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Cloning of the quail PIWI gene and characterization of PIWI binding to small RNAs.

Chen R, Chang G, Zhang Y, Dai A, Ma T, Li J, Zhai F, Hua D, Xia M, Chen G - PLoS ONE (2012)

Bottom Line: The present study cloned and analyzed the sequences of the PIWIL1 protein.Small RNAs showed a strong peak at 24-27 nt in the testicular RNA library, mapped primarily to repeat sequences and were similar to rasiRNAs.MicroRNAs (miRNAs) were abundant in the ovarian RNA library at a peak of 22 nt.

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, China.

ABSTRACT
The PIWI protein regulates gene expression at the epigenetic and post-transcriptional level with a variety of endogenous small non-coding RNAs. In poultry, the biological function of the PIWI protein and PIWI binding to small RNAs had not been determined. The present study cloned and analyzed the sequences of the PIWIL1 protein. We also characterized PIWIL1 binding to small RNAs from adult quail testis, where the PIWIL1 protein is specifically expressed. Small RNAs showed a strong peak at 24-27 nt in the testicular RNA library, mapped primarily to repeat sequences and were similar to rasiRNAs. MicroRNAs (miRNAs) were abundant in the ovarian RNA library at a peak of 22 nt.

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Related in: MedlinePlus

Properties of unannotated unique reads in the testis.A: Chromosomal distribution of exons (top), repeat sequences (middle) and unannotated unique reads (bottom). The number of bases in exons of Refseq genes and repeats are plotted as a percentage of overall chromosome length. The numbers of piRNAs are normalized to chromosome length and plotted. B: Density analysis of exons (red), repeat sequences (green) and unannotated unique reads (with the positive strand in blue and the negative strand in purple) along chromosome 16. The densities of exons and repeats were using a 50 kB window, scanning the genome in increments of 1000 bases. Unannotaed uniques densities were determined by calculating a moving average of reads in a 5 kB sliding window (100 base increments) along each chromosome. Only reads that map 1 to 5 times to the genome were used in density analysis.
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pone-0051724-g004: Properties of unannotated unique reads in the testis.A: Chromosomal distribution of exons (top), repeat sequences (middle) and unannotated unique reads (bottom). The number of bases in exons of Refseq genes and repeats are plotted as a percentage of overall chromosome length. The numbers of piRNAs are normalized to chromosome length and plotted. B: Density analysis of exons (red), repeat sequences (green) and unannotated unique reads (with the positive strand in blue and the negative strand in purple) along chromosome 16. The densities of exons and repeats were using a 50 kB window, scanning the genome in increments of 1000 bases. Unannotaed uniques densities were determined by calculating a moving average of reads in a 5 kB sliding window (100 base increments) along each chromosome. Only reads that map 1 to 5 times to the genome were used in density analysis.

Mentions: An examination of the unannotated unique reads that mapped to 1–5 discrete loci revealed a non-uniform distribution in the genome (Figures 4A, S3, and S4). Unannotated unique reads were primarily found in chromosome W, followed by chromosomes Z and 16, which is consistent with the distribution of the repeat sequences. The majority of the coding sequences are concentrated in chromosome 16, and only a small number are found in chromosome Z. There are no coding sequences in chromosome W. We propose that the unannotated unique reads came primarily from repeat sequences followed by genic sequences. Correspondingly, the most unannotated unique reads were located in the repeat sequences on chromosome 16, and few unannotated unique reads were derived from chromosome 16 genes (Figure 4B). A detailed view revealed the distribution of unannotated unique reads along both strands of the genome, which differed from the single stranded-bias of piRNAs in mammals.


Cloning of the quail PIWI gene and characterization of PIWI binding to small RNAs.

Chen R, Chang G, Zhang Y, Dai A, Ma T, Li J, Zhai F, Hua D, Xia M, Chen G - PLoS ONE (2012)

Properties of unannotated unique reads in the testis.A: Chromosomal distribution of exons (top), repeat sequences (middle) and unannotated unique reads (bottom). The number of bases in exons of Refseq genes and repeats are plotted as a percentage of overall chromosome length. The numbers of piRNAs are normalized to chromosome length and plotted. B: Density analysis of exons (red), repeat sequences (green) and unannotated unique reads (with the positive strand in blue and the negative strand in purple) along chromosome 16. The densities of exons and repeats were using a 50 kB window, scanning the genome in increments of 1000 bases. Unannotaed uniques densities were determined by calculating a moving average of reads in a 5 kB sliding window (100 base increments) along each chromosome. Only reads that map 1 to 5 times to the genome were used in density analysis.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3526641&req=5

pone-0051724-g004: Properties of unannotated unique reads in the testis.A: Chromosomal distribution of exons (top), repeat sequences (middle) and unannotated unique reads (bottom). The number of bases in exons of Refseq genes and repeats are plotted as a percentage of overall chromosome length. The numbers of piRNAs are normalized to chromosome length and plotted. B: Density analysis of exons (red), repeat sequences (green) and unannotated unique reads (with the positive strand in blue and the negative strand in purple) along chromosome 16. The densities of exons and repeats were using a 50 kB window, scanning the genome in increments of 1000 bases. Unannotaed uniques densities were determined by calculating a moving average of reads in a 5 kB sliding window (100 base increments) along each chromosome. Only reads that map 1 to 5 times to the genome were used in density analysis.
Mentions: An examination of the unannotated unique reads that mapped to 1–5 discrete loci revealed a non-uniform distribution in the genome (Figures 4A, S3, and S4). Unannotated unique reads were primarily found in chromosome W, followed by chromosomes Z and 16, which is consistent with the distribution of the repeat sequences. The majority of the coding sequences are concentrated in chromosome 16, and only a small number are found in chromosome Z. There are no coding sequences in chromosome W. We propose that the unannotated unique reads came primarily from repeat sequences followed by genic sequences. Correspondingly, the most unannotated unique reads were located in the repeat sequences on chromosome 16, and few unannotated unique reads were derived from chromosome 16 genes (Figure 4B). A detailed view revealed the distribution of unannotated unique reads along both strands of the genome, which differed from the single stranded-bias of piRNAs in mammals.

Bottom Line: The present study cloned and analyzed the sequences of the PIWIL1 protein.Small RNAs showed a strong peak at 24-27 nt in the testicular RNA library, mapped primarily to repeat sequences and were similar to rasiRNAs.MicroRNAs (miRNAs) were abundant in the ovarian RNA library at a peak of 22 nt.

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, China.

ABSTRACT
The PIWI protein regulates gene expression at the epigenetic and post-transcriptional level with a variety of endogenous small non-coding RNAs. In poultry, the biological function of the PIWI protein and PIWI binding to small RNAs had not been determined. The present study cloned and analyzed the sequences of the PIWIL1 protein. We also characterized PIWIL1 binding to small RNAs from adult quail testis, where the PIWIL1 protein is specifically expressed. Small RNAs showed a strong peak at 24-27 nt in the testicular RNA library, mapped primarily to repeat sequences and were similar to rasiRNAs. MicroRNAs (miRNAs) were abundant in the ovarian RNA library at a peak of 22 nt.

Show MeSH
Related in: MedlinePlus