ArticleProceedings of the National Academy of Sciences of the United States of America2013
Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 42 citations in OpenAlex.
- Domain acquisition enabled functional expansion of the TFIIS transcription factor family.Cell & bioscience · 2025Review
- Two paralogous PHD finger proteins participate in natural genome editing in Paramecium tetraurelia.Journal of cell science · 2024Article
- Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes.Yeast (Chichester, England) · 2024Article
- The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.Nature communications · 2023Article
- A crucial role for dynamic expression of components encoding the negative arm of the circadian clock.Nature communications · 2023Article
- Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1.Current genetics · 2023Review
- SPOC domain proteins in health and disease.Genes & development · 2023Review
- The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.Nature communications · 2023Article
- The biological relevance of the FspTF transcription factor, homologous of Bqt4, inFrontiers in microbiology · 2023Article
- Dissecting and predicting different types of binding sites in nucleic acids based on structural information.Briefings in bioinformatics · 2022Article
- PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.Nature communications · 2021Article
- Contributions of methionine to recognition of trimethyllysine in aromatic cage of PHD domains: implications of polarizability, hydrophobicity, and charge on binding.Chemical science · 2021Article
- Interrogation of the cell wall integrity pathway inGene: X · 2020Article
- Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions.Epigenetics & chromatin · 2020Article
- BORDER proteins protect expression of neighboring genes by promoting 3' Pol II pausing in plants.Nature communications · 2019Article
- Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing.Nucleic acids research · 2019Article
- Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Multisubunit RNA Polymerase Cleavage Factors Modulate the Kinetics and Energetics of Nucleotide Incorporation: An RNA Polymerase I Case Study.Biochemistry · 2017Article
- A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO.Structure (London, England : 1993) · 2017Article
- Analysis of Histone Antibody Specificity with Peptide Microarrays.Journal of visualized experiments : JoVE · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 5 institutions in 4 countries.
Funding
Abstract
Bypass of Ess1 (Bye1) is a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. Here we show that Bye1 binds with its TFIIS-like domain (TLD) to RNA polymerase (Pol) II, and report crystal structures of the Bye1 TLD bound to Pol II and three different Pol II-nucleic acid complexes. Like TFIIS, Bye1 binds with its TLD to the Pol II jaw and funnel. In contrast to TFIIS, however, it neither alters the conformation nor the in vitro functions of Pol II. In vivo, Bye1 is recruited to chromatin via its TLD and occupies the 5'-region of active genes. A plant homeo domain (PHD) in Bye1 binds histone H3 tails with trimethylated lysine 4, and this interaction is enhanced by the presence of neighboring posttranslational modifications (PTMs) that mark active transcription and conversely is impaired by repressive PTMs. We identify putative human homologs of Bye1, the proteins PHD finger protein 3 and death-inducer obliterator, which are both implicated in cancer. These results establish Bye1 as the founding member of a unique family of chromatin transcription factors that link histones with active PTMs to transcribing Pol II.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.