Integration of lncRNA–miRNA–mRNA reveals novel insights into oviposition regulation in honey bees

Background The honey bee (Apis mellifera) is a highly diverse species commonly used for honey production and pollination services. The oviposition of the honey bee queen affects the development and overall performance of the colony. To investigate the ovary activation and oviposition processes on a molecular level, a genome-wide analysis of lncRNAs, miRNAs and mRNA expression in the ovaries of the queens was performed to screen for differentially expressed coding and noncoding RNAs. Further analysis identified relevant candidate genes or RNAs. Results The analysis of the RNA profiles in different oviposition phase of the queens revealed that 740 lncRNAs, 81 miRNAs and 5,481 mRNAs were differently expressed during the ovary activation; 88 lncRNAs, 13 miRNAs and 338 mRNAs were differently expressed during the oviposition inhibition process; and finally, 100 lncRNAs, four miRNAs and 497 mRNAs were differently expressed during the oviposition recovery process. In addition, functional annotation of differentially expressed RNAs revealed several pathways that are closely related to oviposition, including hippo, MAPK, notch, Wnt, mTOR, TGF-beta and FoxO signaling pathways. Furthermore, in the QTL region for ovary size, 73 differentially expressed genes and 14 differentially expressed lncRNAs were located, which are considered as candidate genes affecting ovary size and oviposition. Moreover, a core set of genes served as bridges among different miRNAs were identified through the integrated analysis of lncRNA-miRNA-mRNA network. Conclusion The observed dramatic expression changes of coding and noncoding RNAs suggest that they may play a critical role in honey bee queens’ oviposition. The identified candidate genes for oviposition activation and regulation could serve as a resource for further studies of genetic markers of oviposition in honey bees.

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Integrated analysis of lncRNA, miRNA and mRNA profiles reveals potential lncRNA functions during early HIV infection

Journal of Translational Medicine ◽

10.1186/s12967-021-02802-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Lianwei Ma ◽

Hui Zhang ◽

Yue Zhang ◽

Hailong Li ◽

Minghui An ◽

...

Keyword(s):

Hiv Infection ◽

Immune Activation ◽

Expression Profiles ◽

Critical Role ◽

Differentially Expressed ◽

Integrated Analysis ◽

Target Mrnas ◽

Immunodeficiency Virus ◽

Mirna Sequencing ◽

Hiv 1

Abstract Background Long noncoding RNAs (lncRNAs) can regulate gene expression in a cis-regulatory fashion or as “microRNA sponges”. However, the expression and functions of lncRNAs during early human immunodeficiency virus (HIV) infection (EHI) remain unclear. Methods 3 HAART-naive EHI patients and 3 healthy controls (HCs) were recruited in this study to perform RNA sequencing and microRNA (miRNA) sequencing. The expression profiles of lncRNAs, mRNAs and miRNAs were obtained, and the potential roles of lncRNAs were analysed based on discovering lncRNA cis-regulatory target mRNAs and constructing lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) networks. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on 175 lncRNA-associated differentially expressed (DE) mRNAs to investigate the potential functions of DE lncRNAs in ceRNA networks. Results A total of 242 lncRNAs, 1240 mRNAs and 21 mature known miRNAs were determined as differentially expressed genes in HAART-naive EHI patients compared to HCs. Among DE lncRNAs, 44 lncRNAs were predicted to overlap with 41 target mRNAs, and 107 lncRNAs might regulate their nearby DE mRNAs. Two DE lncRNAs might regulate their cis-regulatory target mRNAs BTLA and ZAP70, respectively, which were associated with immune activation. In addition, the ceRNA networks comprised 160 DE lncRNAs, 21 DE miRNAs and 175 DE mRNAs. Seventeen DE lncRNAs were predicted to regulate HIF1A and TCF7L2, which are involved in the process of HIV-1 replication. Twenty DE lncRNAs might share miRNA response elements (MREs) with FOS, FOSB and JUN, which are associated with both immune activation and HIV-1 replication. Conclusions This study revealed that lncRNAs might play a critical role in HIV-1 replication and immune activation during EHI. These novel findings are helpful for understanding of the pathogenesis of HIV infection and provide new insights into antiviral therapy.

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Identification of long noncoding RNAs reveals the effects of dinotefuran on the brain in Apis mellifera (Hymenopptera: Apidae)

BMC Genomics ◽

10.1186/s12864-021-07811-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Minjie Huang ◽

Jie Dong ◽

Haikun Guo ◽

Minghui Xiao ◽

Deqian Wang

Keyword(s):

