Publications by authors named "Irina A Il'icheva"
Article Synopsis
- * The study aims to identify the positions of intragenic and extragenic Pol III promoters regulating tRNA transcription by examining the DNA properties in the flanking regions of tRNA genes across different organisms, including eukaryotes and archaea.
- * Findings reveal that, while the consensus sequences of A- and B-boxes are similar across all organisms studied, the structural and mechanical properties of DNA in the flanking regions show significant variability both within
Article Synopsis
- - RNA polymerase II (POL II) plays a key role in transcribing both mRNAs and lncRNAs, with structural features of their core promoters showing similarities and differences.
- - Analysis of core promoters for lncRNAs reveals a complex 3D structure, including significant regions like the "INR" near the transcription start site (TSS) and the "TATA-box" further upstream.
- - Textual analysis indicates that lncRNA core promoters have higher informational entropy and a lower occurrence of consensus TATA box sequences compared to mRNA promoters, potentially affecting transcription efficiency.
Eukaryotic and archaeal RNA polymerase II (POL II) machinery is highly conserved, regardless of the extreme changes in promoter sequences in different organisms. The goal of our work is to find the cause of this conservatism. The representative sets of aligned promoter sequences of fifteen organisms belonging to different evolutional stages were studied.
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- DNA fragmentation during Next Generation Sequencing (NGS) preparation exhibits biased cleavage rates for different dinucleotides, with notable differences in methylated and unmethylated CpG dinucleotides.
- Analysis of the 1000 Genomes project revealed that methylated CpG dinucleotides have a significantly higher cleavage rate compared to unmethylated ones.
- A Support Vector Machine classifier was developed to differentiate between cancerous and healthy tissues based on their CpG island statuses, achieving an accuracy of 84% by using NGS sequencing data to identify epigenetic markers.
Article Synopsis
- - Nucleoside phosphorylases are important enzymes that break down nucleosides into bases and sugar phosphates, playing a key role in repairing nucleotides and potentially serving as cancer markers due to their elevated levels in tumors.
- - The review focuses on the structural analysis of nucleosides with nucleoside phosphorylases from the NP-1 family, showing that these nucleosides adopt unique conformations when bound to the enzymes, distinct from their free form.
- - These bound nucleosides are in energetically strained forms due to interactions with the enzyme, with specific ions in the active site affecting the shape of the sugars, highlighting how enzyme-substrate complexes are formed in this enzyme group.
Article Synopsis
- Eukaryotic and archaeal RNA polymerases show remarkable similarity in structure and function, despite different core promoter sequences across species, leading to a focus on understanding the common features that define Pol II promoters.
- Analysis of various physical and structural characteristics from minimal core promoters of diverse evolutionary species revealed unique properties, especially around the TATA-box region, indicating specific mechanical behaviors and differences among organisms.
- Findings highlight that while metazoan and Schizosaccharomyces pombe core promoters share structural similarities, yeast promoters are distinctly organized, with implications for genetic engineering applications related to promoter modulation.
Article Synopsis
- Next Generation Sequencing (NGS) involves cutting DNA into small fragments and then sequencing them in large amounts to create a complete genetic sequence.
- Sequencing errors are minimized by repeating the process several times, but previous studies indicated that some DNA break rates are influenced by the specific nucleotide sequences.
- This research found that DNA fragmentation caused by hydrodynamic forces also introduces a similar bias, suggesting that understanding these factors could help explain uneven coverage of genomic regions.
Article Synopsis
- * The intensity of cleavage at specific phosphodiester bonds varied based on the nucleotide sequence and their positions within the DNA fragment.
- * Our findings revealed that the cleavage rates were particularly enhanced for bonds after deoxycytidine, and this sequence-specific cleavage behavior can help identify important functional regions in the genome.