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Biological functions of natural antisense transcripts

100%
Rosikiewicz W., Makałowska I.
Acta Biochimica Polonica
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2016
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vol. 63
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issue 4
665-673
EN
Natural antisense transcripts (NATs) are RNA molecules that originate from opposite DNA strands of the same genomic locus (cis-NAT) or unlinked genomic loci (trans-NAT). NATs may play various regulatory functions at the transcriptional level via transcriptional interference. NATs may also regulate gene expression levels post-transcriptionally via induction of epigenetic changes or double-stranded RNA formation, which may lead to endogenous RNA interference, RNA editing or RNA masking. The true biological significance of the natural antisense transcripts remains controversial despite many years of research. Here, we summarize the current state of knowledge and discuss the sense-antisense overlap regulatory mechanisms and their potential.
2
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Retroposition as a source of antisense long non-coding RNAs with possible regulatory functions

81%
Bryzghalov O., Szcześniak M., Makałowska I.
Acta Biochimica Polonica
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2016
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vol. 63
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issue 4
825-833
EN
Long non-coding RNAs (lncRNAs) are a class of intensely studied, yet enigmatic molecules that make up a substantial portion of the human transcriptome. In this work, we link the origins and functions of some lncRNAs to retroposition, a process resulting in the creation of intronless copies (retrocopies) of the so-called parental genes. We found 35 human retrocopies transcribed in antisense and giving rise to 58 lncRNA transcripts. These lncRNAs share sequence similarity with the corresponding parental genes but in the sense/antisense orientation, meaning they have the potential to interact with each other and to form RNA:RNA duplexes. We took a closer look at these duplexes and found that 10 of the lncRNAs might regulate parental gene expression and processing at the pre-mRNA and mRNA levels. Further analysis of the co-expression and expression correlation provided support for the existence of functional coupling between lncRNAs and their mate parental gene transcripts.
3
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Ewolucja struktury genów

81%
Makałowska I., Kabza M., Ciomborowska J.
Kosmos
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2009
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vol. 58
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issue 1-2
5-16
EN
With the growing number of sequenced genomes comparative studies of lineage specific genomic features become both very rewarding and challenging. Large scale multiple genomes analyses allow to decipher many genomic features. They show that main differences between related species concern not as much the number of genes or the presence of species specific genes as the differences in the gene structure organization. Although much has been learned about gene structure evolution many problems remain unsolved. Alternative splicing is one of the main mechanisms leading to the proteome diversification. The raise of new splice variants is strictly connected with the exon and intron loss and gain. Main mechanisms of how the new exons originate are known, but question which of them, if any, plays the main role remains open. Another unsolved mystery is the intron origination. The dispute between "intro-early" and "intron-late" hypotheses supporters leads us to many interesting findings but the problem remains unsolved. One of the most fascinating discoveries in the genome studies is the role of so called 'junk DNA' in the evolution of human and other vertebrates. Repetitive elements and retrogenes are one of the most important elements in the gene structure evolution. They provide signals, motifs and coding sequences for new exons, splice sites or regulatory elements. Another phenomenon discovered in the process of whole genomes analyses is the common presence of overlapping genes and, at the same time, their low conservation level.
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