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MicroRNA expression profiling of the porcine developing hypothalamus and pituitary tissue.

Zhang L, Cai Z, Wei S, Zhou H, Zhou H, Jiang X, Xu N - Int J Mol Sci (2013)

Bottom Line: The 37 differentially expressed miRNAs in hypothalamus represented 6 different expression patterns, while the 30 differentially expressed miRNAs in pituitary represented 7 different expression patterns.The current functional analysis showed that the differentially expressed miRNAs in hypothalamus and pituitary shared many biological processes, with the main differences being found in tissue-specific processes including: CDP-diacylglycerol biosynthetic/metabolic process; phosphatidic acid biosynthetic/metabolic process; energy reserve metabolic process for hypothalamus; adult behavior; sterol transport/homeostasis; and cholesterol/reverse cholesterol transport for pituitary.Overall, this study identified miRNA profiles and differentially expressed miRNAs among various developmental stages in hypothalamus and pituitary and indicated miRNA profiles change with age and brain location, enhancing our knowledge about spatial and temporal expressions of miRNAs in the porcine developing brain.

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science, Zhejiang University, Hangzhou 310058, China. nyxu@zju.edu.cn.

ABSTRACT
MicroRNAs (miRNAs), a class of small non-coding RNA molecules, play important roles in gene expressions at transcriptional and post-transcriptional stages in mammalian brain. So far, a growing number of porcine miRNAs and their function have been identified, but little is known regarding the porcine developing hypothalamus and pituitary. In the present study, Solexa sequencing analysis showed 14,129,397 yielded reads, 6,680,678 of which were related to 674 unique miRNAs. After a microarray assay, we detected 175 unique miRNAs in the hypothalamus, including 136 previously known miRNAs and 39 novel candidates, while a total of 140 miRNAs, including 104 known and 36 new candidate miRNAs, were discovered in pituitary. More importantly, 37 and 30 differentially expressed miRNAs from several developmental stages of hypothalamus and pituitary were revealed, respectively. The 37 differentially expressed miRNAs in hypothalamus represented 6 different expression patterns, while the 30 differentially expressed miRNAs in pituitary represented 7 different expression patterns. To clarify potential target genes and specific functions of these differentially expressed miRNAs in hypothalamus and pituitary, TargetScan and Gorilla prediction tools were then applied. The current functional analysis showed that the differentially expressed miRNAs in hypothalamus and pituitary shared many biological processes, with the main differences being found in tissue-specific processes including: CDP-diacylglycerol biosynthetic/metabolic process; phosphatidic acid biosynthetic/metabolic process; energy reserve metabolic process for hypothalamus; adult behavior; sterol transport/homeostasis; and cholesterol/reverse cholesterol transport for pituitary. Overall, this study identified miRNA profiles and differentially expressed miRNAs among various developmental stages in hypothalamus and pituitary and indicated miRNA profiles change with age and brain location, enhancing our knowledge about spatial and temporal expressions of miRNAs in the porcine developing brain.

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The chart of sequencing data analysis through various filters and the number of miRNAs detected.
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f1-ijms-14-20326: The chart of sequencing data analysis through various filters and the number of miRNAs detected.

Mentions: A small RNA library was constructed using pooled RNA of hypothalamus and pituitary, followed by Solexa sequencing to discover new miRNA candidates. As shown in Figure 1, a total of 14,129,397 reads were obtained from our small RNA library. In addition, 6,646,023 reads with simple sequences, the length of sequences <15 nt or >26 nt, junk sequences, or sequences <3 copies were observed. After excluding the reads described above, the remaining 7,483,374 reads were compared with Hit mRNA, RFam and Repbase to remove possible mRNA, rRNA, tRNA, snRNA, snoRNA and repeat sequences. Finally, 6,680,678 reads with different length distribution (Figure S1) were held for miRNA identification.


MicroRNA expression profiling of the porcine developing hypothalamus and pituitary tissue.

Zhang L, Cai Z, Wei S, Zhou H, Zhou H, Jiang X, Xu N - Int J Mol Sci (2013)

The chart of sequencing data analysis through various filters and the number of miRNAs detected.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3821617&req=5

f1-ijms-14-20326: The chart of sequencing data analysis through various filters and the number of miRNAs detected.
Mentions: A small RNA library was constructed using pooled RNA of hypothalamus and pituitary, followed by Solexa sequencing to discover new miRNA candidates. As shown in Figure 1, a total of 14,129,397 reads were obtained from our small RNA library. In addition, 6,646,023 reads with simple sequences, the length of sequences <15 nt or >26 nt, junk sequences, or sequences <3 copies were observed. After excluding the reads described above, the remaining 7,483,374 reads were compared with Hit mRNA, RFam and Repbase to remove possible mRNA, rRNA, tRNA, snRNA, snoRNA and repeat sequences. Finally, 6,680,678 reads with different length distribution (Figure S1) were held for miRNA identification.

Bottom Line: The 37 differentially expressed miRNAs in hypothalamus represented 6 different expression patterns, while the 30 differentially expressed miRNAs in pituitary represented 7 different expression patterns.The current functional analysis showed that the differentially expressed miRNAs in hypothalamus and pituitary shared many biological processes, with the main differences being found in tissue-specific processes including: CDP-diacylglycerol biosynthetic/metabolic process; phosphatidic acid biosynthetic/metabolic process; energy reserve metabolic process for hypothalamus; adult behavior; sterol transport/homeostasis; and cholesterol/reverse cholesterol transport for pituitary.Overall, this study identified miRNA profiles and differentially expressed miRNAs among various developmental stages in hypothalamus and pituitary and indicated miRNA profiles change with age and brain location, enhancing our knowledge about spatial and temporal expressions of miRNAs in the porcine developing brain.

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science, Zhejiang University, Hangzhou 310058, China. nyxu@zju.edu.cn.

ABSTRACT
MicroRNAs (miRNAs), a class of small non-coding RNA molecules, play important roles in gene expressions at transcriptional and post-transcriptional stages in mammalian brain. So far, a growing number of porcine miRNAs and their function have been identified, but little is known regarding the porcine developing hypothalamus and pituitary. In the present study, Solexa sequencing analysis showed 14,129,397 yielded reads, 6,680,678 of which were related to 674 unique miRNAs. After a microarray assay, we detected 175 unique miRNAs in the hypothalamus, including 136 previously known miRNAs and 39 novel candidates, while a total of 140 miRNAs, including 104 known and 36 new candidate miRNAs, were discovered in pituitary. More importantly, 37 and 30 differentially expressed miRNAs from several developmental stages of hypothalamus and pituitary were revealed, respectively. The 37 differentially expressed miRNAs in hypothalamus represented 6 different expression patterns, while the 30 differentially expressed miRNAs in pituitary represented 7 different expression patterns. To clarify potential target genes and specific functions of these differentially expressed miRNAs in hypothalamus and pituitary, TargetScan and Gorilla prediction tools were then applied. The current functional analysis showed that the differentially expressed miRNAs in hypothalamus and pituitary shared many biological processes, with the main differences being found in tissue-specific processes including: CDP-diacylglycerol biosynthetic/metabolic process; phosphatidic acid biosynthetic/metabolic process; energy reserve metabolic process for hypothalamus; adult behavior; sterol transport/homeostasis; and cholesterol/reverse cholesterol transport for pituitary. Overall, this study identified miRNA profiles and differentially expressed miRNAs among various developmental stages in hypothalamus and pituitary and indicated miRNA profiles change with age and brain location, enhancing our knowledge about spatial and temporal expressions of miRNAs in the porcine developing brain.

Show MeSH