ArticlePLoS genetics2019
Transcription-driven chromatin repression of Intragenic transcription start sites.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 91 citations in OpenAlex.
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- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis.The Plant cell · 2024Article
- Arabidopsis transcription factor ANAC102 predominantly expresses a nuclear protein and acts as a negative regulator of methyl viologen-induced oxidative stress responses.Journal of experimental botany · 2024Article
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis.EMBO reports · 2024Article
- Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding.The Journal of biological chemistry · 2024Article
- Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis.Nucleic acids research · 2023Article
- Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants.Proteomes · 2023Review
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
- LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis.The EMBO journal · 2023Article
- Two isoforms of Arabidopsis protoporphyrinogen oxidase localize in different plastidal membranes.Plant physiology · 2023Article
- Cotranscriptional RNA processing and modification in plants.The Plant cell · 2023Review
- Review
- Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.The EMBO journal · 2023Article
- Translating across kingdoms: target of rapamycin promotes protein synthesis through conserved and divergent pathways in plants.Journal of experimental botany · 2022Review
- Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis.Nature communications · 2022Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.