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Down but Not Out: The Role of MicroRNAs in Hibernating Bats.

Yuan L, Geiser F, Lin B, Sun H, Chen J, Zhang S - PLoS ONE (2015)

Bottom Line: A total of 196 miRNAs (including 77 novel bat-specific miRNAs) were identified, and of these, 49 miRNAs showed significant differences in expression during hibernation, including 33 in the brain and 25 in WAT (P≤0.01 &│logFC│≥1).Putative target gene prediction combined with KEGG pathway and GO annotation showed that many essential processes of both organs are significantly correlated with differentially expressed miRNAs during bat hibernation.Thus, our novel findings of miRNAs and Interspersed Elements in a hibernating bat suggest that brain and WAT are active with respect to the miRNA expression activity during hibernation.

View Article: PubMed Central - PubMed

Affiliation: Guangdong Entomological Institute, Guangzhou, China; Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, China; Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangzhou, China.

ABSTRACT
MicroRNAs (miRNAs) regulate many physiological processes through post-transcriptional control of gene expression and are a major part of the small noncoding RNAs (snRNA). As hibernators can survive at low body temperatures (Tb) for many months without suffering tissue damage, understanding the mechanisms that enable them to do so are of medical interest. Because the brain integrates peripheral physiology and white adipose tissue (WAT) is the primary energy source during hibernation, we hypothesized that both of these organs play a crucial role in hibernation, and thus, their activity would be relatively increased during hibernation. We carried out the first genomic analysis of small RNAs, specifically miRNAs, in the brain and WAT of a hibernating bat (Myotis ricketti) by comparing deeply torpid with euthermic individual bats using high-throughput sequencing (Solexa) and qPCR validation of expression levels. A total of 196 miRNAs (including 77 novel bat-specific miRNAs) were identified, and of these, 49 miRNAs showed significant differences in expression during hibernation, including 33 in the brain and 25 in WAT (P≤0.01 &│logFC│≥1). Stem-loop qPCR confirmed the miRNA expression patterns identified by Solexa sequencing. Moreover, 31 miRNAs showed tissue- or state-specific expression, and six miRNAs with counts >100 were specifically expressed in the brain. Putative target gene prediction combined with KEGG pathway and GO annotation showed that many essential processes of both organs are significantly correlated with differentially expressed miRNAs during bat hibernation. This is especially evident with down-regulated miRNAs, indicating that many physiological pathways are altered during hibernation. Thus, our novel findings of miRNAs and Interspersed Elements in a hibernating bat suggest that brain and WAT are active with respect to the miRNA expression activity during hibernation.

No MeSH data available.


Related in: MedlinePlus

Illustration of genomic repeat-derived reads in four libraries.LINE, Long INterspersed Elements; SINE, Short INterspersed Elements; LTR, Transposable elements with Long Terminal Repeats; DNA, DNA transposons; SSR, Simple Sequence Repeats; Low, Low Complexity Sequences; unknown, derived from unannotated/intergenic regions.
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pone.0135064.g002: Illustration of genomic repeat-derived reads in four libraries.LINE, Long INterspersed Elements; SINE, Short INterspersed Elements; LTR, Transposable elements with Long Terminal Repeats; DNA, DNA transposons; SSR, Simple Sequence Repeats; Low, Low Complexity Sequences; unknown, derived from unannotated/intergenic regions.

Mentions: Less than 5% of total small RNA reads from the bat libraries perfectly matched the Myotis lucifugus genome >20 times (S4 Table); thus, we removed these unique reads to avoid self-contradiction of miRNA prediction. Therefore, a total of 3.16×107 remained after mapping the sequences to the M. lucifugus genome (Table 1 and S2 Fig). The size distribution of perfectly matched small RNA reads is shown in Fig 1A. We identified a total of 2.47×107 potential miRNA reads, including 159,807 distinct reads, by searching against miRBase and filtering the ncRNAs and low-expressing reads (S5 Table). Subsequently, 1.51×107 (47.7% in total) miRNA reads met the fold-back structure (hairpin) and MirCheck criteria, and miRNA reads were the most abundant fraction (range from 32.7% in HA to 55.6% in AB, Table 1 and Fig 1B). Other small RNAs, such as ncRNAs, genomic repeats, transcript repeats, and unknown genomic regions, comprised 20.4%, 2.3%, 2.8% and 26.8%, respectively (Table 1 and Fig 1B). Upon further inspection of genomic repeat-derived siRNAs, we determined that Short INterspersed Element (SINE) and Long INterspersed Element (LINE) were the major contributors to the four libraries (Table 1 and Fig 2).


