{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T10:02:54Z","timestamp":1753869774286,"version":"3.41.2"},"reference-count":43,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2025,2,23]],"date-time":"2025-02-23T00:00:00Z","timestamp":1740268800000},"content-version":"vor","delay-in-days":22,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Reproduction Devel"],"published-print":{"date-parts":[[2025,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>Intergenic transcription, either failure to terminate at the transcription end site (TES), or transcription initiation at other intergenic regions, is present in cultured cells and enhanced in the presence of stressors such as viral infection. Such intergenic transcription has not been characterized in natural biological samples such as pre\u2010implantation embryos which express more than 10,000 genes and undergo drastic changes in DNA methylation. Using Automatic Readthrough Transcription Detection (ARTDeco) and poly(A)\u2010selected RNA\u2010seq libraries from in vivo developed bovine oocytes and embryos, we found abundant intergenic transcripts that we termed as read\u2010outs (transcribed from 5 to 15\u2009kb after TES) and read\u2010ins (transcribed 1\u2009kb upstream of reference genes, extending up to 15\u2009kb upstream). Read\u2010throughs (continued transcription from TES of expressed reference genes, 4\u201315\u2009kb in length), however, were much fewer. For example, the numbers of read\u2010outs and read\u2010ins ranged from 3084 to 6565 or 33.36% to 66.67% of expressed reference genes at different stages of embryo development. The less copious read\u2010throughs were at an average of 10% and significantly correlated with reference gene expression (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Interestingly, intergenic transcription did not seem to be random because many intergenic transcripts (1504 read\u2010outs, 1045 read\u2010ins, and 1021 read\u2010throughs) were associated with common reference genes across all stages of pre\u2010implantation development. Their expression also seemed to be regulated by developmental stages because many were differentially expressed (log<jats:sub>2<\/jats:sub> fold change \u2265\u20092, <jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Additionally, while gradual but un\u2010patterned decreases in DNA methylation densities 10\u2009kb both up\u2010 and downstream of the intergenic transcribed regions were observed, the correlation between intergenic transcription and DNA methylation was insignificant. Finally, transcription factor binding motifs and polyadenylation signals were found in 27.2% and 12.15% of intergenic transcripts, respectively, suggesting considerable novel transcription initiation and RNA processing. In summary, in vivo developed oocytes and pre\u2010implantation embryos express large numbers of intergenic transcripts, which are not related to the overall DNA methylation profiles either up\u2010 or downstream.<\/jats:p>","DOI":"10.1002\/mrd.70017","type":"journal-article","created":{"date-parts":[[2025,2,23]],"date-time":"2025-02-23T16:04:31Z","timestamp":1740326671000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Poly(A)\u2010Selected Intergenic Transcripts in In Vivo Developed Bovine Oocytes and Pre\u2010Implantation Embryos"],"prefix":"10.1002","volume":"92","author":[{"given":"Saurav","family":"Ranjitkar","sequence":"first","affiliation":[{"name":"Department of Animal Science University of Connecticut Storrs Connecticut USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad","family":"Shiri","sequence":"additional","affiliation":[{"name":"Department of Computer Science Old Dominion University Norfolk Virginia USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiangwen","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Computer Science Old Dominion University Norfolk Virginia USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiuchun","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Animal Science University of Connecticut Storrs Connecticut USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,2,23]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02350-x"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab203"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20061281"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(04)00127-8"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.4222606"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10142-016-0524-x"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.00512"},{"key":"e_1_2_12_10_1","unstructured":"Geng F.\u2010S. 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