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Park D, Cenik C. Long-read RNA sequencing reveals allele-specific N 6-methyladenosine modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602538. [PMID: 39026828 PMCID: PMC11257478 DOI: 10.1101/2024.07.08.602538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA promises the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNA. We utilized human and mouse cells with known genetic variants to assign allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses revealed the importance of sequences adjacent to the DRACH-motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discovered allele-specific m6A modification (ASM) events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long reads and surpassing the capabilities of antibody-based short-read approaches. This technological advancement promises to advance our understanding of the role of genetics in determining mRNA modifications.
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Affiliation(s)
- Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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Quan J, Yang M, Wang X, Cai G, Ding R, Zhuang Z, Zhou S, Tan S, Ruan D, Wu J, Zheng E, Zhang Z, Liu L, Meng F, Wu J, Xu C, Qiu Y, Wang S, Lin M, Li S, Ye Y, Zhou F, Lin D, Li X, Deng S, Zhang Y, Yao Z, Gao X, Yang Y, Liu Y, Zhan Y, Liu Z, Zhang J, Ma F, Yang J, Chen Q, Yang J, Ye J, Dong L, Gu T, Huang S, Xu Z, Li Z, Yang J, Huang W, Wu Z. Multi-omic characterization of allele-specific regulatory variation in hybrid pigs. Nat Commun 2024; 15:5587. [PMID: 38961076 PMCID: PMC11222378 DOI: 10.1038/s41467-024-49923-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.
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Affiliation(s)
- Jianping Quan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
| | - Ming Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Xingwang Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Rongrong Ding
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Zhanwei Zhuang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shenping Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Suxu Tan
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Donglin Ruan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiajin Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Enqin Zheng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zebin Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Langqing Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fanming Meng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou, Guangdong, China
| | - Jie Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Cineng Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yibin Qiu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shiyuan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Meng Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shaoyun Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yong Ye
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fuchen Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Danyang Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xuehua Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shaoxiong Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuling Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zekai Yao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xin Gao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Yingshan Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yiyi Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuexin Zhan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhihong Liu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Jiaming Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fucai Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jifei Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qiaoer Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jisheng Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jian Ye
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Linsong Dong
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Sixiu Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zheng Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China.
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China.
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Nagy N, Hádinger N, Tóth O, Rácz GA, Pintér T, Gál Z, Urbán M, Gócza E, Hiripi L, Acsády L, Vértessy BG. Characterization of dUTPase expression in mouse postnatal development and adult neurogenesis. Sci Rep 2024; 14:13139. [PMID: 38849394 PMCID: PMC11161619 DOI: 10.1038/s41598-024-63405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
The enzyme dUTPase has an essential role in maintaining genomic integrity. In mouse, nuclear and mitochondrial isoforms of the enzyme have been described. Here we present the isoform-specific mRNA expression levels in different murine organs during development using RT-qPCR. In this study, we analyzed organs of 14.5-day embryos and of postnatal 2-, 4-, 10-week- and 13-month-old mice. We demonstrate organ-, sex- and developmental stage-specific differences in the mRNA expression levels of both isoforms. We found high mRNA expression level of the nuclear isoform in the embryo brain, and the expression level remained relatively high in the adult brain as well. This was surprising, since dUTPase is known to play an important role in proliferating cells, and mass production of neural cells is completed by adulthood. Thus, we investigated the pattern of the dUTPase protein expression specifically in the adult brain with immunostaining and found that dUTPase is present in the germinative zones, the subventricular and the subgranular zones, where neurogenesis occurs and in the rostral migratory stream where neuroblasts migrate to the olfactory bulb. These novel findings suggest that dUTPase may have a role in cell differentiation and indicate that accurate dTTP biosynthesis can be vital, especially in neurogenesis.
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Affiliation(s)
- Nikolett Nagy
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary.
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary.
| | - Nóra Hádinger
- Laboratory of Thalamus Research, Institute of Experimental Medicine, HUN-REN, Szigony utca 43, 1083, Budapest, Hungary
| | - Otília Tóth
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary
| | - Gergely Attila Rácz
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary
| | - Tímea Pintér
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - Zoltán Gál
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - Martin Urbán
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - Elen Gócza
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
| | - László Hiripi
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert utca 4, 2100, Gödöllő, Hungary
- Laboratory Animal Science Coordination Center, Semmelweis University, Nagyvárad tér 4, 1089, Budapest, Hungary
| | - László Acsády
- Laboratory of Thalamus Research, Institute of Experimental Medicine, HUN-REN, Szigony utca 43, 1083, Budapest, Hungary
| | - Beáta G Vértessy
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar tudósok körútja 2, 1117, Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary.
