Article
Microbiology
Patrizia D'Aquila, Francesco De Rango, Ersilia Paparazzo, Giuseppe Passarino, Dina Bellizzi
Summary: Adaptive antibiotic resistance is a transient metabolic adaptation of bacteria in response to low concentrations of antibiotics. Epigenetic modifications triggered by low concentrations of various antibiotics may modulate the sensitivity of bacteria to antibiotics. Understanding the molecular mechanisms behind adaptive resistance can suggest strategies to avoid it.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Yan Shi, Xingtan Zhang, Xiaojun Chang, Maokai Yan, Heming Zhao, Yuan Qin, Haifeng Wang
Summary: The study investigated the role of DNA methylation in regulating CAM photosynthesis by analyzing the DNA methylome and transcriptome of pineapple leaves. Differences in DNA methylation patterns and gene expression levels were observed between non-photosynthetic and photosynthetic tissues, with thousands of genes related to the CAM pathway showing differential methylation and expression levels.
Article
Biochemistry & Molecular Biology
Weilin Zhu, Chunling Yang, Qingyun Liu, Min Peng, Qiangyong Li, Huanling Wang, Xiuli Chen, Bin Zhang, Pengfei Feng, Tiancong Chen, Digang Zeng, Yongzhen Zhao
Summary: In this study, a comprehensive comparative analysis was conducted using whole genome bisulfite sequencing (WGBS) and transcriptome sequencing to investigate the DNA methylation profiles and differentially expressed genes in two strains of Litopenaeus vannamei with significantly different cold tolerance. The results revealed that differentially methylated regions (DMRs) were mainly located in gene exons and introns. The DMR-related genes (DMRGs) were significantly enriched in cell parts, catalytic activity, and metabolic processes, as revealed by Gene Ontology (GO) analysis. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed significant enrichment of these DMRGs in various metabolic pathways. These findings provide important insights into DNA methylation patterns and identification of cold tolerance genes in shrimp.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Yan Shi, Yuan Qin, Fenglan Li, Haifeng Wang
Summary: The role of DNA methylation in regulating potato response to Fusarium toxin deoxynivalenol (DON) stress and potato disease resistance was investigated in this study. The results showed that different concentrations of DON treatment caused significant changes in global DNA methylation levels in potato tubers. Differentially methylated regions (DMRs)-associated differentially expressed genes (DEGs) were enriched in resistance-related metabolic pathways. In addition, DON stress potentially induced resistance in potato tubers, possibly related to epigenetic memory created after DNA methylation changes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Veterinary Sciences
Xiuxiu Miao, Lewen Liu, Liying Liu, Geng Hu, Guixian Wu, Yuanmei Wang, Yanan Zhao, Jingchao Yang, Xianyao Li
Summary: By analyzing the mRNA and miRNA expression profiles of the cecum of Shouguang chickens, it was found that there were significant differences in the expression of mRNA and miRNA between the SE-infected group and the control group. The differentially expressed mRNAs were mainly enriched in immune-related processes and KEGG pathways, while the differentially expressed miRNAs were mainly enriched in metabolic-related GO-BP terms and KEGG pathways. Further experiments showed that miR-20b-5p regulates the immune or metabolic responses in Shouguang chickens after SE infection by directly targeting SCNN1A.
BMC VETERINARY RESEARCH
(2022)
Article
Reproductive Biology
Chuan Chen, Yawei Gao, Wenqiang Liu, Shaorong Gao
Summary: This article introduces the importance of epigenetic regulation in embryo development and somatic cell reprogramming. Using low-input sequencing techniques, researchers have revealed the epigenetic landscape during rapid transcriptome transitions and highlighted the essential roles of specific epigenetic regulators in transcription activity and chromatin remodeling.
BIOLOGY OF REPRODUCTION
(2022)
Review
Cell Biology
Shihang Zhou, Hongliang Zeng, Jinhua Huang, Li Lei, Xiaoliang Tong, Si Li, Ying Zhou, Haoran Guo, Manal Khan, Liping Luo, Rong Xiao, Jing Chen, Qinghai Zeng
Summary: Melanogenesis is a complex process involving multiple genes and signaling pathways, with epigenetics playing a key role in regulating the expression of key genes. Epigenetic-based therapy provides novel opportunities for treating dermatoses caused by pigmentation disturbances.
