Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/516187

Integrative methylome and transcriptome analysis of Japanese flounder (Paralichthys olivaceus) skeletal muscle during development

he, f.·Zhang, J.·Wu, S.·Huang, Y.·Wen, H.·Zhang, M.·Li, J.·Li, Y.·Qi, X.
View original source ↗Export metadata ↓

Abstract

DNA methylation is an important epigenetic modification in vertebrate and is essential for epigenetic gene regulation in skeletal muscle development. We showed the genome-wide DNA methylation profile in skeletal muscle tissue of larval 7dph (JP1), juvenile 90dph (JP2), adult female 24 months (JP3) and adult male 24 months (JP4) Japanese flounder. The distribution and levels of methylated DNA within genomic features (1stexons, gene body, introns, TSS200, TSS1500 and intergenic) show different developmental landscapes. We also successfully identified differentially methylated regions (DMRs) and different methylated genes (DMGs) through a comparative analysis, indicating that DMR in gene body, intron and intergenic regions were more compared to other regions of all DNA elements. A gene ontology analysis indicated that the DMGs were mainly related to regulation of skeletal muscle fiber development process, Axon guidance, Adherens junction, and some ATPase activity. Methylome and transcriptome clearly revealed a exhibit a negative correlation. And integration analysis revealed a total of 425, 398 and 429 negatively correlated genes with methylation in the JP2_VS_JP1, JP3_VS_JP1 and JP4_VS_JP1 comparison groups, respectively. And these genes were functionally associated with pathways including Adherens junction, Axon guidance, Focal adhesion, cell junctions, Actin cytoskeleton and Wnt signaling pathways. In addition, we validated the MethylRAD results by bisulfite sequencing PCR (BSP) in some of the differentially methylated skeletal muscle growth-related genes (Myod1, Six1 and Ctnnb1). In this study, we have generated the genome-wide profile of methylome and transcriptome in Japanese flounder for the first time, and our results bring new insights into the epigenetic regulation of developmental processes in Japanese flounder. This study contributes to the knowledge on epigenetics in vertebrates.\n\nAuthor summaryEpigenetic mechanisms like DNA methylation have recently reported as vital regulators of some species skeletal muscle development through the control of genes related to growth. To date, although genome-wide DNA methylation profiles of many organisms have been reported and the Japanese flounder reference genome and whole transcriptome data are publically available, the methylation pattern of Japanese flounder skeletal muscle tissue remains minimally studied and the global DNA methylation data are yet to be known. Here we investigated the genome-wide DNA methylation patterns in Japanese flounder, throughout its development. These findings help to enrich research in molecular and developmental biology in vertebrates.

Explore related subjects

epidemiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

he, f., Zhang, J., Wu, S., Huang, Y., Wen, H., Zhang, M., Li, J., Li, Y., Qi, X.. 2019-01-09. Integrative methylome and transcriptome analysis of Japanese flounder (Paralichthys olivaceus) skeletal muscle during development. https://doi.org/10.1101/516187

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2019

Modeling cholera transmission and vaccination in a refugee camp

BackgroundCholera remains a major public health concern, particularly in refugee camps, which may contend with overcrowding and scarcity of resources. Maela, the largest long-standing refugee camp in Thailand, experienced four cholera outbreaks between 2005 and 2010. In 2013, a cholera vaccine campaign was implemented in the camp. To assist in the evaluation of the campaign and planning for subsequent campaigns, we developed a mathematical model of cholera in Maela. MethodsWe formulated a Susceptible-Infectious-Water-Recovered-based cholera transmission model and estimated parameters using incidence data from 2010. We next evaluated the reduction in cases conferred by several immunization strategies, varying timing, effectiveness, and resources (i.e., vaccine availability). Finally, we generated post-campaign case forecasts, to determine whether a booster campaign was needed. ResultsWe found that preexposure vaccination can substantially reduce the risk of cholera even when the < 50% of the population is given the full two-dose series. Additionally, the preferred number of doses per person should be considered in the context of one vs. two dose effectiveness and vaccine availability. For reactive vaccination, a trade-off between timing and effectiveness was revealed, indicating that it may be beneficial to give one dose to more people rather than two doses to fewer people, given that a two-dose schedule would incur a delay in administration of the second dose. Forecasting using realistic coverage levels predicted that there was no need for a booster campaign in 2014 (consistent with our predictions, there was not a cholera epidemic in the 2014 season). ConclusionsOur analyses suggest that vaccination in conjunction with ongoing water sanitation and hygiene efforts provides an effective strategy for cholera outbreaks in refugee camps. Effective preexposure vaccination depends on timing and effectiveness. If a camp is facing an outbreak, delayed distribution of vaccines can substantially alter the effectiveness of reactive vaccination, suggesting that quick distribution of vaccines may be more important than ensuring every individual receives both vaccine doses.