Immune Response ◽

Honey Bee ◽

Honey Bees ◽

Transforming Growth Factor ◽

Sublethal Effects ◽

Inflammatory Responses ◽

Noncoding Rnas ◽

Enrichment Analysis ◽

Long Noncoding Rnas ◽

Gene Set Enrichment Analysis

Abstract Background Dinotefuran (CAS No. 165252–70-0), a neonicotinoid insecticide, has been used to protect various crops against invertebrate pests and has been associated with numerous negative sublethal effects on honey bees. Long noncoding RNAs (lncRNAs) play important roles in mediating various biological and pathological processes, involving transcriptional and gene regulation. The effects of dinotefuran on lncRNA expression and lncRNA function in the honey bee brain are still obscure. Results Through RNA sequencing, a comprehensive analysis of lncRNAs and mRNAs was performed following exposure to 0.01 mg/L dinotefuran for 1, 5, and 10 d. In total, 312 lncRNAs and 1341 mRNAs, 347 lncRNAs and 1458 mRNAs, and 345 lncRNAs and 1155 mRNAs were found to be differentially expressed (DE) on days 1, 5 and 10, respectively. Gene set enrichment analysis (GSEA) indicated that the dinotefuran-treated group showed enrichment in carbohydrate and protein metabolism and immune-inflammatory responses such as glycine, serine and threonine metabolism, pentose and glucuronate interconversion, and Hippo and transforming growth factor-β (TGF-β) signaling pathways. Moreover, the DE lncRNA TCONS_00086519 was shown by fluorescence in situ hybridization (FISH) to be distributed mainly in the cytoplasm, suggesting that it may serve as a competing endogenous RNA and a regulatory factor in the immune response to dinotefuran. Conclusion This study characterized the expression profile of lncRNAs upon exposure to neonicotinoid insecticides in young adult honey bees and provided a framework for further study of the role of lncRNAs in honey bee growth and the immune response.

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Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma

International Journal of Genomics ◽

10.1155/2013/480534 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 22

Author(s):

Wei Cao ◽

Wei Wu ◽

Fachun Shi ◽

Xiaobing Chen ◽

Lihua Wu ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Noncoding Rna ◽

Cell Cancer ◽

Differentially Expressed ◽

Integrated Analysis ◽

Aberrant Expression ◽

A Genome

Tumorigenesis is a complex dynamic biological process that includes multiple steps of genetic and epigenetic alterations, aberrant expression of noncoding RNA, and changes in the expression profiles of coding genes. We call the collection of those perturbations in genome space the “cancer initiatome.” Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and they have key regulatory functions in chromatin remodeling and gene expression. Spatiotemporal variation in the expression of lncRNAs has been observed in development and disease states, including cancer. A few dysregulated lncRNAs have been studied in cancers, but the role of lncRNAs in the cancer initiatome remains largely unknown, especially in esophageal squamous cell carcinoma (ESCC). We conducted a genome-wide screen of the expression of lncRNAs and coding RNAs from ESCC and matched adjacent nonneoplastic normal tissues. We identified differentially expressed lncRNAs and coding RNAs in ESCC relative to their matched normal tissue counterparts and validated the result using polymerase chain reaction analysis. Furthermore, we identified differentially expressed lncRNAs that are co-located and co-expressed with differentially expressed coding RNAs in ESCC and the results point to a potential interaction between lncRNAs and neighboring coding genes that affect ether lipid metabolism, and the interaction may contribute to the development of ESCC. These data provide compelling evidence for a potential novel genomic biomarker of esophageal squamous cell cancer.

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Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

10.21203/rs.3.rs-25292/v1 ◽

2020 ◽

Author(s):

Tao Jiang ◽

Meide Zhang ◽

Chunxiu Wen ◽

Xiaoliang Xie ◽

Wei Tian ◽

...

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Regulatory Networks ◽

Anthocyanin Biosynthesis ◽

Salvia Miltiorrhiza ◽

Flower Color ◽

Differentially Expressed ◽

Integrated Analysis ◽

Anthocyanin Content ◽

Transcriptomics Data

Abstract Background: The study objectives were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis . Results: We analyzed the metabolomics and transcriptomics data of Salvia miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of Salvia miltiorrhiza . Integrated analysis of transcriptomic and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of Salvia miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in Salvia miltiorrhiza flowers. The low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in Salvia miltiorrhiza flowers. Conclusions: Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in Salvia miltiorrhiza .

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Reclassification of seven honey bee symbiont strains as Bombella apis

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004950 ◽

2021 ◽

Vol 71 (9) ◽

Author(s):

Eric A. Smith ◽

Kirk E. Anderson ◽

Vanessa Corby-Harris ◽

Quinn S. McFrederick ◽

Audrey J. Parish ◽

...

Keyword(s):

Honey Bee ◽

Honey Bees ◽

Type Species ◽

Phylogenetic Analyses ◽

Acetic Acid Bacterium ◽

Content Type ◽

Link Type ◽

Us Economy ◽

Genome Wide ◽

Honey Bee Queen

Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture’s most important pollinator. One factor that may influence colony health is the microbial community. Although honey bee worker guts have a characteristic community of bee-specific microbes, the honey bee queen digestive tracts are colonized predominantly by a single acetic acid bacterium tentatively named ‘Parasaccharibacter apium’. This bacterium is related to flower-associated microbes such as Saccharibacter floricola , and initial phylogenetic analyses placed it as sister to these environmental bacteria. We used a combination of phylogenetic and sequence identity methods to better resolve evolutionary relationships among ‘P. apium’, strains in the genus Saccharibacter , and strains in the closely related genus Bombella . Interestingly, measures of genome-wide average nucleotide identity and aligned fraction, coupled with phylogenetic placement, indicate that many strains labelled as ‘P. apium’ and Saccharibacter species are all the same species as Bombella apis . We propose reclassifying these strains as Bombella apis and outline the data supporting that classification below.

