Harnessing male germline epigenomics for the genetic improvement in cattle

Sperm is essential for successful artificial insemination in dairy cattle,and its quality can be influenced by both epi-genetic modification and epigenetic inheritance.The bovine germline differentiation is characterized by epigenetic reprogramming,while intergenerational and transgenerational epigenetic inheritance can influence the offspring’s development through the transmission of epigenetic features to the offspring via the germline.Therefore,the selec-tion of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers.We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.

Nutritional epigenetics education improves diet and attitude of parents of children with autism or attention deficit/hyperactivity disorder

BACKGROUND Unhealthy maternal diet leads to heavy metal exposures from the consumption of ultra-processed foods that may impact gene behavior across generations,creating conditions for the neurodevelopmental disorders known as autism and attention deficit/hyperactivity disorder(ADHD).Children with these disorders have difficulty metabolizing and excreting heavy metals from their bloodstream,and the severity of their symptoms correlates with the heavy metal levels measured in their blood.Psychiatrists may play a key role in helping parents reduce their ultra-processed food and dietary heavy metal intake by providing access to effective nutritional epigenetics education.AIM To test the efficacy of nutritional epigenetics instruction in reducing parental ultra-processed food intake.METHODS The study utilized a semi-randomized test and control group pretest-posttest pilot study design with participants recruited from parents having a learning-disabled child with autism or ADHD.Twenty-two parents who met the inclusion criteria were randomly selected to serve in the test(n=11)or control(n=11)group.The test group participated in the six-week online nutritional epigenetics tutorial,while the control group did not.The efficacy of the nutritional epigenetics instruction was determined by measuring changes in parent diet and attitude using data derived from an online diet survey administered to the participants during the pre and post intervention periods.Diet intake scores were derived for both ultra-processed and whole/organic foods.Paired sample t-tests were conducted to determine any differences in mean diet scores within each group.RESULTS There was a significant difference in the diet scores of the test group between the pre-and post-intervention periods.The parents in the test group significantly reduced their intake of ultra-processed foods with a preintervention diet score of 70(mean=5.385,SD=2.534)and a post-intervention diet score of 113(mean=8.692,SD=1.750)and the paired t-test analysis showing a significance of P<0.001.The test group also significantly increased their consumption of whole and/or organic foods with a pre-intervention diet score of 100(mean=5.882,SD=2.472)and post-intervention diet score of 121(mean=7.118,SD=2.390)and the paired t-test analysis showing a significance of P<0.05.CONCLUSION Here we show nutritional epigenetics education can be used to reduce ultra-processed food intake and improve attitude among parents having learning-disabled children with autism or ADHD.

Crop Epigenomics： Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base res- olution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methyl- ation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be tar- geted for reactivation leading to phenotypic variation.

Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer

BACKGROUND Aberrant methylation is common during the initiation and progression of colorectal cancer(CRC),and detecting these changes that occur during early adenoma(ADE)formation and CRC progression has clinical value.AIM To identify potential DNA methylation markers specific to ADE and CRC.METHODS Here,we performed SeqCap targeted bisulfite sequencing and RNA-seq analysis of colorectal ADE and CRC samples to profile the epigenomic-transcriptomic landscape.RESULTS Comparing 22 CRC and 25 ADE samples,global methylation was higher in the former,but both showed similar methylation patterns regarding differentially methylated gene positions,chromatin signatures,and repeated elements.High-grade CRC tended to exhibit elevated methylation levels in gene promoter regions compared to those in low-grade CRC.Combined with RNA-seq gene expression data,we identified 14 methylation-regulated differentially expressed genes,of which only AGTR1 and NECAB1 methylation had prognostic significance.CONCLUSION Our results suggest that genome-wide alterations in DNA methylation occur during the early stages of CRC and demonstrate the methylation signatures associated with colorectal ADEs and CRC,suggesting prognostic biomarkers for CRC.

Re-searching nasopharyngeal carcinoma

Nasopharyngeal carcinoma(NPC)has been a focus of medical research for more than 100 years,with significant interest emerging over the last 58 years following the identification of the link between the disease and Epstein-Barr virus(EBV)infection.NPC possesses several distinctive characteristics among human cancers,notably its well-documented global epidemiology,which reveals localized high-incidence regions primarily in Southeast Asia,particularly in the Southern provinces of China near the Pearl river,as well as in Greenland and North Africa.Epidemiological data indicate a marked male predominance,early disease onset,and a nearly 100%prevalence of latent EBV infection in the tumors.Due to lack of consistent pattern of cancer-related mutations in NPC genomes and excessive DNA-methylation in the tumor cells,NPC can be considered"an epigenetic cancer".Despite extensive researches,convincing biological explanations for these unique characteristics remain elusive.Recently,suggestive evidence has been published that specific local variants of EBV may represent major high risk factors.In spite of tumor and virus specific immunity,it has not been possible to use this for improved treatment.Ongoing studies on the role of the local microflora and tumor microenvironment are essential for a comprehensive understanding of host-EBV-tumor interactions.Ultimately,this knowledge aims to enhance diagnosis,disease fractionation,treatment strategies,and potentially prevention of NPC.

Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs

Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and growth.Recent studies unveiled a potential link between these two systems,implicating the potential mechanism of coordinated transcriptional and post-transcrip-tional regulation in porcine prenatal myogenesis and postnatal skeletal muscle growth.Methods:Immunofluorescence and co-IP assays were carried out between the 5mC writers and m^(6)A writers to investigate the molecular basis underneath.Large-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis(WGCNA)to identify the co-expression patterns of m^(6)A and 5mC regulators and their potential role in pig myogenesis.Whole-genome bisulfite sequencing(WGBS)and methylated RNA immu-noprecipitation sequencing(MeRIP-seq)were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages(days 30,60,120 and 180).Results:Significantly correlated expression between 5mC writers and m^(6)A writers and co-occurrence of 5mC and m^(6)A modification were revealed from public datasets of C2C12 myoblasts.The protein-protein interactions between the DNA methylase and the m^(6)A methylase were observed in mouse myoblast cells.Further,by analyzing tran-scriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages,we identified a 5mC/m^(6)A epigenetic module eigengene and decoded its potential functions in pre-or post-transcriptional regulation in postnatal skeletal muscle development and growth of pigs.Following integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m^(6)A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m^(6)A modifications as a consequence of 5mC/m^(6)A crosstalk in the postnatal myogenesis progress of pigs.Last,we identified a group of myogenesis-related genes collaboratively regulated by both 5mC and m^(6)A modifications in postnatal skeletal muscle growth in pigs.Conclusions:Our study discloses a potential epigenetic mechanism in skeletal muscle development and provides a novel direction for animal breeding and drug development of related human muscle-related diseases.

Elevated blood pressure: Our family's fault?The genetics of essential hypertension

AIM: To provide an updated review on current genetic aspects possibly affecting essential hypertension(EH), and to further elucidate their role in EH. METHODS: We searched for genetic and epigenetic factors in major studies associated with EH between Jan 2008-Oct 2013 using PubMed. We limited our search to reviews that discussed mostly human studies, and were accessible through the university online re-source. We found 11 genome wide association studies(GWAS), as well as five methylation and three miRNA studies that fit our search criteria. A distinction was not made between genes with protective effects or nega-tive effects, as this article is only meant to be a sum-mary of genes associated with any aspect of EH.RESULTS: We found 130 genes from the studies that met our inclusion/exclusion criteria. Of note, genes withmultiple study references include: STK39, CYP17A1, MTHFR-NPPA, MTHFR-NPPB, ATP2B1, CSK, ZNF652, UMOD, CACNB2, PLEKHA7, SH2B3, TBX3-TBX5, ULK4, CSK-ULK3, CYP1A2, NT5C2, CYP171A, PLCD3, SH2B3, ATXN2, CACNB2, PLEKHA7, SH2B3, TBX3-TBX5, ULK4, and HFE. The following genes overlapped between the genetic studies and epigenetic studies: WNK4 and BDKRB2. Several of the identified genes were found to have functions associated with EH. Many epigenetic factors were also correlated with EH. Of the epigenetic factors, there were no articles discussing siRNA and its effects on EH that met the search criteria, thus the topic was not included in this review. Among the miRNA tar-gets found to be associated with EH, many of the genes involved were also identified in the GWAS studies.CONCLUSION: Genetic hypertension risk algorithms could be developed in the future but may be of limited benefit due to the multi-factorial nature of EH. With emerging technologies, like next-generation sequenc-ing, more direct causal relationships between genetic and epigenetic factors affecting EH will likely be discov-ered creating a tremendous potential for personalized medicine using pharmacogenomics.