epidemiology↗
bioRxiv2019

Prevalence and risk factors of postpartum depression among women living in urban slums of Dhaka, Bangladesh

Postpartum depression (PPD) is a serious pubic health concern and known to have the adverse effects on mothers perinatal wellbeing; and childs physical and codnitive development. There were limited literatures on PPD in Bangladesh, especially in urban slum context. The aim of this study was to assess the burden and risk factors of PPD among the urban slum women. A cross-sectional study was conducted between November-December 2017 in three urban slums on 376 women within first 12 months of postpartum. A validated Bangla version of Edinburgh Postnatal Depression Scale was used to measure the depression status. Respondents socio-economic characteristics and other risk factors were collected with structured validated questionaire by trained interviewers. Unadjusted Prevalence Ratio (PR) and Adjusted Prevalence Ratio (APR) were estimated with Generalized Linear Model(GLM) and Generalized Estimating Equation (GEE) respectively to identify the risk factors of PPD. The prevalence of PPD was 39.4% within first 12 months following the child birth. Job involvement after child delivery (APR=1.9, 95% CI= 1.1, 3.3), job loss due to pregnancy (APR=1.5, 95% CI= 1.0, 2.1), perinatal and postnatal death (APR=1.4, 95% CI= 0.97, 2.0), unintended pregnancy (APR=1.8, 95% CI= 1.3, 2.5), management of delivery cost by borrowing, selling or mortgaging assets (APR=1.3, 95% CI= 0.94, 1.9), depressive symptom during pregnancy (APR=2.5, 95% CI= 1.7, 3.8) and intimate partner violence (APR=2.0, 95% CI= 1.2, 3.3), were identified as risk factors. PPD was not associated with poverty, mother in law and any child related factors. The burden of postpartum depression is high in the urban slum of Bangladesh. Maternal mental health services should be integrated with existing maternal health services. Research is required for the innovation of effective, low cost and culturally appropriate PPD case management and preventive intervention in urban slum of Bangladesh.

epidemiology↗
bioRxiv2019

Plasmodium caprae infection is negatively correlated with infection of Theileria ovis and Anaplasma ovis in goats

Theileria, Babesia, and Anaplasma are tick-borne pathogens affecting livestock industries worldwide. In this study, we surveyed the presence of Babesia ovis, Theileria ovis, Theileria lestoquardi, Anaplasma ovis, Anaplasma phagocytophilum, and Anaplasma marginale in 200 goats from 3 different districts in Sistan and Baluchestan province, Iran. Species-specific diagnostic PCR and sequence analysis revealed that 1.5%, 12.5%, and 80% of samples were positive for T. lestoquardi, T. ovis, and A. ovis, respectively. Co-infections of goats with up to 3 pathogens were seen in 22% of the samples. We observed a positive correlation between A. ovis and T. ovis infection. In addition, by analyzing the data with respect to Plasmodium caprae infection in these goats, a negative correlation was found between P. caprae and A. ovis and between P. caprae and T. ovis. This study contributes to understanding the epidemiology of vector-borne pathogens and their interplay in goats.\n\nImportanceTick-borne pathogens include economically important pathogens restricting livestock farming worldwide. In endemic areas livestock are exposed to different tick species carrying various pathogens which could result in co-infection with several tick-borne pathogens in a single host. The co-infection and interaction among pathogens are important in determining the outcome of disease. Little is known about pathogen interactions in the vector and the host. In this study, we show for the first time that co-infection of P. caprae, a mosquito transmitted pathogen, with T. ovis and A. ovis. Analysis of goat blood samples revealed a positive correlation between A. ovis and T. ovis. Moreover, a negative correlation was seen between P. caprae, a mosquito transmitted pathogen, and the tick-borne pathogens T. ovis or A. ovis.

epidemiology↗