- EMDB-36252: RNA polymerase II elongation complex containing 40 bp upstream DN... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: EMDB / ID: EMD-36252
タイトル
RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome
マップデータ
試料
複合体: RNA polymerase II - nucleosome complex
複合体: RNA polymerase II
複合体: Histones
複合体: DNA
複合体: RNA
タンパク質・ペプチド: x 16種
DNA: x 2種
RNA: x 1種
リガンド: x 2種
キーワード
Transcription-DNA-RNA complex / RNAPII
機能・相同性
機能・相同性情報
regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / : / RPB4-RPB7 complex / inner kinetochore / pericentric heterochromatin formation / muscle cell differentiation / oocyte maturation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / : / RPB4-RPB7 complex / inner kinetochore / pericentric heterochromatin formation / muscle cell differentiation / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / : / nucleus organization / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / spermatid development / transcription initiation at RNA polymerase I promoter / pericentric heterochromatin / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / : / : / : / : / : / negative regulation of tumor necrosis factor-mediated signaling pathway / : / single fertilization / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II core promoter sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / Replacement of protamines by nucleosomes in the male pronucleus / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / 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 / translation initiation factor binding / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / embryo implantation / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / transcription elongation by RNA polymerase II / lipopolysaccharide binding / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / ribonucleoside binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / multicellular organism growth / Transcriptional regulation of granulopoiesis / DNA-directed RNA polymerase / UCH proteinases / HCMV Early Events / male gonad development / osteoblast differentiation 類似検索 - 分子機能
DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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 H4 / Histone H3.3 類似検索 - 構成要素
Japan Agency for Medical Research and Development (AMED)
JP22ama121009
日本
Japan Science and Technology
JPMJER1901
日本
引用
ジャーナル: J Biol Chem / 年: 2023 タイトル: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. 著者: Munetaka Akatsu / Haruhiko Ehara / Tomoya Kujirai / Risa Fujita / Tomoko Ito / Ken Osumi / Mitsuo Ogasawara / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka / 要旨: RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the ...RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.