AGEING RESEARCH REVIEWS
(2021)
Review
Plant Sciences
Jie Liu, Meng Ke, Yuhan Sun, Shihui Niu, Wenli Zhang, Yun Li
Summary: Plant rejuvenation involves resetting gene expression patterns, chromatin remodeling, and histone modifications, resulting in the restoration of juvenile characteristics. The epigenetic mechanisms underlying this process are still in the early stages of study.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Genetics & Heredity
Ning Tang, Zhengyan Cao, Peiyin Wu, Yanni Liu, Juan Lou, Yang Hu, Xiaofan Sun, Shuo Si, Zexiong Chen
Summary: This study characterized the morphological and molecular features of prickle initiation in prickless and prickly Z. armatum, and identified candidate genes and transcription factors involved in prickle formation. Furthermore, the involvement of phytohormones, transcription factors, and epigenetic modifications in prickle initiation was also demonstrated.
Review
Immunology
Xiaohong Xiang, Jiefu Zhu, Guie Dong, Zheng Dong
Summary: Recent studies have demonstrated the important role of epigenetic regulation in various pathological processes of kidney transplantation, which may contribute to the discovery of novel diagnostic biomarkers and therapeutic interventions.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Marek Bednarczyk, Aleksandra Dunislawska, Katarzyna Stadnicka, Ewa Grochowska
Summary: Epigenetics studies heritable changes in gene function that do not alter DNA sequence. Environmental factors like temperature can affect embryo development and gene expression, making chicken embryos a useful model for understanding these effects. Epigenetic modifications can have long-lasting impacts on postembryonic development by influencing gene expression.
Review
Gastroenterology & Hepatology
Vivienne Woo, Theresa Alenghat
Summary: The complex relationship between the gastrointestinal tract and microbiota is regulated by epigenetic modifications, including modifications to DNA or histones and regulation of non-coding RNAs. Further research is needed to fully understand the mechanisms of epigenetic regulation.
Article
Pharmacology & Pharmacy
Taixiong Xue, Xingyu Qiu, Hongyao Liu, Cailing Gan, Zui Tan, Yuting Xie, Yuxi Wang, Tinghong Ye
Summary: Fibrosis, a common process of chronic inflammatory diseases, leads to scar formation and functional failure in organs. Epigenetic mechanisms play a crucial role in fibrosis, involving DNA methylation, histone modification, ncRNAs, and m6A modification. Targeted therapy based on epigenetics holds great potential for treating fibrosis.
PHARMACOLOGICAL RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Lingtong Ren, Anfang Liu, Qigui Wang, Honggan Wang, Deqiang Dong, Lingbin Liu
Summary: This study explored the embryonic muscle development of Chengkou Mountain Chicken, identifying numerous differentially expressed genes related to muscle development. Key genes for embryonic development were validated, providing a preliminary explanation of their role in muscle development. Overall, this study broadened our understanding of the phenotypic mechanism for myofiber formation and offered valuable information for enhancing chicken quality.
Review
Medicine, Research & Experimental
Ajinath Kale, Himanshu Sankrityayan, Hans-Joachim Anders, Anil Bhanudas Gaikwad
Summary: Klotho is a novel anti-aging protein expressed at highest levels in the kidney, with its regulation contributing to kidney disease progression. Levels of Klotho decrease during kidney injury and other diseases, but supplementation or overexpression can attenuate kidney disease. Various epigenetic and non-epigenetic mechanisms regulate Klotho expression, with natural products showing potential in this regulation.
Article
Biotechnology & Applied Microbiology
Jingwei Yuan, Shijun Li, Zheya Sheng, Meikun Zhang, Xuming Liu, Zhengdong Yuan, Ning Yang, Jilan Chen
Summary: High genetic diversity is observed in Tibetan native chickens, with intense inbreeding in the Nyingchi population. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the Tibetan native chicken populations.
