{"entity": "researcher", "timestamp": "2026-10-10T11:28:51.071Z", "family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "affiliations": ["SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1"}}, "publications": [{"entity": "publication", "iuid": "9be1ae6123ae437e8fde8d91b37b6931", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9be1ae6123ae437e8fde8d91b37b6931.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9be1ae6123ae437e8fde8d91b37b6931"}}, "title": "OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.", "authors": [{"family": "Alekseenko", "given": "Alisa", "initials": "A", "orcid": "0000-0002-4269-4894", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85f8ac2ec1a54cf79e4b1fbfc8a44aaf.json"}}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.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": "2022-06-00", "journal": {"title": "NAR Genomics and Bioinformatics", "issn": "2631-9268", "volume": "4", "issue": "2", "pages": "lqac048", "issn-l": null}, "abstract": "Detection of low-frequency DNA variants (below 1%) is becoming increasingly important in biomedical research and clinical practice, but is challenging to do with standard sequencing approaches due to high error rates. The use of double-stranded unique molecular identifiers (dsUMIs) allows correction of errors by comparing reads arising from the same original DNA duplex. However, the implementation of such approaches is still challenging. Here, we present a novel method, one-pot dsUMI sequencing (OPUSeq), which allows incorporation of dsUMIs in the same reaction as the library PCR. This obviates the need for adapter pre-synthesis or additional enzymatic steps. OPUSeq can be incorporated into standard DNA library preparation approaches and coupled with hybridization target capture. We demonstrate successful error correction and detection of variants down to allele frequency of 0.01%. Using OPUSeq, we also show that the use of enzymatic fragmentation can lead to the appearance of spurious double-stranded variants, interfering with detection of variant fractions below 0.1%.", "doi": "10.1093/nargab/lqac048", "pmid": "35769342", "labels": {"SciLifeLab Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC9235115"}, {"db": "pii", "key": "lqac048"}], "notes": [], "created": "2022-11-25T19:21:46.596Z", "modified": "2026-09-23T13:33:02.090Z"}, {"entity": "publication", "iuid": "127ab2b4417f4ac0ace77e0f2c278dbc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/127ab2b4417f4ac0ace77e0f2c278dbc"}}, "title": "TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.", "authors": [{"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}}, {"family": "Marques", "given": "Sueli", "initials": "S", "orcid": "0000-0003-3368-4392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36fa155444764068a6515a6ec93a7a2e.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.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": "2020-10-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "48", "issue": "18", "pages": "e104"}, "abstract": "Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5' and 3' ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5' and 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.", "doi": "10.1093/nar/gkaa691", "pmid": "32816037", "labels": {"SciLifeLab Fellow": null, "Vicente Pelechano": null}, "xrefs": [{"db": "pii", "key": "5894951"}, {"db": "pmc", "key": "PMC7544212"}], "notes": [], "created": "2020-11-08T15:50:59.020Z", "modified": "2026-09-11T13:23:25.817Z"}, {"entity": "publication", "iuid": "aed3c1e3d03b42278b08c1b74653acde", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/aed3c1e3d03b42278b08c1b74653acde.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/aed3c1e3d03b42278b08c1b74653acde"}}, "title": "The RNA exosome shapes the expression of key protein-coding genes.", "authors": [{"family": "Wu", "given": "Mengjun", "initials": "M"}, {"family": "Karadoulama", "given": "Evdoxia", "initials": "E"}, {"family": "Lloret-Llinares", "given": "Marta", "initials": "M"}, {"family": "Rouviere", "given": "Jerome Olivier", "initials": "JO"}, {"family": "Vaagens\u00f8", "given": "Christian Skov", "initials": "CS"}, {"family": "Moravec", "given": "Martin", "initials": "M"}, {"family": "Li", "given": "Bingnan", "initials": "B"}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Wu", "given": "Guifen", "initials": "G"}, {"family": "Gockert", "given": "Maria", "initials": "M"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Jensen", "given": "Torben Heick", "initials": "TH", "orcid": "0000-0001-5127-1239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f63375fe0a24f95b0b6bb6674d7a3b1.json"}}, {"family": "Sandelin", "given": "Albin", "initials": "A", "orcid": "0000-0002-7109-7378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9618b5e69c14c6e9df631a8abfcd77c.