Histone methyltransferase SETDB1 is required for prostate cancer cell proliferation, migration and invasion

SETDB1 has been established as an oncogene in a number of human carcinomas. The present study was to evaluate the expression of SETDB1 in prostate cancer （PCa） tissues and cells and to preliminarily investigate the role of SETDB1 in prostate tumorigenesis in vitro. Quantitative reverse transcription polymerase chain reaction （qRT-PCR） and immunohistochemistry （IHC） were used to detect the expression of SETDB1 in PCa tissues, adjacent normal tissues, benign prostatic hyperplasia （BPH） tissues, PCa cell lines and normal prostate epithelial cells. The results suggested that SETDB1 was upregulated in human PCa tissues compared with normal tissues at the mRNA and protein levels. The role of SETDB1 in proliferation was analyzed with cell counting kit-8, colony-forming efficiency and flow cytometry assays. The results indicated that downregulation of SETDB1 by siRNA inhibited PCa cell growth, and induced GO/G1 cell cycle arrest. The PCa cell migration and invasion decreased by silcencing SETDBt which were assessed by using in vitro scratch and transwell invasion assay respectively. Our data suggested that SETDB1 is overexpressed in human PCa. Silencing SETDB1 inhibited PCa cell proliferation, migration and invasion.

Review: Pathogenesis of cholestatic liver diseases

Cholestatic liver diseases(CLD)begin to develop after an impairment of bile flow start to affect the biliary tree.Cholangiocytes actively participate in the liver response to injury and repair and the intensity of this reaction is a determinant factor for the development of CLD.Progressive cholangiopathies may ultimately lead to end-stage liver disease requiring at the end orthotopic liver transplantation.This narrative review will discuss cholangiocyte biology and pathogenesis mechanisms involved in four intrahepatic CLD:Primary biliary cholangitis,primary sclerosing cholangitis,cystic fibrosis involving the liver,and polycystic liver disease.

Phytoestrogens and prevention of breast cancer: The contentious debate

Phytoestrogens have multiple actions within target cells, including the epigenome, which could be beneficial to the development and progression of breast cancer. In this brief review the action of phytoestrogens on oestrogen receptors, cell signalling pathways, regulation of the cell cycle, apoptosis, steroid synthesis and epigenetic events in relation to breast cancer are discussed. Phytoestrogens can bind weakly to oestrogen receptors(ERs) and some have a preferential affinity for ERβ which can inhibit the transcriptional growthpromoting activity of ERα. However only saturating doses of phytoestrogens, stimulating both ERα and β, exert growth inhibitory effects. Such effects on growth may be through phytoestrogens inhibiting cell signalling pathways. Phytoestrogens have also been shown to inhibit cyclin D1 expression but increase the expression of cyclin-dependent kinase inhibitors(p21 and p27) and the tumour suppressor gene p53. Again these effects are only observed at high(> 10) μmol/L doses of phytoestrogens. Finally the effects of phytoestrogens on breast cancer may be mediated by their ability toinhibit local oestrogen synthesis and induce epigenetic changes. There are, though, difficulties in reconciling epidemiological and experimental data due to the fact experimental doses, both in vivo and in vitro, far exceed the circulating concentrations of "free" unbound phytoestrogens measured in women on a high phytoestrogen diet or those taking phytoestrogen supplements.

Histone Deacetylase Inhibition:An Important Mechanism in the Treatment of Lymphoma

Lymphomas enconlpass a group of malignancies that originate in the lymph nodes or other lymphoid tissues. Epigenetic modification, especially by histone deacetylase （HDACs）, plays a key role during the occurrence and development of lymphomas. Consequently, HDAC inhibitors （HDACIs）, a class of gene expression-modulating drugs, have emerged as promising mechanism-based agents for the treatment of lymphomas. This review presents the rationale of HDAC inhibition, describes the epigenetic-based mechanisms of action of HDACIs, discusses their clinical efficiency, and summarizes the current and future developments in this field.

Dental anomalies in first-degree relatives of transposed canine probands

The aim of this study was to investigate and compare the inheritance pattern and prevalence of inheritable dental anomalies in a sample of patients with maxillary canine—first premolar transposition and their first-degree relatives with a sample of palatally displaced canine families. Thirty-five consecutive maxillary canine—first premolar transposition probands and 111 first-degree relatives were matched to 35 consecutive palatally displaced canine probands and 115 first-degree relatives. These were assessed for palatally displaced canines and incisor-premolar hypodontia. Parental age at birth of the proband was also noted. The results revealed that（i） there is no difference in the overall prevalence of palatally displaced canine or incisor-premolar hypodontia between the groups of relatives;（ii） first-degree relatives of bilateral palatally displaced canine probands have a higher prevalence of palatally displaced canine and incisor-premolar hypodontia than those with unilateral palatally displaced canine; and（iii） maternal age at birth of the maxillary canine—first premolar transposition probands was significantly higher than that of the palatally displaced canine probands.The results suggest that maxillary canine—first premolar transposition and palatally displaced canine are unlikely to be different genetic entities and also indicate environmental or epigenetic influences on dental development.

