Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III inStaphylococcus aureus

AbstractBackgroundMitogenome diversity is staggering among early branching animals with respect to size, gene density and content, gene orders, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals.ResultsWe characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5’ and/or 3’ untranslated regions (UTRs) of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, mtMutS, was found to undergo alternative polyadenylation (APA), and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected.ConclusionsMt-mRNA processing in octocorals bearing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represents a first step towards understanding its functional and evolutionary implications.

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Antisense regulation by transposon‐derived RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus

EMBO Reports ◽

10.1038/embor.2013.47 ◽

2013 ◽

Vol 14 (6) ◽

pp. 527-533 ◽

Cited By ~ 18

Author(s):

Birgit Märtens ◽

Salim Manoharadas ◽

David Hasenöhrl ◽

Andrea Manica ◽

Udo Bläsi

Keyword(s):

Sulfolobus Solfataricus ◽

Hyperthermophilic Archaeon ◽

Antisense Regulation

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Regulation of antisense RNA expression during cardiac MHC gene switching in response to pressure overload

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.01111.2005 ◽

2006 ◽

Vol 290 (6) ◽

pp. H2351-H2361 ◽

Cited By ~ 39

Author(s):

F. Haddad ◽

A. X. Qin ◽

P. W. Bodell ◽

L. Y. Zhang ◽

H. Guo ◽

...

Keyword(s):

Gene Expression ◽

Left Ventricle ◽

Mrna Expression ◽

Antisense Rna ◽

Pressure Overload ◽

Antisense Transcription ◽

Regulatory Sequences ◽

Rna Regulation ◽

Regulation Scheme ◽

Antisense Regulation

Hypertension has been shown to cause cardiac hypertrophy and a shift in myosin heavy chain (MHC) gene expression from the faster α- to slower β-MHC isoform. The expression of the β- and α-MHC pre-mRNAs, mRNAs, as well as the newly discovered antisense β-RNA were analyzed in three regions of the normal control (NC) and 12-day pressure-overloaded (AbCon) hearts: the left ventricle apex, left ventricle base, and the septum. The RNA analyses in the AbCon heart targeted both the 5′ and the 3′ ends of each RNA molecule. β-MHC mRNA expression significantly increased relative to control in all three regions, regardless of the target site (5′ or 3′ end). In contrast, β-MHC pre-mRNA expression in the AbCon heart depended on the site of the measurement (5′ vs. 3′ end). For example, whereas the pre-mRNA did not change when targeted at the 3′ end (last intron), it increased significantly in the AbCon heart when measurement targeted the 5′ end (2nd intron) of the 25-kb molecule. Analyses of the antisense β-RNA revealed that its expression in the AbCon heart was significantly decreased relative to control regardless of its measurement site. A negative correlation was observed between the β-mRNA expression and the antisense β-RNA ( P < 0.05), suggesting an inhibitory role of antisense RNA on the sense β-MHC gene expression. In contrast, a positive correlation was observed between the antisense β-RNA and the α-MHC pre-mRNA ( P < 0.05). This latter observation along with the α-MHC gene position relative to that of the β-antisense suggest that the α-MHC sense and β-antisense transcription are coregulated likely via common intergenic regulatory sequences. Our results suggest that the increased β-MHC expression in the AbCon heart not only is the result of increased β-MHC transcription but also involves an antisense β-RNA regulation scheme. Although the exact mechanism concerning antisense regulation is not clear, it could involve modulation of both transcriptional activity of the β-MHC gene and posttranscriptional processing.

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Antisense regulation of human gene MAP3K13: True phenomenon or artifact?

Molecular Biology ◽

10.1134/s0026893308040055 ◽

2008 ◽

Vol 42 (4) ◽

pp. 514-520

Author(s):

A. V. Marakhonov ◽

A. V. Baranova ◽

M. Yu. Skoblov

Keyword(s):

Human Gene ◽

Antisense Regulation

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Photodynamic antisense regulation using psoralen-conjugated oligo(nucleoside phosphorothioate)s (I). Growth regulation of cervical carcinoma cells

Nucleic Acids Symposium Series ◽

10.1093/nass/42.1.223 ◽

1999 ◽

Vol 42 (1) ◽

pp. 223-224 ◽

Cited By ~ 1

Author(s):

R. Iwase ◽

A. Yamayoshi ◽

J.-i. Nishida ◽

T. Yamaoka ◽

N. Wake ◽

...

Keyword(s):

Cervical Carcinoma ◽

Growth Regulation ◽

Carcinoma Cells ◽

Antisense Regulation

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MicC, a Second Small-RNA Regulator of Omp Protein Expression in Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.186.20.6689-6697.2004 ◽

2004 ◽

Vol 186 (20) ◽

pp. 6689-6697 ◽

Cited By ~ 166

Author(s):

Shuo Chen ◽

Aixia Zhang ◽

Lawrence B. Blyn ◽

Gisela Storz

Keyword(s):

Escherichia Coli ◽

Small Rna ◽

Two Component System ◽

Base Pairs ◽

Protein Ratio ◽

Protein Levels ◽

Antisense Regulation ◽

Rna Genes ◽

Rna Transcript

ABSTRACT In a previous bioinformatics-based search for novel small-RNA genes encoded by the Escherichia coli genome, we identified a region, IS063, located between the ompN and ydbK genes, that encodes an ∼100-nucleotide small-RNA transcript. Here we show that the expression of this small RNA is increased at a low temperature and in minimal medium. Twenty-two nucleotides at the 5′ end of this transcript have the potential to form base pairs with the leader sequence of the mRNA encoding the outer membrane protein OmpC. The deletion of IS063 increased the expression of an ompC-luc translational fusion 1.5- to 2-fold, and a 10-fold overexpression of the small RNA led to a 2- to 3-fold repression of the fusion. Deletion and overexpression of the IS063 RNA also resulted in increases and decreases, respectively, in OmpC protein levels. Taken together, these results suggest that IS063 is a regulator of OmpC expression; thus, the small RNA has been renamed MicC. The antisense regulation was further demonstrated by the finding that micC mutations were suppressed by compensatory mutations in the ompC mRNA. MicC was also shown to inhibit ribosome binding to the ompC mRNA leader in vitro and to require the Hfq RNA chaperone for its function. We suggest that the MicF and MicC RNAs act in conjunction with the EnvZ-OmpR two-component system to control the OmpF/OmpC protein ratio in response to a variety of environmental stimuli.

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