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "48", "issue": "15", "pages": "8509-8528"}, "abstract": "The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify \u223c2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3' end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.", "doi": "10.1093/nar/gkaa594", "pmid": "32710631", "labels": {"SciLifeLab Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7470964"}, {"db": "pii", "key": "5876282"}], "notes": [], "created": "2020-11-08T15:50:45.945Z", "modified": "2026-09-23T11:52:38.080Z"}, {"entity": "publication", "iuid": "a80d534b3097447888f8c79c3323f9e7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a80d534b3097447888f8c79c3323f9e7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a80d534b3097447888f8c79c3323f9e7"}}, "title": "Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.", "authors": [{"family": "Thomas", "given": "Quentin Angelo", "initials": "QA", "orcid": "0000-0002-3522-5125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de6fa033a00e46d0b068dcdebd13a25e.json"}}, {"family": "Ard", "given": "Ryan", "initials": "R", "orcid": "0000-0002-9070-9747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b7dd13a6df4e1aa77fced747dc0f2a.json"}}, {"family": "Liu", "given": "Jinghan", "initials": "J", "orcid": "0000-0001-7816-4791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c1e737ce8d9491192727f16ede2e359.json"}}, {"family": "Li", "given": "Bingnan", "initials": "B"}, {"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}, {"family": "Marquardt", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-1709-2717", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c0e928664724466ad7e558bef348c86.json"}}], "type": "journal article", "published": "2020-05-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "2589"}, "abstract": "RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.", "doi": "10.1038/s41467-020-16390-7", "pmid": "32444691", "labels": {"SciLifeLab Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC7244574"}, {"db": "pii", "key": "10.1038/s41467-020-16390-7"}], "notes": [], "created": "2020-11-08T15:50:38.178Z", "modified": "2026-09-23T08:36:29.221Z"}, {"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": {"SciLifeLab Fellow": ""}, "xrefs": [{"db": "pmc", "key": "PMC6886497"}, {"db": "pii", "key": "gr.243378.118"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2020-11-08T15:49:22.722Z", "modified": "2026-09-23T13:44:15.227Z"}, {"entity": "publication", "iuid": "a2d40dfd2cfb4370ada520f89da4f85f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2d40dfd2cfb4370ada520f89da4f85f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2d40dfd2cfb4370ada520f89da4f85f"}}, "title": "Dissecting chronic myeloid leukaemia overlapping transcriptome with TIF-Seq2", "authors": [{"family": "Wang", "given": "Jingwen", "initials": "J", "orcid": "0000-0001-9688-8793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a565028feaf4adea7c9678710c9ade1.json"}}, {"family": "Li", "given": "Bingnan", "initials": "B", "orcid": "0000-0001-8143-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55e50e72ddd0473298d9b77d218a226c.json"}}, {"family": "Marques", "given": "Sueli", "initials": "S", "orcid": "0000-0003-3368-4392", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36fa155444764068a6515a6ec93a7a2e.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM", "orcid": "0000-0002-3962-2865", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19807fc4d94a44e088f35ef1e94e81ce.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.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": "2019-11-29", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/859488", "pmid": null, "labels": {"SciLifeLab Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:15:29.305Z", "modified": "2026-09-23T15:04:46.746Z"}, {"entity": "publication", "iuid": "6594895db8b1418ebaee5a295c155588", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6594895db8b1418ebaee5a295c155588.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6594895db8b1418ebaee5a295c155588"}}, "title": "Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination", "authors": [{"family": "Ard", "given": "Ryan", "initials": "R", "orcid": "0000-0002-9070-9747", "researcher": {"href": 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"initials": "S", "orcid": "0000-0003-1709-2717", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c0e928664724466ad7e558bef348c86.json"}}], "type": "posted-content", "published": "2019-10-28", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/805853", "pmid": null, "labels": {"SciLifeLab Fellow": ""}, "xrefs": [], "notes": [], "created": "2026-08-20T11:15:00.743Z", "modified": "2026-09-23T14:40:31.490Z"}, {"entity": "publication", "iuid": "e4de9798c17c4e53aa06f60b3c552dd5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e4de9798c17c4e53aa06f60b3c552dd5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e4de9798c17c4e53aa06f60b3c552dd5"}}, "title": "Chromatin-sensitive cryptic promoters encode alternative protein isoforms in yeast", "authors": [{"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": 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