Down but Not Out: The Role of MicroRNAs in Hibernating Bats.

Yuan L, Geiser F, Lin B, Sun H, Chen J, Zhang S - PLoS ONE (2015)

Illustration of genomic repeat-derived reads in four libraries.LINE, Long INterspersed Elements; SINE, Short INterspersed Elements; LTR, Transposable elements with Long Terminal Repeats; DNA, DNA transposons; SSR, Simple Sequence Repeats; Low, Low Complexity Sequences; unknown, derived from unannotated/intergenic regions.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4526555&req=5

pone.0135064.g002: Illustration of genomic repeat-derived reads in four libraries.LINE, Long INterspersed Elements; SINE, Short INterspersed Elements; LTR, Transposable elements with Long Terminal Repeats; DNA, DNA transposons; SSR, Simple Sequence Repeats; Low, Low Complexity Sequences; unknown, derived from unannotated/intergenic regions.
Mentions: Less than 5% of total small RNA reads from the bat libraries perfectly matched the Myotis lucifugus genome >20 times (S4 Table); thus, we removed these unique reads to avoid self-contradiction of miRNA prediction. Therefore, a total of 3.16×107 remained after mapping the sequences to the M. lucifugus genome (Table 1 and S2 Fig). The size distribution of perfectly matched small RNA reads is shown in Fig 1A. We identified a total of 2.47×107 potential miRNA reads, including 159,807 distinct reads, by searching against miRBase and filtering the ncRNAs and low-expressing reads (S5 Table). Subsequently, 1.51×107 (47.7% in total) miRNA reads met the fold-back structure (hairpin) and MirCheck criteria, and miRNA reads were the most abundant fraction (range from 32.7% in HA to 55.6% in AB, Table 1 and Fig 1B). Other small RNAs, such as ncRNAs, genomic repeats, transcript repeats, and unknown genomic regions, comprised 20.4%, 2.3%, 2.8% and 26.8%, respectively (Table 1 and Fig 1B). Upon further inspection of genomic repeat-derived siRNAs, we determined that Short INterspersed Element (SINE) and Long INterspersed Element (LINE) were the major contributors to the four libraries (Table 1 and Fig 2).

Bottom Line: A total of 196 miRNAs (including 77 novel bat-specific miRNAs) were identified, and of these, 49 miRNAs showed significant differences in expression during hibernation, including 33 in the brain and 25 in WAT (P≤0.01 &│logFC│≥1).Putative target gene prediction combined with KEGG pathway and GO annotation showed that many essential processes of both organs are significantly correlated with differentially expressed miRNAs during bat hibernation.Thus, our novel findings of miRNAs and Interspersed Elements in a hibernating bat suggest that brain and WAT are active with respect to the miRNA expression activity during hibernation.

View Article: PubMed Central - PubMed

Affiliation: Guangdong Entomological Institute, Guangzhou, China; Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, China; Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangzhou, China.

ABSTRACT
MicroRNAs (miRNAs) regulate many physiological processes through post-transcriptional control of gene expression and are a major part of the small noncoding RNAs (snRNA). As hibernators can survive at low body temperatures (Tb) for many months without suffering tissue damage, understanding the mechanisms that enable them to do so are of medical interest. Because the brain integrates peripheral physiology and white adipose tissue (WAT) is the primary energy source during hibernation, we hypothesized that both of these organs play a crucial role in hibernation, and thus, their activity would be relatively increased during hibernation. We carried out the first genomic analysis of small RNAs, specifically miRNAs, in the brain and WAT of a hibernating bat (Myotis ricketti) by comparing deeply torpid with euthermic individual bats using high-throughput sequencing (Solexa) and qPCR validation of expression levels. A total of 196 miRNAs (including 77 novel bat-specific miRNAs) were identified, and of these, 49 miRNAs showed significant differences in expression during hibernation, including 33 in the brain and 25 in WAT (P≤0.01 &│logFC│≥1). Stem-loop qPCR confirmed the miRNA expression patterns identified by Solexa sequencing. Moreover, 31 miRNAs showed tissue- or state-specific expression, and six miRNAs with counts >100 were specifically expressed in the brain. Putative target gene prediction combined with KEGG pathway and GO annotation showed that many essential processes of both organs are significantly correlated with differentially expressed miRNAs during bat hibernation. This is especially evident with down-regulated miRNAs, indicating that many physiological pathways are altered during hibernation. Thus, our novel findings of miRNAs and Interspersed Elements in a hibernating bat suggest that brain and WAT are active with respect to the miRNA expression activity during hibernation.

No MeSH data available.


Related in: MedlinePlus