Article
Biotechnology & Applied Microbiology
Weiwei Fu, Rui Wang, Naiyi Xu, Jinxin Wang, Ran Li, Hojjat Asadollahpour Nanaei, Qinghua Nie, Xin Zhao, Jianlin Han, Ning Yang, Yu Jiang
Summary: Galbase is an easily accessible repository that integrates public chicken multi-omics data, providing new opportunities for in-depth functional genomic studies on chicken and identification of genetic variations responsible for chicken complex traits.
Article
Biotechnology & Applied Microbiology
Jing Yang, Zhiqiong Mao, Xiqiong Wang, Jingjie Zhuang, Sijia Gong, Zhouyang Gao, Guiyun Xu, Ning Yang, Congjiao Sun
Summary: The study comprehensively investigated the regulatory mechanisms of eggshell brownness in different eggshell color and time following oviposition. Results suggest that Pp IX is synthesized de novo and stored in the shell gland, with ALAS1 identified as a key gene regulating Pp IX synthesis. Additionally, three transporters in the Pp IX pathway and three metabolites in shell glands and uterine fluid may influence eggshell browning.
Article
Agriculture, Dairy & Animal Science
Qiang Huang, Chaoliang Wen, Wei Yan, Congjiao Sun, Shuang Gu, Jiangxia Zheng, Ning Yang
Summary: Improving feed efficiency is an important goal in chicken breeding and production. This study found that the development of the gizzard, liver, and cecum is related to the feed efficiency of chickens.
Article
Agriculture, Dairy & Animal Science
Qianqian Zhou, Fangren Lan, Shuang Gu, Guangqi Li, Guiqin Wu, Yiyuan Yan, Xiaochang Li, Jiaming Jin, Chaoliang Wen, Congjiao Sun, Ning Yang
Summary: In this study, the researchers investigated the effects of host genetics and gut microbiota on feed efficiency in laying hens. They found that genetic factors and gut microbiota both play important roles in determining feed efficiency, with RFI having the highest microbial influence. They also identified three microbial genera that were negatively correlated with RFI and positively contributed to improving feed efficiency.
Article
Genetics & Heredity
Xiuan Zhang, Jianbo Li, Xiqiong Wang, Yuchen Jie, Congjiao Sun, Jiangxia Zheng, Junying Li, Ning Yang, Sirui Chen
Summary: In this study, a sex-reversed chicken flock was created by injecting an aromatase inhibitor, fadrozole, and high-resolution profiles of gene expression and chromatin accessibility in embryonic gonads were constructed. The results showed that fadrozole affected the transcriptional activities of genes related to sex determination and differentiation and regulated the expression of genes related to gonadal development through nearby open chromatin regions. After sexual maturity, the sex-reversed chickens were found to be infertile, and promising genes related to spermatogenesis and infertility were identified through RNA-seq. This study provides important insights into the molecular basis of sex differentiation and infertility in sex-reversed chickens and lays a foundation for further research on bird sex development.
EPIGENETICS & CHROMATIN
(2023)
Article
Agriculture, Dairy & Animal Science
Xingzheng Li, Jianlou Song, Xuefeng Shi, Mingyi Huang, Lei Liu, Guoqiang Yi, Ning Yang, Guiyun Xu, Jiangxia Zheng
Summary: The study revealed the crucial roles of liver FMO3 and cecal microbes in TMA metabolism in ducks, with the limited oxidation ability of FMO3 explaining the weakening of TMA metabolism in ducks.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Biology
Junxiao Ren, Zhengzheng Hu, Quanlin Li, Shuang Gu, Fangren Lan, Xiqiong Wang, Jianbo Li, Junying Li, Liwa Shao, Ning Yang, Congjiao Sun
Summary: Chicken embryonic diapause is a state of temporary arrest of embryonic development triggered by cold stress-induced IRF1 expression, mediated by the PKC-NF-kappa B signaling pathway. This is in contrast to mammalian diapause which is mTOR-dependent. The study characterized the dynamic transcriptomic and phosphoproteomic profiles of chicken embryos in different diapause states and identified key regulators of diapause.
