Вирусная реклама как средство привлечения внимания к услугам организации

ВКР посвящена изучению вирусной рекламы как средства привлечения внимания к услугам организации. Автором был разработан комплекс необходимых рекламных продуктов и мероприятий для привлечения внимания к услугам магазина детских товаров нового сегмента целевой аудитории

High-throughput sequencing (HTS) data- and structure-based identification of mirtrons in <i>Arabidopsis</i> and rice.

<p>(A) A “match 5′ end” mirtron resided within the 15^th intron of AT3G60950.1. (B) A “match 3′ end” mirtron resided within the second intron of AT1G76680.1. (C) A “match both ends” mirtron resided within the first intron of AT4G27410.1. (D) A “match 5′ end” mirtron resided within the 5^th intron of LOC_Os04g09380.1. (E) A “match 3′ end” mirtron resided within the 13^th intron of LOC_Os09g04260.1. (F) A “match both ends” mirtron resided within the first intron of LOC_Os03g57750.2. For all the panels, the short reads perfectly mapped to the mirtron precursors along with their normalized read counts in RPM (reads per million) are shown (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s005" target="_blank">Table S1</a> for the small RNA HTS data sources and see “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#s3" target="_blank">Materials and Methods</a>” for read count normalization). The mature mirtrons with significantly higher expression levels compared to the coordinates on the other arms were highlighted in red color, and the coordinates were in blue. For the mirtron precursors generating mirtrons with indistinguishable expression levels on both arms, their mature mirtrons were highlighted in green color. The mature mirtrons and their coordinates were also indicated in the stem-loop structures of their precursors. The parenthesis-dot formed secondary structure expression along with the free energy, and the stem-loop structures were all predicted and generated by RNAshapes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163-Steffen1" target="_blank">[17]</a>.</p

Degradome sequencing data-based identification of the targets of the mature mirtrons in <i>Arabidopsis</i> and rice.

<p>For all the sub-figures (A to D), the first panels depict the degradome signals all along the target transcripts, and the other panels provide detailed views of the cleavage signals within the regions surrounding the target recognition sites (denoted by gray horizontal lines). The transcript IDs are shown in the first panels, and the mirtron IDs are listed in the other panels (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s007" target="_blank">Table S3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s008" target="_blank">S4</a> for the sequence information corresponding to the mirtron IDs). The <i>x</i> axes measure the positions of the signals along the transcripts, and the <i>y</i> axes measure the signal intensities based on normalized counts (in RPM, reads per million), allowing cross-library comparison. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s006" target="_blank">Table S2</a> for the degradome data sets used in this analysis.</p

Sequence characteristics of the mature mirtrons identified in <i>Arabidopsis</i> and rice.

<p>(A) Sequence length distribution patterns. (B) 5′ terminal nucleotide compositions. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s007" target="_blank">Table S3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s008" target="_blank">S4</a> for sequence information.</p

The use of high-throughput sequencing methods for plant microRNA research

<div><p>MicroRNA (miRNA) acts as a critical regulator of gene expression at post-transcriptional and occasionally transcriptional levels in plants. Identification of reliable miRNA genes, monitoring the procedures of transcription, processing and maturation of the miRNAs, quantification of the accumulation levels of the miRNAs in specific biological samples, and validation of miRNA–target interactions become the basis for thoroughly understanding of the miRNA-mediated regulatory networks and the underlying mechanisms. Great progresses have been achieved for sequencing technology. Based on the high degree of sequencing depth and coverage, the high-throughput sequencing (HTS, also called next-generation sequencing) technology provides unprecedentedly efficient way for genome-wide or transcriptome-wide studies. In this review, we will introduce several HTS platform-based methods useful for plant miRNA research, including RNA-seq (RNA sequencing), RNA-PET-seq (paired end tag sequencing of RNAs), sRNA-seq (small RNA sequencing), dsRNA-seq (double-stranded RNA sequencing), ssRNA-seq (single-stranded RNA sequencing) and degradome-seq (degradome sequencing). In particular, we will provide some special cases to illustrate the novel use of HTS methods for investigation of the processing modes of the miRNA precursors, identification of the RNA editing sites on miRNA precursors, mature miRNAs and target transcripts, re-examination of the current miRNA registries, and discovery of novel miRNA species and novel miRNA–target interactions. Summarily, we opinioned that integrative use of the above mentioned HTS methods could make the studies on miRNAs more efficient.</p></div

Examples of the chloroplast genes generating PASRs (promoter-associated small RNAs) or TASRs (terminus-associated small RNAs) dominantly in green organ (leaves) of <i>Arabidopsis</i>.