‘Omics’of suicidal behaviour:A path to personalised psychiatry

Psychiatric disorders,including suicide,are complex disorders that are affected by many different risk factors.It has been estimated that genetic factors contribute up to 50%to suicide risk.As the candidate gene approach has not identified a gene or set of genes that can be defined as biomarkers for suicidal behaviour,much is expected from cutting edge technological approaches that can interrogate several hundred,or even millions,of biomarkers at a time.These include the‘-omic’approaches,such as genomics,transcriptomics,epigenomics,proteomics and metabolomics.Indeed,these have revealed new candidate biomarkers associated with suicidal behaviour.The most interesting of these have been implicated in inflammation and immune responses,which have been revealed through different study approaches,from genome-wide single nucleotide studies and the micro-RNA transcriptome,to the proteome and metabolome.However,the massive amounts of data that are generated by the‘-omic’technologies demand the use of powerful computational analysis,and also specifically trained personnel.In this regard,machine learning approaches are beginning to pave the way towards personalized psychiatry.

Changes in the epigenome and transcriptome of rice in response to Magnaporthe oryzae infection

DNA methylation participates in regulating the expression of coding and non-coding regions in plants. To investigate the association between DNA methylation and pathogen infection, we used whole-genome bisulfite sequencing to survey temporal DNA methylation changes in rice after infection with the rice blast fungus Magnaporthe oryzae. In contrast to previous findings in Arabidopsis, global DNA methylation levels in rice increased slightly after rice blast infection. We identified over 38,000 differentially methylated regions(DMRs), and hypermethylated DMRs far outnumbered hypomethylated DMRs. Most DMRs were located in transposable element regions. Using transcriptome analysis, we identified 8830 differentially expressed genes(DEGs) after 1, 3, and 5 days of infection. Over one-third of DEGs, most of which were CHH-type DMRs, were associated with DMRs. Functional analysis of the CHH DMR-DEGs indicated their involvement in many important biological processes, including cell communication and response to external stimulus. The transcription of many NBS-LRR family genes was affected by changes in DNA methylation, suggesting that DNA methylation plays essential roles in the response of rice to M. oryzae infection. More broadly, the DNA methylation analysis presented here sheds light on epigenomic involvement in plant defense against fungal pathogens.

Aberrant DNA methylation profile in cholangiocarcinoma

Cholangiocarcinoma(CCA)is a notoriously lethal epith-elial cancer originating from the biliary system.As radical resection offers a poor success rate and limited effective adjuvant modalities exist in its advanced stage,the disease leads to a fairly poor prognosis.As the incidence of CCA is increasing,although the mortality rate remains stable,and few other definite etiologies have yet to be established,renewing our knowledge of its fundamental carcinogenesis is advisable.The latest advances in molecular carcinogenesis have highlighted the roles of epigenetic perturbations and cancer-related inflammation in CCA.This review focuses on the reciprocal effects between aberrant DNA methylation and inflammatory microenvironment in CCA.

Frontiers in research on maternal diabetes-induced neural tube defects:Past,present and future

Diabetes mellitus rightly regarded as a silent-epidemic is continually on the rise and estimated to have a global prevalence of 6.4 % as of 2010.Diabetes during pregnancy is a well known risk factor for congenital anomalies in various organ systems that contribute to neonatal mortality,including cardiovascular,gastrointestinal,genitourinary and neurological systems,among which the neural tube defects are frequently reported.Over the last two to three decades,several groups around the world have focussed on identifying the molecular cues and cellular changes resulting in altered gene expression and the morphological defects and in diabetic pregnancy.In recent years,the focus has gradually shifted to looking at pre-programmed changes and activation of epigenetic mechanisms that cause altered gene expression.While several theories such as oxidative stress,hypoxia,and apoptosis triggered due to hyperglycemic conditions have been proposed and proven for being the cause for these defects,the exact mechanism or the link between how high glucose can alter gene expression/transcriptome and activate epigenetic mechanisms is largely unknown.Although preconceptual control of diabetes,(i.e.,managing glu-cose levels during pregnancy),and in utero therapies has been proposed as an effective solution for managing diabetes during pregnancy,the impact that a fluctuating glycemic index can have on foetal development has not been evaluated in detail.A tight glycemic control started before pregnancy has shown to reduce the incidence of congenital abnormalities in diabetic mothers.On the other hand,a tight glycemic control after organogenesis and embryogenesis have begun may prove insufficient to prevent or reverse the onset of congenital defects.The importance of determining the extent to which glycemic levels in diabetic mothers should be regulated is critical as foetal hypoglycemia has also been shown to be teratogenic.Finally,the major question remaining is if this whole issue is negligible and not worthy of investigation as the efficient management of diabetes during pregnancy is well in place in many countries.