Review
Biochemistry & Molecular Biology
Xiuan Zhang, Jianbo Li, Sirui Chen, Ning Yang, Jiangxia Zheng
Summary: Sex determination and differentiation in birds involves genetic factors controlling the sex determination program, while sex differentiation is influenced by hormones and can be reversed when disturbed. The regulatory mechanism of avian cell autonomous sex identity and sex development is still not clearly understood and requires further exploration. However, avian sex research findings have provided theoretical bases for gender control technologies in poultry production, which are being improved through interdisciplinary cooperation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Chaoliang Wen, Qinli Gou, Shuang Gu, Qiang Huang, Congjiao Sun, Jiangxia Zheng, Ning Yang
Summary: This study investigated the composition of microbial communities in chicken muscle tissue and their relationship with meat quality. The results showed that the microbial composition in muscle tissue can affect the fat content, and there is also a correlation between fat content in different muscle tissues. These findings provide important insights for improving meat quality in chickens.
Article
Agriculture, Dairy & Animal Science
Yiming Yuan, Gang Zheng, Zhen You, Lulu Wang, Ziyi Wang, Congjiao Sun, Changjun Liu, Xianyao Li, Peng Zhao, Yongqiang Wang, Ning Yang, Ling Lian
Summary: This study used whole genome bisulfite sequencing (WGBS) and RNA-seq to identify genes playing important roles in the tumor transformation of Marek's disease (MD). 8 genes, including CD4 and HMGB1, were found to be negatively correlated with methylation and showed high expression in the MDV-infected group. Overexpression of CD4 and HMGB1 significantly promoted MDCC-MSB-1 cell proliferation, suggesting their potential promoting roles in MD tumorigenesis.
Article
Multidisciplinary Sciences
Zhangyuan Pan, Ying Wang, Mingshan Wang, Yuzhe Wang, Xiaoning Zhu, Shenwen Gu, Conghao Zhong, Liqi An, Mingzhu Shan, Joana Damas, Michelle M. Halstead, Dailu Guan, Nares Trakooljul, Klaus Wimmers, Ye Bi, Shang Wu, Mary E. Delany, Xuechen Bai, Hans H. Cheng, Congjiao Sun, Ning Yang, Xiaoxiang Hu, Harris A. Lewin, Lingzhao Fang, Huaijun Zhou
Summary: This study identified and characterized regulatory elements in the chicken genome by integrating genome-wide sequencing datasets from 23 adult tissues. It annotated 1.57 million regulatory elements, predicted enhancer-gene pairs, and super-enhancers. These findings have significant implications for understanding gene regulation in chicken domestication, selection, and complex trait regulation.
Article
Biotechnology & Applied Microbiology
Xinwei Jiang, Boxuan Zhang, Fangren Lan, Conghao Zhong, Jiaming Jin, Xiaochang Li, Qianqian Zhou, Junying Li, Ning Yang, Chaoliang Wen, Congjiao Sun
Summary: Blood biochemical indicators are regulated by both host genetics and gut microbiota, and their interrelationships can affect growth traits in chickens. The heritability and microbiability of these indicators vary, and several candidate genes and microbial species have been identified as potentially involved in their regulation.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Ziyi Wang, Yiming Yuan, Gang Zheng, Meng Sun, Qinyuan Wang, Junfeng Wu, Junying Li, Congjiao Sun, Yongqiang Wang, Ning Yang, Ling Lian
Summary: This study reveals the distribution of ALVE in 11 chicken breeds, including the identification of 23 novel ALVEs in Chinese domestic breeds. Most of these insertion sites are located in intergenic regions and introns.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Chaoliang Wen, Chunning Mai, Ronglang Cai, Qinli Gou, Boxuan Zhang, Junying Li, Congjiao Sun, Ning Yang
Summary: Duration of fertility (DF) is an important economic trait in poultry production, and its correlation with egg production and breeding efficiency has been analyzed. The heritability of DF traits is low, but improvement of DF is possible through selection. Fertility duration day (FDD) is an effective selection criterion for improving DF, and it can be incorporated into a breeding program to enhance reproductive efficiency.
GENETICS SELECTION EVOLUTION
(2022)