DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA479740 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7472330.fastq.gz | Fastqsanger.gz | |||
| SRR7472340.fastq.gz | Fastqsanger.gz | |||
| SRR7472350.fastq.gz | Fastqsanger.gz | |||
| SRR7472360.fastq.gz | Fastqsanger.gz | |||
| SRR7472331.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 37 |
Similar Datasets
Project description:DNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of gene body methylation and its association with transcription and splicing in honey bee, an organism that targets methylation specifically to gene bodies. Our data show that gene body methylation globally fluctuates during honey bee development, with relatively high CG methylation in the embryo and adult stages and lower methylation in the larvae. We did not find a significant correlation between developmentally associated genic methylation dynamics and gene expression profiles. Furthermore, most developmentally regulated gene expression alterations occur in unmethylated genes. Tissue-specific methylation patterns, either at the level of complete genes or exons, are rare, implying robust maintenance of gene body methylation throughout the honeybee life cycle. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, we report a Dnmt3-associated non-CG methylation signal in the gene bodies of adult bee heads that resembles the methylation patterns of mammalian brain tissue. Based on these results, we suggest that honey bee DNA methylation is distinctly regulated in the soma and germline. In the germline, methylation is efficiently maintained to preserve methylation patterns across generations. In contrast, methylation can fluctuate in somatic cells with limited division potential, as long as overall methylation of exons and genes remains at an adequate functional level. Additionally, we propose that heightened non-CG methylation may be a conserved characteristic of animal nervous systems.
2019-10-01 | GSE116629 | GEO
Project description:BackgroundDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.ResultsOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.ConclusionsBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.
| S-EPMC6786280 | biostudies-literature
Project description:Honey bee colonies were maintained in an apiary at the University of British Columbia. During the summer of 2018, 40 queens were reared from a single colony and half were allowed to open mate, while the other half were kept as virgins in plastic queen cages. Two weeks after emergence, the virgin queens were given two, eight-minute carbon dioxide treatments on 2 sequential days, then re-introduced to their nucleus colonies. This process stimulates virgin queens to begin laying71, and we conducted these treatments in order to minimize the physiological differences between virgin and mated queens. Virgin and mated queens were retrieved from their nucleus colonies and half of each (10) were subjected to heat-shock (42 ͦC, 2 h), and then maintained at 30 ͦC for 2 d. The other half were held only at 30 ͦC for 2 d. Four to six weeks after mating, the queens were anesthetized with carbon dioxide, beheaded, then their spermathecae (including the tracheal net) were removed with fine forceps. Both ovaries were also removed and weighed. During the same summer, 200 drones from a different colony in the same apiary were collected and maintained in the laboratory overnight at ambient temperature with excess syrup (50% sucrose). The next day, semen was harvested with glass capillaries according to the methods described above. Because many drones were not sexually mature, 60 semen samples (out of the 200 drones) were collected. Capillaries were placed in petri dishes and half (30) were heat-shocked as described above, then kept at 25 ͦC for 2 d. The other half were only kept at 25 ͦC for 2 d. Ten samples from each experimental group were used for sperm viability assays as described above.
2019-07-19 | PXD013728 | Pride
Project description:Apis cerana, Apis florea, Apis dorsata, Apis mellifera, Trigona Genome sequencing and assembly
| PRJNA1127320 | ENA
Project description:Foragers facilitate horizontal pathogen transmission in honey bee colonies, yet their systemic immune function wanes during transition to this life stage. In general, the insect immune system can be categorized into mechanisms operating at both the barrier epithelial surfaces and at the systemic level. As proposed by the intergenerational transfer theory of aging, such immunosenescence may result from changes in group resource allocation. Yet, the relative influence of pathogen transmission and resource allocation on immune function in bees from different stages has not been examined in the context of barrier immunity. We find that expression levels of antimicrobial peptides (AMPs) in honey bee barrier epithelia of the digestive tract do not follow a life stage-dependent decrease. In addition, correlation of AMP transcript abundance with microbe levels reveals a number of microbe-associated changes in AMPs levels that are equivalent between nurses and foragers. These results favor a model in which barrier effectors are maintained in foragers as a first line of defense, while systemic immune effectors are dismantled to optimize hive-level resources. These findings have important implications for our understanding of immunosenescence in honey bees and other social insects.
