- EMDB-34415: RNA polymerase II transcribing a chromatosome (type I) -
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Basic information
Entry
Database: EMDB / ID: EMD-34415
Title
RNA polymerase II transcribing a chromatosome (type I)
Map data
Sample
Complex: RNA polymerase II transcribing a chromatosome (type I)
Complex: RNA polymerase II
Protein or peptide: x 12 types
Complex: DNA,RNA
RNA: x 1 types
DNA: x 2 types
Complex: Histone
Protein or peptide: x 5 types
Ligand: x 2 types
Keywords
chromatin / nucleosome / TRANSCRIPTION
Function / homology
Function and homology information
regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of DNA recombination / RPB4-RPB7 complex / Apoptosis induced DNA fragmentation / chromosome condensation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of DNA recombination / RPB4-RPB7 complex / Apoptosis induced DNA fragmentation / chromosome condensation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / negative regulation of tumor necrosis factor-mediated signaling pathway / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / protein localization to CENP-A containing chromatin / RNA polymerase II, core complex / pericentric heterochromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / translation initiation factor binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / P-body / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / chromatin DNA binding / ribonucleoside binding / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / single-stranded DNA binding / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones Similarity search - Function
DNA-directed RNA polymerase subunit beta / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit ...DNA-directed RNA polymerase subunit beta / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / DNA-directed RNA polymerase subunit / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H1.2 / Histone H4 / Histone H3.1 Similarity search - Component
Japan Agency for Medical Research and Development (AMED)
JP22ama121009
Japan
Japan Science and Technology
JPMJER1901
Japan
Citation
Journal: Nat Commun / Year: 2022 Title: Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1. Authors: Rina Hirano / Haruhiko Ehara / Tomoya Kujirai / Tamami Uejima / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka / Abstract: In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in ...In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in the chromatosome has remained enigmatic. Here we report the cryo-electron microscopy (cryo-EM) structures of transcribing RNAPII-chromatosome complexes (forms I and II), in which RNAPII is paused at the entry linker DNA region of the chromatosome due to H1 binding. In the form I complex, the H1 bound to the nucleosome restricts the linker DNA orientation, and the exit linker DNA is captured by the RNAPII DNA binding cleft. In the form II complex, the RNAPII progresses a few bases ahead by releasing the exit linker DNA from the RNAPII cleft, and directly clashes with the H1 bound to the nucleosome. The transcription elongation factor Spt4/5 masks the RNAPII DNA binding region, and drastically reduces the H1-mediated RNAPII pausing.
Macromolecule #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
Macromolecule
Name: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
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