{"entity": "researcher", "timestamp": "2026-04-13T05:58:48.160Z", "family": "Ard", "given": "Ryan", "initials": "R", "orcid": "0000-0002-9070-9747", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b7dd13a6df4e1aa77fced747dc0f2a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b7dd13a6df4e1aa77fced747dc0f2a"}}, "publications": [{"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": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16390-7"}, {"db": "pmc", "key": "PMC7244574"}], "notes": [], "created": "2020-11-08T15:50:38.178Z", "modified": "2022-11-04T11:32:14.968Z"}, {"entity": "publication", "iuid": "dd2ce89e67a9412a97fa4367a5fdc073", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dd2ce89e67a9412a97fa4367a5fdc073.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dd2ce89e67a9412a97fa4367a5fdc073"}}, "title": "Transcription-driven chromatin repression of Intragenic transcription start sites.", "authors": [{"family": "Nielsen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-2336-1146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4712573bdc943768cc289b977b74f35.json"}}, {"family": "Ard", "given": "Ryan", "initials": "R", "orcid": "0000-0002-9070-9747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b7dd13a6df4e1aa77fced747dc0f2a.json"}}, {"family": "Leng", "given": "Xueyuan", "initials": "X", "orcid": "0000-0003-1758-413X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a25df91a0dbd4cfdb2153413d594f0b6.json"}}, {"family": "Ivanov", "given": "Maxim", "initials": "M", "orcid": "0000-0001-7548-3316", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/118c370e68264073b11197ae6ecdc5ab.json"}}, {"family": "Kindgren", "given": "Peter", "initials": "P", "orcid": "0000-0003-0947-2648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4859124d29c242f080ed0b695e38d57c.json"}}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"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": "2019-02-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "15", "issue": "2", "pages": "e1007969"}, "abstract": "Progression of RNA polymerase II (RNAPII) transcription relies on the appropriately positioned activities of elongation factors. The resulting profile of factors and chromatin signatures along transcription units provides a \"positional information system\" for transcribing RNAPII. Here, we investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. This repression is characterized by reduced promoter-specific molecular signatures and increased molecular signatures associated with RNAPII elongation. The conserved FACT histone chaperone complex is required for this repression mechanism. Genome-wide Transcription Start Site (TSS) mapping reveals thousands of discrete intragenic TSS positions in fact mutants, including downstream promoters that initiate alternative transcript isoforms. We find that histone H3 lysine 4 mono-methylation (H3K4me1), an Arabidopsis RNAPII elongation signature, is enriched at FACT-repressed intragenic TSSs. Our analyses suggest that FACT is required to repress intragenic TSSs at positions that are in part characterized by elevated H3K4me1 levels. In sum, conserved and plant-specific chromatin features correlate with the co-transcriptional repression of intragenic TSSs. Our insights into TSS repression by RNAPII transcription promise to inform the regulation of alternative transcript isoforms and the characterization of gene regulation through the act of pervasive transcription across eukaryotic genomes.", "doi": "10.1371/journal.pgen.1007969", "pmid": "30707695", "labels": {"Vicent Pelechano": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-01434"}, {"db": "pmc", "key": "PMC6373976"}], "notes": [], "created": "2020-10-09T14:05:14.182Z", "modified": "2022-11-04T11:32:16.833Z"}]}