| S-EPMC3540063 | biostudies-literature
Project description:Apis mellifera syriaca is the native honeybee subspecies of Jordan and much of the Middle East. It expresses behavioral adaptations to a regional climate with very high temperatures, nectar dearth in summer, attacks of the Oriental wasp Vespa orientalis and in most cases it is resistant to varroa mites. The Thorax control sample of A. m. syriaca in this experiment was originally collected and stored since 2001 from Wadi Ben Hammad a remote valley in the southern region of Jordan. Using morphometric and Mitochondrial DNA markers it was proved that bees from this area had show higher similarity than other samples collected from the Middle East as represented by reference samples collected in 1952 by Brother Adam. The samples L1-L5 are collected from the National Center for Agricultural Research and Extension breading apiary which was originally established for the conservation of Apis mellifera syriaca. Goal was to use the genetic information in the breeding for varroa resistant bees and to determine the successfulness of this conservation program. Project funded by USAID-MERC grant number: TA-MOU-09-M29-075.
2016-02-01 | GSE43554 | GEO
Project description:Apis mellifera intermissa (Buttel-Reepen, 1906) is the native honeybee subspecies of Algeria. A.m.intermissa occurs in Tunisia, Algeria and Morocco, between the Atlas and the Mediterranean and Atlantic coasts (Ruttner, 1988), in an area of more than 2500 km long. Intermissa indicates the position through this bee races between tropical Africa and European breeds (Peyvel, 1994). The settlement area of the Tellian extends from Tunisia to Morocco. Ruttner et al (1978) describes the pure Tellian. It is a black hair of his coat poverty brings out the black color. It is a small size, there are some times light illumination on the tergites. This bee is very aggressive, nervous, sick to take part, as swarms huge fall and even produced many brood and can build up to one hundred queen cells (Le Conte, 2002). A.m.intermissa is prone to swarming, shows an aggressive behaviour and an abundant use of propolis (Ruttner 1988). This study is part of the project funded by the USAID Grant No. TA-MOU-08-M29-075.
2016-02-01 | GSE45464 | GEO
Project description:Honey bee drones, queens and workers have vastly different phenotypes. Here we profile the the expression level of mRNAs and microRNAs of honeybee, drones, queens and workers at the L5 larval stage (91 hours +/- 1).
2015-09-06 | GSE61253 | GEO
Project description:Honey bee symbionts extracted from short read sequencing data
| PRJNA387664 | ENA
Project description:Bees are important plant pollinators in both natural and agricultural ecosystems. Managed and wild bees have experienced high average annual colony losses, population declines, and local extinctions in many geographic regions. Multiple factors, including virus infections, impact bee health and longevity. The majority of bee-infecting viruses are positive-sense single-stranded RNA viruses. Bee-infecting viruses often cause asymptomatic infections but may also cause paralysis, deformity or death. The severity of infection is governed by bee host immune responses and influenced by additional biotic and abiotic factors. Herein, we highlight studies that have contributed to the current understanding of antiviral defense in bees, including the Western honey bee (Apis mellifera), the Eastern honey bee (Apis cerana) and bumble bee species (Bombus spp.). Bee antiviral defense mechanisms include RNA interference (RNAi), endocytosis, melanization, encapsulation, autophagy and conserved immune pathways including Jak/STAT (Janus kinase/signal transducer and activator of transcription), JNK (c-Jun N-terminal kinase), MAPK (mitogen-activated protein kinases) and the NF-?B mediated Toll and Imd (immune deficiency) pathways. Studies in Dipteran insects, including the model organism Drosophila melanogaster and pathogen-transmitting mosquitos, provide the framework for understanding bee antiviral defense. However, there are notable differences such as the more prominent role of a non-sequence specific, dsRNA-triggered, virus limiting response in honey bees and bumble bees. This virus-limiting response in bees is akin to pathways in a range of organisms including other invertebrates (i.e., oysters, shrimp and sand flies), as well as the mammalian interferon response. Current and future research aimed at elucidating bee antiviral defense mechanisms may lead to development of strategies that mitigate bee losses, while expanding our understanding of insect antiviral defense and the potential evolutionary relationship between sociality and immune function.
| S-EPMC6115922 | biostudies-literature