name":"Genome Dynamics and Function Program, Genome Decoding Department, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Madrid Autonomous University, 28049 Madrid, Spain"},{"name":"Institute of Health Research Jim\u00e9nez D\u00edaz Foundation, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9427-2581","authenticated-orcid":false,"given":"Pablo","family":"Fern\u00e1ndez-Navarro","sequence":"additional","affiliation":[{"name":"Cancer and Environmental Epidemiology Unit, National Center for Epidemiology, Institute of Health Carlos III, 28029 Madrid, Spain"},{"name":"Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda \u00c1ngeles","family":"Cobos-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Genome Dynamics and Function Program, Genome Decoding Department, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Madrid Autonomous University, 28049 Madrid, Spain"},{"name":"Institute of Health Research Jim\u00e9nez D\u00edaz Foundation, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4688-5508","authenticated-orcid":false,"given":"Iria","family":"Gonz\u00e1lez-Vasconcellos","sequence":"additional","affiliation":[{"name":"Genome Dynamics and Function Program, Genome Decoding Department, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Madrid Autonomous University, 28049 Madrid, Spain"},{"name":"Institute of Health Research Jim\u00e9nez D\u00edaz Foundation, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ra\u00fal","family":"S\u00e1nchez P\u00e9rez","sequence":"additional","affiliation":[{"name":"Department of Congenital Cardiac Surgery, Hospital Universitario La Paz, 28046 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00c1ngel","family":"Aroca","sequence":"additional","affiliation":[{"name":"Department of Congenital Cardiac Surgery, Hospital Universitario La Paz, 28046 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4520-6785","authenticated-orcid":false,"given":"Jos\u00e9","family":"Fern\u00e1ndez-Piqueras","sequence":"additional","affiliation":[{"name":"Genome Dynamics and Function Program, Genome Decoding Department, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Madrid Autonomous University, 28049 Madrid, Spain"},{"name":"Institute of Health Research Jim\u00e9nez D\u00edaz Foundation, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4168-6251","authenticated-orcid":false,"given":"Javier","family":"Santos","sequence":"additional","affiliation":[{"name":"Genome Dynamics and Function Program, Genome Decoding Department, Severo Ochoa Molecular Biology Center (CBMSO), CSIC-Madrid Autonomous University, 28049 Madrid, Spain"},{"name":"Institute of Health Research Jim\u00e9nez D\u00edaz Foundation, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,3,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.cell.2014.09.001","article-title":"Complementary sequence-mediated exon circularization","volume":"159","author":"Zhang","year":"2014","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/nsmb.2959","article-title":"Exon-intron circular RNAs regulate transcription in the nucleus","volume":"22","author":"Li","year":"2015","journal-title":"Nat. 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