H-W Chang, A K Shaytan, F-K Hsieh, O I Kulaeva, M P Kirpichnikov, V M Studitsky
{"title":"Structural Analysis of the Key Intermediate Formed during Transcription through a Nucleosome.","authors":"H-W Chang, A K Shaytan, F-K Hsieh, O I Kulaeva, M P Kirpichnikov, V M Studitsky","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":23241,"journal":{"name":"Trends in cell & molecular biology","volume":"8 ","pages":"13-23"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214391/pdf/nihms548583.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32786545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Valérie de Crécy-Lagard, Christian Marck, Henri Grosjean
{"title":"Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set?","authors":"Valérie de Crécy-Lagard, Christian Marck, Henri Grosjean","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A comparative genomic analysis of the recently sequenced human body louse unicellular endosymbiont Candidatus Riesia pediculicola with a reduced genome (582 Kb), revealed that it is the only known organism that might have lost all post-transcriptional base and ribose modifications of the tRNA body, retaining only modifications of the anticodon-stem-loop essential for mRNA decoding. Such a minimal tRNA modification set was not observed in other insect symbionts or in parasitic unicellular bacteria, such as Mycoplasma genitalium (580 Kb), that have also evolved by considerably reducing their genomes. This could be an example of a minimal tRNA modification set required for life, a question that has been at the center of the field for many years, especially for understanding the emergence and evolution of the genetic code.</p>","PeriodicalId":23241,"journal":{"name":"Trends in cell & molecular biology","volume":"7 ","pages":"11-34"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539174/pdf/nihms385606.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31154870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}