{"entity": "researcher", "timestamp": "2026-09-06T15:49:30.882Z", "family": "Zhang", "given": "Yujie", "initials": "Y", "orcid": "0000-0002-4926-028X", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782"}}, "publications": [{"entity": "publication", "iuid": "3e3213fffbd449ba9410298238eb3a2f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3213fffbd449ba9410298238eb3a2f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3e3213fffbd449ba9410298238eb3a2f"}}, "title": "High-throughput 5\u2032P sequencing enables the study of degradation-associated ribosome stalls", "authors": [{"family": "Zhang", "given": "Yujie", "initials": "Y", "orcid": "0000-0002-4926-028X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal-article", "published": "2021-05-00", "journal": {"title": "Cell Rep Methods", "issn": "2667-2375", "issn-l": null, "volume": "1", "issue": "1", "pages": "100001"}, "abstract": "RNA degradation is critical for gene expression and mRNA quality control. mRNA degradation is connected to the translation process up to the degree that 5'-3' mRNA degradation follows the last translating ribosome. Here, we present an improved high-throughput 5'P degradome RNA-sequencing method (HT-5Pseq). HT-5Pseq is easy, scalable, and uses affordable duplex-specific nuclease-based rRNA depletion. We investigate in vivo ribosome stalls focusing on translation termination. By comparing ribosome stalls identified by ribosome profiling, disome-seq and HT-5Pseq, we find that degradation-associated ribosome stalls are often enriched in Arg preceding the stop codon. On the contrary, mRNAs depleted for those stalls use more frequently a TAA stop codon preceded by hydrophobic amino acids. Finally, we show that termination stalls found by HT-5Pseq, and not by other approaches, are associated with decreased mRNA stability. Our work suggests that ribosome stalls associated with mRNA decay can be easily captured by investigating the 5'P degradome.", "doi": "10.1016/j.crmeth.2021.100001", "pmid": "35474692", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9017187"}, {"db": "pii", "key": "S2667-2375(21)00001-1"}], "notes": [], "created": "2021-12-02T18:38:13.745Z", "modified": "2025-12-04T17:06:21.371Z"}, {"entity": "publication", "iuid": "8249df0550d04d96b38854567bfb885f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8249df0550d04d96b38854567bfb885f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8249df0550d04d96b38854567bfb885f"}}, "title": "High-throughput 5\u2019P sequencing enables the study of degradation-associated ribosome stalls", "authors": [{"family": "Zhang", "given": "Yujie", "initials": "Y", "orcid": "0000-0002-4926-028X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "posted-content", "published": "2020-06-23", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.06.22.165134", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:57:34.697Z", "modified": "2026-08-20T09:57:34.754Z"}, {"entity": "publication", "iuid": "5ae608853bc545c9b08e1b8c6a0abab9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae608853bc545c9b08e1b8c6a0abab9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ae608853bc545c9b08e1b8c6a0abab9"}}, "title": "Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.", "authors": [{"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Hennig", "given": "Bianca P", "initials": "BP", "orcid": "0000-0002-7733-8160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c64ef90520aa408c8c2ed17fae8fd95c.json"}}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Zhang", "given": "Yujie", "initials": "Y", "orcid": "0000-0002-4926-028X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbd52b8ae0744815b568a3ebc2af3782.json"}}, {"family": "Piazza", "given": "Ilaria", "initials": "I", "orcid": "0000-0001-5895-6134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5258dce396444d9a8f5e5bc2fd13b282.json"}}, {"family": "Pareja Sanchez", "given": "Yerma", "initials": "Y", "orcid": "0000-0003-2008-5390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c66abc222f14d7b80591307113af56e.json"}}, {"family": "Chabbert", "given": "Christophe D", "initials": "CD", "orcid": "0000-0001-7851-4640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/490051f9ae674750a4dd3ee10c27b2b0.json"}}, {"family": "Adjalley", "given": "Sophie H", "initials": "SH", "orcid": "0000-0002-5666-7088", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e0ba3a91cf9b4039a83e915d1698e581.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Genome Res", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "29", "issue": "12", "pages": "1974-1984"}, "abstract": "Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site (TSS) usage, chromatin organization, and posttranscriptional consequences in Saccharomyces cerevisiae We show that TSSs of chromatin-sensitive internal cryptic transcripts retain comparable features of canonical TSSs in terms of DNA sequence, directionality, and chromatin accessibility. We define the 5' and 3' boundaries of cryptic transcripts and show that, contrary to RNA degradation-sensitive ones, they often overlap with the end of the gene, thereby using the canonical polyadenylation site, and associate to polyribosomes. We show that chromatin-sensitive cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Finally, we confirm the presence of the predicted polypeptides by reanalyzing N-terminal proteomic data sets. Our work suggests that a fraction of chromatin-sensitive internal cryptic promoters initiates the transcription of alternative truncated mRNA isoforms. The expression of these chromatin-sensitive isoforms is conserved from yeast to human, expanding the functional consequences of cryptic transcription and proteome complexity.", "doi": "10.1101/gr.243378.118", "pmid": "31740578", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "gr.243378.118"}, {"db": "pmc", "key": "PMC6886497"}], "notes": [], "created": "2020-11-08T15:49:22.722Z", "modified": "2022-11-04T11:32:15.727Z"}]}