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Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

Scientific Reports ◽

10.1038/s41598-019-49548-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Kai Xing ◽

Kejun Wang ◽

Hong Ao ◽

Shaokang Chen ◽

Zhen Tan ◽

...

Keyword(s):

Candidate Genes ◽

Signaling Pathway ◽

Meat Quality ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Mapk Signaling ◽

Fat Deposition ◽

Differentially Expressed ◽

Integrated Analysis ◽

Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

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Effect of honey bee queen mating condition on worker ovary activation

Insectes Sociaux ◽

10.1007/s00040-012-0275-1 ◽

2012 ◽

Vol 60 (2) ◽

pp. 123-133 ◽

Cited By ~ 12

Author(s):

M. Peso ◽

E. L. Niño ◽

C. M. Grozinger ◽

A. B. Barron

Keyword(s):

Honey Bee ◽

Ovary Activation ◽

Honey Bee Queen

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Genomic signatures of honey bee association in an acetic acid symbiont

10.1101/367490 ◽

2018 ◽

Cited By ~ 1

Author(s):

Eric A. Smith ◽

Irene L. G. Newton

Keyword(s):

Acetic Acid ◽

Honey Bee ◽

Honey Bees ◽

Phylogenetic Analyses ◽

Acetic Acid Bacterium ◽

Genomic Changes ◽

Genomic Signatures ◽

Us Economy ◽

Honey Bee Queen ◽

Honey Bee Queens

AbstractHoney bee queens are central to the success and productivity of their colonies; queens are the only reproductive members of the colony, and therefore queen longevity and fecundity can directly impact overall colony health. Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture’s most important pollinator. Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. One factor that may influence queen and colony health is the microbial community. Although honey bee worker guts have a characteristic community of bee-specific microbes, the honey bee queen digestive tracts are colonized by a few bacteria, notably an acetic acid bacterium not seen in worker guts: Bombella apis. This bacterium is related to flower-associated microbes such as Saccharibacter floricola and other species in the genus Saccharibacter, and initial phylogenetic analyses placed it as sister to these environmental bacteria. We used comparative genomics of multiple honey bee-associated strains and the nectar-associated Saccharibacter to identify genomic changes associated with the ecological transition to bee association. We identified several genomic differences in the honey bee-associated strains, including a complete CRISPR/Cas system. Many of the changes we note here are predicted to confer upon them the ability to survive in royal jelly and defend themselves against mobile elements, including phages. Our results are a first step towards identifying potential benefits provided by the honey bee queen microbiota to the colony’s matriarch.

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Genome-Wide Association Studies and Transcriptome Changes during Acclimation and Deacclimation in Divergent Brassica napus Varieties

International Journal of Molecular Sciences ◽

10.3390/ijms21239148 ◽

2020 ◽

Vol 21 (23) ◽

pp. 9148 ◽

Cited By ~ 1

Author(s):

David P. Horvath ◽

Jiaping Zhang ◽

Wun S. Chao ◽

Ashok Mandal ◽

Mukhlesur Rahman ◽

...

Keyword(s):

Oxidative Stress ◽

Cold Acclimation ◽

Candidate Genes ◽

Calcium Binding ◽

Association Studies ◽

Differentially Expressed ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

A Genome

Information concerning genes and signals regulating cold acclimation processes in plants is abundant; however, less is known about genes and signals regulating the deacclimation process. A population of primarily winter B. napus varieties was used to conduct a genome-wide association study and to compare the transcriptomes from two winter B. napus varieties showing time-dependent differences in response to cold acclimation and deacclimation treatments. These studies helped to identify loci, candidate genes, and signaling processes impacting deacclimation in B. napus. GWAS identified polymorphisms at five different loci associated with freezing tolerance following deacclimation. Local linkage decay rates near these polymorphisms identified 38 possible candidate genes. Several of these genes have been reported as differentially regulated by cold stress in arabidopsis (Arabidopsis thaliana), including a calcium-binding EF-hand family protein (encoded by BnaCnng10250D) that was also differentially expressed during deacclimation in this study. Thousands of other genes differentially expressed during the acclimation and deacclimation treatments implicated processes involving oxidative stress, photosynthesis, light-regulated diurnal responses, and growth regulation. Generally, responses observed during acclimation were reversed within one week of deacclimation. The primary differences between the two winter B. napus varieties with differential deacclimation responses involved protection from oxidative stress and the ability to maintain photosynthesis.

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