{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR315/SRR315579/SRR315579.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR315/SRR315580/SRR315580.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["HHMI/UCSD"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA144267"],"scientific_name":["Homo sapiens"],"long_description":["While liganded nuclear receptors are well established to regulate Pol II protein-coding transcription units, their role in regulation of DNA repeats remains largely unknown. Here, we report that ~2-3% of the ~1-200,000 human DR2 Alu repeats, particularly those in proximity to retinoic acid-activated Pol II transcription units, are bound and activated by retinoic acid receptor in human embryonic stem cells, triggering their Pol  III-dependent transcription. The non-coding DR2 Alu transcripts are processed in a Dicer-dependent fashion into a series of small RNA products with sizes ranging ~28-65nt and exhibit substantial co-localization with P bodies. These small RNAs cause degradation of a subset of mRNAs critical for the \"stem cell\" state, which harbor complimentary sequences in their 3' untranslated regions. This regulation requires Ago3- dependent stabilization of full-length and processed DR2 Alu transcripts, and recruitment of Ago3-associated decapping complexes to the target mRNAs. Thus, the RAR/Pol III-dependent DR2 Alu transcriptional program in stem cells serves as a functional complement to the RAR/Pol II-dependent counterpart. Overall design: ChIP-seq of H3K36me3 samples before and after RA (retinoic acid) treatments."],"tag":["xref:PubMed:23064648"],"repository":["ENA"],"description_synonyms":["Tretin M, tretinoin, Refissa, trans-Retinoic Acid, Colony-Forming Units, Degradation, Vitamin A, Progenitor Cell, mRNA Stability, 8E-tetraenoic acid, beta all trans Retinoic Acid, 6-trimethyl-1-cyclohexen-1-yl)-2, mRNA decay, AGN 100335, Potassium Salt, Retinoic Acid, Stability, reduced, Cordes vas, Mother Cells, 3, 4, mRNA Transcript, 6, Retin-A, tiny, Vesanoid, Stieva-A, Progenitor, 6-trimethylcyclohex-1-en-1-yl)nona-2, Retinoic acid, Retinoic, all-trans-beta-Retinoic acid, Renova, Salt, hypoplasia, all trans Retinoic Acid, Atralin, Mother, Tretinoin Potassium Salt, Betarretin, 8E)-3, trans Retinoic Acid, Tretinoin Sodium Salt, 6-trimethyl-1-cyclohexenyl)nona-2, beta-all-trans-Retinoic, Altreno, RNA., mRNA Transcript Degradation, Decay, Vitamin A Acid, (2E, trans-Retinoic, Veltin, all-trans-vitamin A1 acid, small, RNA Degradation, RNA, Colony Forming Unit, Tretinoin Zinc Salt, 8-all-trans-tetraenoic acid, Progenitor Cells, 4E, Dermairol, Tretinoin Potassium, Ro 1-5488, Tri-luma, Cell, Tretinoin, trans-retinoic acid, all-trans retinoic acid, all-trans-Retinoic Acid, 8-nonatetraenoic acid, Tretinoin Sodium, all-trans-vitamin A acid, Colony-Forming Unit, macromolecular stability of mRNA, Biacna, 6-trimethylcyclohex-1-enyl)nona-2, Stem Cell, Retin A, mRNA Instability, retinoic acid, all-trans-tretinoin, all-trans-Retinoic, mRNA Decay, 6-trimethyl-1-cyclohexene-1-yl)-2, RNA Decay, Acide retinoique (French), RNA Instability, Mother Cell, beta-Retinoic acid, Acid, tretinoina, underdeveloped, mRNA, Stem, 6E, Tretinoin Zinc, beta-all-trans-Retinoic Acid, tretinoinum, Colony Forming Units, mRNA Degradation, 6-trimethylcyclohexen-1-yl)nona-2E, Transcript Degradation, Zinc Salt, Sodium Salt, 7-dimethyl-9-(2, all-(E)-retinoic acid, Avita, Cells, vitamin A acid, Retisol-A, (all-E)-3, 8-tetraenoic acid, Instability, tretinoine"],"name_synonyms":["Human, Modern., human being, Man (Taxonomy), Homo sapiens, man, Man, human, Modern Man"],"additional_accession":[]},"is_claimable":false,"name":"Homo sapiens","description":"Retinoic Acid-Induced DR2 Alu Transcripts in Stem Cells Generate Functional Small RNAs that Mediate Target mRNA Degradation","dates":{"last_updated":"2025-09-24","first_public":"2013-05-31"},"accession":"PRJNA144267","cross_references":{"GEO":["GSE30876"],"taxon":["9606"],"PubMed":["23064648"]}}