<p>(A) The PASR peak was identified on the sense strand of <i>ATCG00540</i> (encoding photosynthetic electron transfer A). The <i>x</i> axis measures the genomic positions surrounding the TSS (transcription start site, marked by a black vertical bar) of this gene. The <i>y</i> axis measures the abundance of the small RNAs perfectly mapped onto the genomic region surrounding the TSS, which is also applied to the other figure panels. (B) The PASR peak was identified on both strands of <i>ATCG01120</i> (chloroplast ribosomal protein S15). The <i>x</i> axis measures the genomic positions surrounding the TSS of this gene. (C) The TASR peak was identified on the sense strand of <i>ATCG00270</i> (photosystem II reaction center protein D). The <i>x</i> axis measures the genomic positions surrounding the transcription terminus (marked by a black vertical bar) of this gene.</p

Examples of paired PASR (promoter-associated small RNA) and TASR (terminus-associated small RNA) peaks potentially mediating site-specific DNA methylation, and analysis of their biogenesis and action pathways.

<p>Examples of paired PASR (promoter-associated small RNA) and TASR (terminus-associated small RNA) peaks potentially mediating site-specific DNA methylation, and analysis of their biogenesis and action pathways.</p

Examples of site-specific DNA methylation potentially mediated by PASRs (promoter-associated small RNAs) and TASRs (terminus-associated small RNAs) in <i>Arabidopsis</i>.

<p>(A) Site-specific DNA methylation signals were observed within the genomic region surrounding the TSS (transcription start site; marked by a vertical dashed line) of <i>AT1G53265</i>. Accordingly, abundant small RNAs (i.e. PASRs) were mapped onto this region. (B) Site-specific DNA methylation signals were detected within the genomic region surrounding the transcription terminus of <i>AT5G54700</i>. Accordingly, abundant small RNAs (i.e. TASRs) were mapped onto this region. <i>Arabidopsis</i> epigenome maps (neomorph.salk.edu/epigenome/epigenome.html) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0169212#pone.0169212.ref032" target="_blank">32</a>] were employed for this analysis.</p

TASRs (terminus-associated small RNAs) identified on both strands of <i>AT3G41762</i>, and small RNA (sRNA) and double-stranded RNA (dsRNA) high-throughput sequencing (HTS)-based evidences showing potential Argonaute (AGO) loading preference and biogenesis pathways of TASRs.

<p>(A) Total: Initially, four sRNA HTS data sets belonging to GEO (Gene Expression Omnibus; <a href="http://www.ncbi.nlm.nih.gov/geo" target="_blank">www.ncbi.nlm.nih.gov/geo</a>) accession ID GSE28591 were utilized to identify TASR peak near the transcription terminus (marked by a red vertical bar) of the gene. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0169212#pone.0169212.g001" target="_blank">Fig 1</a> for the analytical workflow. (B) AGO: Eight sRNA HTS data sets belonging to GSE28591 were divided into AGO1 data group (GSM707682, GSM707683, GSM707684 and GSM707685) and AGO4 data group (GSM707686, GSM707687, GSM707688 and GSM707689). To analyze the AGO loading preference of the TASRs, an accumulation level-based comparison was performed between the two AGO-associated sRNA HTS data groups. The higher accumulation levels of the TASRs were detected in the AGO4 data group, and were denoted by black lines. (C) RDR-, DCL-dependence: sRNA HTS data sets from different mutants (including <i>dcl</i> and <i>rdr</i> mutants) involved in sRNA biogenesis pathways were recruited for this analysis. Prominently repressed abundances of TASRs observed in specific mutants were denoted by black lines. (D) Pol IV-dependence: sRNA HTS data sets from two mutants (<i>nrpd1a</i> and <i>nrpd1b</i>, and <i>nrpd1a</i> was denoted by black lines) of RNA polymerase (Pol) IV were used to analyze the dependence of TASR biogenesis on Pol IV. For all the figure panels, the dsRNA sequencing read-covered regions (the positions were provided on the top right) were highlighted in semitransparent red (for sense strand) and green (for antisense strand) background color. For the detailed explanation of the HTS data sets, please refer to “Data sources” within the “Materials and Methods” section.</p

Sequence characteristics of the PASRs (promoter-associated small RNAs) and the TASRs (terminus-associated small RNAs).

<p>(A) Sequence length distribution of the PASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (B) Sequence length distribution of the PASRs identified on the antisense strands of the protein-coding genes of <i>Arabidopsis</i>. (C) Sequence length distribution of the TASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (D) Sequence length distribution of the TASRs identified on the antisense strands of the protein-coding genes of <i>Arabidopsis</i>. (E) 5’ terminal nucleotide compositions of the PASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (F) 5’ terminal nucleotide compositions of the PASRs identified on the antisense strands of the protein-coding genes of <i>Arabidopsis</i>. (G) 5’ terminal nucleotide compositions of the TASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (H) 5’ terminal nucleotide compositions of the antisense strands of the protein-coding genes of <i>Arabidopsis</i>.</p