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Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III

The small nuclear RNAs 4.5SH and 4.5SI were characterized only in mouse-like rodents; their genes originate from 7SL RNA and tRNA, respectively. Similar to many genes transcribed by RNA polymerase III (pol III), the genes of 4.5SH and 4.5SI RNAs include boxes A and B, forming an intergenic pol III-d...

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Autores principales: Stasenko, Danil V., Tatosyan, Karina A., Borodulina, Olga R., Kramerov, Dmitri A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10137851/
https://www.ncbi.nlm.nih.gov/pubmed/37107560
http://dx.doi.org/10.3390/genes14040802
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author Stasenko, Danil V.
Tatosyan, Karina A.
Borodulina, Olga R.
Kramerov, Dmitri A.
author_facet Stasenko, Danil V.
Tatosyan, Karina A.
Borodulina, Olga R.
Kramerov, Dmitri A.
author_sort Stasenko, Danil V.
collection PubMed
description The small nuclear RNAs 4.5SH and 4.5SI were characterized only in mouse-like rodents; their genes originate from 7SL RNA and tRNA, respectively. Similar to many genes transcribed by RNA polymerase III (pol III), the genes of 4.5SH and 4.5SI RNAs include boxes A and B, forming an intergenic pol III-directed promoter. In addition, their 5′-flanking sequences have TATA-like boxes at position −31/−24, also required for efficient transcription. The patterns of the three boxes notably differ in the 4.5SH and 4.5SI RNA genes. The A, B, and TATA-like boxes were replaced in the 4.5SH RNA gene with the corresponding boxes in the 4.5SI RNA gene to evaluate their effect on the transcription of transfected constructs in HeLa cells. Simultaneous replacement of all three boxes decreased the transcription level by 40%, which indicates decreased promoter activity in a foreign gene. We developed a new approach to compare the promoter strength based on the competition of two co-transfected gene constructs when the proportion between the constructs modulates their relative activity. This method demonstrated that the promoter activity of 4.5SI is 12 times that of 4.5SH. Unexpectedly, the replacement of all three boxes of the weak 4.5SH promoter with those of the strong 4.5SI gene significantly reduced, rather than enhanced, the promoter activity. Thus, the strength of a pol III-directed promoter can depend on the nucleotide environment of the gene.
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spelling pubmed-101378512023-04-28 Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III Stasenko, Danil V. Tatosyan, Karina A. Borodulina, Olga R. Kramerov, Dmitri A. Genes (Basel) Article The small nuclear RNAs 4.5SH and 4.5SI were characterized only in mouse-like rodents; their genes originate from 7SL RNA and tRNA, respectively. Similar to many genes transcribed by RNA polymerase III (pol III), the genes of 4.5SH and 4.5SI RNAs include boxes A and B, forming an intergenic pol III-directed promoter. In addition, their 5′-flanking sequences have TATA-like boxes at position −31/−24, also required for efficient transcription. The patterns of the three boxes notably differ in the 4.5SH and 4.5SI RNA genes. The A, B, and TATA-like boxes were replaced in the 4.5SH RNA gene with the corresponding boxes in the 4.5SI RNA gene to evaluate their effect on the transcription of transfected constructs in HeLa cells. Simultaneous replacement of all three boxes decreased the transcription level by 40%, which indicates decreased promoter activity in a foreign gene. We developed a new approach to compare the promoter strength based on the competition of two co-transfected gene constructs when the proportion between the constructs modulates their relative activity. This method demonstrated that the promoter activity of 4.5SI is 12 times that of 4.5SH. Unexpectedly, the replacement of all three boxes of the weak 4.5SH promoter with those of the strong 4.5SI gene significantly reduced, rather than enhanced, the promoter activity. Thus, the strength of a pol III-directed promoter can depend on the nucleotide environment of the gene. MDPI 2023-03-27 /pmc/articles/PMC10137851/ /pubmed/37107560 http://dx.doi.org/10.3390/genes14040802 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Stasenko, Danil V.
Tatosyan, Karina A.
Borodulina, Olga R.
Kramerov, Dmitri A.
Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III
title Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III
title_full Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III
title_fullStr Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III
title_full_unstemmed Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III
title_short Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III
title_sort nucleotide context can modulate promoter strength in genes transcribed by rna polymerase iii
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10137851/
https://www.ncbi.nlm.nih.gov/pubmed/37107560
http://dx.doi.org/10.3390/genes14040802
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