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Structural Analysis of the Key Intermediate Formed during Transcription through a Nucleosome.

ABSTRACT: Transcription through chromatin by different RNA polymerases produces different biological outcomes and is accompanied by either nucleosome survival at the original location (Pol II-type mechanism) or backward nucleosome translocation along DNA (Pol III-type mechanism). It has been proposed that differences in the structure of the key intermediates formed during transcription dictate the fate of the nucleosomes. To evaluate this possibility, structure of the key intermediate formed during transcription by Pol III-type mechanism was studied by DNase I footprinting and molecular modeling. The Pol III-type mechanism is characterized by less efficient formation of the key intermediate required for nucleosome survival (Ø-loop, Pol II-type mechanism), most likely due to steric interference between the RNA polymerase and DNA in the Ø-loop. The data suggest that the lower efficiency of Ø-loop formation induces formation of a lower nucleosomal barrier and nucleosome translocation during transcription by Pol III-type mechanism.

SUBMITTER: Chang HW

PROVIDER: S-EPMC4214391 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Structural Analysis of the Key Intermediate Formed during Transcription through a Nucleosome.

Chang H-W HW Shaytan A K AK Hsieh F-K FK Kulaeva O I OI Kirpichnikov M P MP Studitsky V M VM

Trends in cell & molecular biology 20130101

Transcription through chromatin by different RNA polymerases produces different biological outcomes and is accompanied by either nucleosome survival at the original location (Pol II-type mechanism) or backward nucleosome translocation along DNA (Pol III-type mechanism). It has been proposed that differences in the structure of the key intermediates formed during transcription dictate the fate of the nucleosomes. To evaluate this possibility, structure of the key intermediate formed during transc ...[more]

PMID: 25364155

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Project description:The reduction of nitrite by deoxygenated hemoglobin chains has been implicated in red cell-induced vasodilation, although the mechanism for this process has not been established. We have previously demonstrated that the reaction of nitrite with deoxyhemoglobin produces a hybrid intermediate with properties of Hb(II)NO(+) and Hb(III)NO that builds up during the reaction retaining potential NO bioactivity. To explain the unexpected stability of this intermediate, which prevents NO release from the Hb(III)NO component, we had implicated the transfer of an electron from the β-93 thiol to NO(+) producing ·SHb(II)NO. To determine if this species is formed and to characterize its properties, we have investigated the electron paramagnetic resonance (EPR) changes taking place during the nitrite reaction. The EPR effects of blocking the thiol group with N-ethyl-maleimide and using carboxypeptidase-A to stabilize the R-quaternary conformation have demonstrated that ·SHb(II)NO is formed and that it has the EPR spectrum expected for NO bound to the heme in the β-chain plus that of a thiyl radical. This new NO-related paramagnetic species is in equilibrium with the hybrid intermediate "Hb(II)NO(+) ↔ Hb(III)NO", thereby further inhibiting the release of NO from Hb(III)NO. The formation of an NO-related paramagnetic species other than the tightly bound NO in Hb(II)NO was also confirmed by a decrease in the EPR signal by -20 °C incubation, which shifts the equilibrium back to the "Hb(II)NO(+) ↔ Hb(III)NO" intermediate. This previously unrecognized NO hemoglobin species explains the stability of the intermediates and the buildup of a pool of potentially bioactive NO during nitrite reduction. It also provides a pathway for the formation of β-93 cysteine S-nitrosylated hemoglobin [SNOHb:S-nitrosohemoglobin], which has been shown to induce vasodilation, by a rapid radical-radical reaction of any free NO with the thiyl radical of this new paramagnetic intermediate.

Dataset Information

Structural Analysis of the Key Intermediate Formed during Transcription through a Nucleosome.

Publications

Structural Analysis of the Key Intermediate Formed during Transcription through a Nucleosome.

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