Are We Learning as Much as Possible from Spaceflight to Better Understand Health and Risks to Health on Earth, as Well as in Space?

The objective of this review is to discuss the changes in human biology and physiology that occur when humans, who evolved on Earth for millions of years, now are subjected to space flight for extended periods of time, and how detailing such changes associated with space flight could help better understand risks for loss of health on Earth. Space programs invest heavily in the selection and training of astronauts. They also are investing in maintaining the health of astronauts, both for extensive stays in low earth orbit on ISS, and in preparation for deep space missions in the future. This effort is critical for the success of such missions as the N is small and the tasks needed to be performed in a hostile environment are complex and demanding. However, space is a unique environment, devoid of many of the “boundary conditions” that shaped human evolution (e.g. 1 g environment, magnetic fields, background radiation, oxygen, water, etc). Therefore, for humans to be successful in space, we need to learn to adapt and minimize the impact of an altered environment on human health. Conversely, we can also learn considerably from this altered environment for life on earth. The question is, are we getting the maximal information from life in space to learn about like on earth? The answer is likely No, and as such, our “Return on Investment” is not as great as it could be. Even though the number of astronauts is not large, what we can learn from them could help shape new questions for research focused on health for those on earth, as well is contribute to “precision health” from the study of astronaut diversity. This latter effort would contribute to both the health of astronauts identifying risks, as well as contribute to health on earth via better understanding of the human genome and epigenome, as well as factors contributing to risk for diseases on earth, particularly as individuals age and regulatory systems become altered. Better use of the International Space Station, and similar platforms in the future, could provide critical insights in aging-associated risks for loss of health on Earth, as well as promote new approaches to using precision medicine to overcome threats to health while in space. To achieve this goal will likely require advanced approaches to collecting such information and use of more systems biology, systems physiology approaches to integrate the information.

Epigenomic reprogramming in peripheral nerve injury

The regenerative capacity of peripheral nerve is significantly different from injury responses in the central nervous system.Regeneration of injured axons,re-myelination and functional recovery are readily observed after injury to peripheral nerve.

α-ketoglutarate promotes the specialization of primordial germ cell-like cells through regulating epigenetic reprogramming

There is growing evidence that cellular metabolism can directly participate in epigenetic dynamics and consequently modulate gene expression.However,the role of metabolites in activating the key gene regulatory network for specialization of germ cell lineage remains largely unknown.Here,we identified some cellular metabolites with significant changes by untargeted metabolomics between mouse epiblast-like cells(EpiLCs)and primordial germ cell-like cells(PGCLCs).More importantly,we found that inhibition of glutaminolysis by bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide(BPTES)impeded PGCLC specialization,but the impediment could be rescued by addition ofα-ketoglutarate(αKG),the intermediate metabolite of oxidative phosphorylation and glutaminolysis.Moreover,adding aKG alone to the PGCLC medium accelerated the PGCLC specialization through promoting H3 K27 me3 demethylation.Thus,our study reveals the importance of metabolite aKG in the germ cell fate determination and highlights the essential role of cellular metabolism in shaping the cell identities through epigenetic events.

Regulation of IL12B Expression in Human Macrophages by TALEN-mediated Epigenome Editing

Although the exact etiology of inflammatory bowel disease(IBD)remains unclear,exaggerated immune response in genetically predisposed individuals has been reported.Th1 and Th17 cells mediate IBD development.Macrophages produce IL-12 and IL-23 that share p40 subunit encoded by IL12B gene as heteromer partner to drive Th1 and Th17 differentiation.The available animal and human data strongly support the pathogenic role of IL-12/IL-23 in IBD development and suggest that blocking p40 might be the potential strategy for IBD treatment.Furthermore,aberrant alteration of some cytokines expression via epigenetic mechanisms is involved in pathogenesis o f IBD.In this study,we analyzed core promoter region of IL12B gene and investigated whether IL12B expression could be regulated through targeted epigenetic modification with gene editing technology.Transcription activator-like effectors(TALEs)are widely used in the field of genome editing and can specifically target DNA sequence in the host genome.We synthesized the TALE DNA-binding domains that target the promoter of human IL12B gene and fused it with the functional catalytic domains of epigenetic enzymes.Transient expression of these engineered enzymes demonstrated that the TALE-DNMT3A targeted the selected IL12B promoter region,induced loci-specific DNA methylation,and down-regulated IL-12B expression in various human cell lines.Collectively,our data suggested that epigenetic editing of IL12B through methylating DNA on its promoter might be developed as a potential therapeutic strategy for IBD treatment.