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Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera.

Jayakodi M, Jung JW, Park D, Ahn YJ, Lee SC, Shin SY, Shin C, Yang TJ, Kwon HW - BMC Genomics (2015)

Bottom Line: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins.A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues.This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. murukarthick@snu.ac.kr.

ABSTRACT

Background: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases.

Results: In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses.

Conclusions: This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

No MeSH data available.


Related in: MedlinePlus

RT-PCR validation of lincRNAs in Asian honey bee (A. cerana) tissues. Twenty-two putative lincRNAs were selected for RT-PCR validation. Each primer set was used to perform RT-PCR on six RNA samples, including brain, antenna (Ant), hypoharyngeal gland (HG), gut, Fat body (FB), and venom gland (VG), and actin was used as a control to show amplification of cDNA samples
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Fig2: RT-PCR validation of lincRNAs in Asian honey bee (A. cerana) tissues. Twenty-two putative lincRNAs were selected for RT-PCR validation. Each primer set was used to perform RT-PCR on six RNA samples, including brain, antenna (Ant), hypoharyngeal gland (HG), gut, Fat body (FB), and venom gland (VG), and actin was used as a control to show amplification of cDNA samples

Mentions: The predicted lncRNAs were further filtered using the A. cerana genome annotation [41] to find those that were intergenic, yielding a total of 2470 lincRNAs from 2376 transcription loci (Fig. 1). From these, we selected 22 putative lincRNAs to validate their prediction and expression using RT-PCR. We used six tissues (antenna, brain, hypoharyngeal gland, gut, fat body, venom gland) for RT-PCR confirmation (Fig. 2) in A. cerana. The RT-PCR bands and tissue expression patterns were largely consistent with the RNA-seq data (Additional file 1: Table S1 (B). For example, we selected some lincRNAs based on expression in all analyzed tissues (Fig. 2 (Gel: AC_lincRNA.4118.1, AC_lincRNA.457.1) or specifically in 2 (Fig. 2 (Gel: AC_lincRNA.15188.1, AC_lincRNA.21243.1), 3 (Fig. 2 (Gel: AC_lincRNA.4523.1, AC_lincRNA.5679.1), or a single (Fig. 2 (Gel: AC_lincRNA.12705.1, AC_lincRNA.20163.1) tissue. Most of the lincRNAs exhibited tissue-specific expression, and many lincRNA were detected in brain, hypoharyngeal gland and fat body tissues (Fig. 2).Fig. 2


Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera.

Jayakodi M, Jung JW, Park D, Ahn YJ, Lee SC, Shin SY, Shin C, Yang TJ, Kwon HW - BMC Genomics (2015)

RT-PCR validation of lincRNAs in Asian honey bee (A. cerana) tissues. Twenty-two putative lincRNAs were selected for RT-PCR validation. Each primer set was used to perform RT-PCR on six RNA samples, including brain, antenna (Ant), hypoharyngeal gland (HG), gut, Fat body (FB), and venom gland (VG), and actin was used as a control to show amplification of cDNA samples
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4559890&req=5

Fig2: RT-PCR validation of lincRNAs in Asian honey bee (A. cerana) tissues. Twenty-two putative lincRNAs were selected for RT-PCR validation. Each primer set was used to perform RT-PCR on six RNA samples, including brain, antenna (Ant), hypoharyngeal gland (HG), gut, Fat body (FB), and venom gland (VG), and actin was used as a control to show amplification of cDNA samples
Mentions: The predicted lncRNAs were further filtered using the A. cerana genome annotation [41] to find those that were intergenic, yielding a total of 2470 lincRNAs from 2376 transcription loci (Fig. 1). From these, we selected 22 putative lincRNAs to validate their prediction and expression using RT-PCR. We used six tissues (antenna, brain, hypoharyngeal gland, gut, fat body, venom gland) for RT-PCR confirmation (Fig. 2) in A. cerana. The RT-PCR bands and tissue expression patterns were largely consistent with the RNA-seq data (Additional file 1: Table S1 (B). For example, we selected some lincRNAs based on expression in all analyzed tissues (Fig. 2 (Gel: AC_lincRNA.4118.1, AC_lincRNA.457.1) or specifically in 2 (Fig. 2 (Gel: AC_lincRNA.15188.1, AC_lincRNA.21243.1), 3 (Fig. 2 (Gel: AC_lincRNA.4523.1, AC_lincRNA.5679.1), or a single (Fig. 2 (Gel: AC_lincRNA.12705.1, AC_lincRNA.20163.1) tissue. Most of the lincRNAs exhibited tissue-specific expression, and many lincRNA were detected in brain, hypoharyngeal gland and fat body tissues (Fig. 2).Fig. 2

Bottom Line: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins.A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues.This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. murukarthick@snu.ac.kr.

ABSTRACT

Background: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases.

Results: In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses.

Conclusions: This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

No MeSH data available.


Related in: MedlinePlus