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He C, Zhu B, Gao W, Wu Q, Zhang C. Study on Allele Specific Expression of Long-Term Residents in High Altitude Areas. Evol Bioinform Online 2024; 20:11769343241257344. [PMID: 38826865 PMCID: PMC11141219 DOI: 10.1177/11769343241257344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
In diploid organisms, half of the chromosomes in each cell come from the father and half from the mother. Through previous studies, it was found that the paternal chromosome and the maternal chromosome can be regulated and expressed independently, leading to the emergence of allele specific expression (ASE). In this study, we analyzed the differential expression of alleles in the high-altitude population and the normal population based on the RNA sequencing data. Through gene cluster analysis and protein interaction network analysis, we found some changes occurred at the gene level, and some negative effects. During the study, we realized that the calmodulin homology domain may have a certain correlation with long-term survival at high altitude. The plateau environment is characterized by hypoxia, low air pressure, strong ultraviolet radiation, and low temperature. Accordingly, the genetic changes in the process of adaptation are mainly reflected in these characteristics. High altitude generation living is also highly related to cancer, immune disease, cardiovascular disease, neurological disease, endocrine disease, and other diseases. Therefore, the medical system in high altitude areas should pay more attention to these diseases.
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Affiliation(s)
- Chao He
- The General Hospital of Tibet Military Region, Lhasa, China
| | - Bin Zhu
- The General Hospital of Tibet Military Region, Lhasa, China
| | - Wenwen Gao
- The General Hospital of Tibet Military Region, Lhasa, China
| | - Qianjin Wu
- The General Hospital of Tibet Military Region, Lhasa, China
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Umapathy VR, Natarajan PM, Swamikannu B. Molecular and Therapeutic Roles of Non-Coding RNAs in Oral Cancer-A Review. Molecules 2024; 29:2402. [PMID: 38792263 PMCID: PMC11123887 DOI: 10.3390/molecules29102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Oral cancer (OC) is among the most common malignancies in the world. Despite advances in therapy, the worst-case scenario for OC remains metastasis, with a 50% survival rate. Therefore, it is critical to comprehend the pathophysiology of the condition and to create diagnostic and treatment plans for OC. The development of high-throughput genome sequencing has revealed that over 90% of the human genome encodes non-coding transcripts, or transcripts that do not code for any proteins. This paper describes the function of these different kinds of non-coding RNAs (ncRNAs) in OC as well as their intriguing therapeutic potential. The onset and development of OC, as well as treatment resistance, are linked to dysregulated ncRNA expression. These ncRNAs' potentially significant roles in diagnosis and prognosis have been suggested by their differing expression in blood or saliva. We have outlined every promising feature of ncRNAs in the treatment of OC in this study.
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Affiliation(s)
- Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Dr. M.G.R. Educational and Research Institute, Thai Moogambigai Dental College and Hospital, Chennai 600107, Tamil Nadu, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Centre of Medical and Bio-Allied Health Sciences and Research Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Bhuminathan Swamikannu
- Department of Prosthodontics, Sree Balaji Dental College and Hospital, Pallikaranai, BIHER, Chennai 600100, Tamil Nadu, India;
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Van Campen H, Bishop JV, Brink Z, Engle TE, Gonzalez-Berrios CL, Georges HM, Kincade JN, Murtazina DA, Hansen TR. Epigenetic Modifications of White Blood Cell DNA Caused by Transient Fetal Infection with Bovine Viral Diarrhea Virus. Viruses 2024; 16:721. [PMID: 38793603 PMCID: PMC11125956 DOI: 10.3390/v16050721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Bovine viral diarrhea virus (BVDV) infections cause USD 1.5-2 billion in losses annually. Maternal BVDV after 150 days of gestation causes transient fetal infection (TI) in which the fetal immune response clears the virus. The impact of fetal TI BVDV infections on postnatal growth and white blood cell (WBC) methylome as an index of epigenetic modifications was examined by inoculating pregnant heifers with noncytopathic type 2 BVDV or media (sham-inoculated controls) on Day 175 of gestation to generate TI (n = 11) and control heifer calves (n = 12). Fetal infection in TI calves was confirmed by virus-neutralizing antibody titers at birth and control calves were seronegative. Both control and TI calves were negative for BVDV RNA in WBCs by RT-PCR. The mean weight of the TI calves was less than that of the controls (p < 0.05). DNA methyl seq analysis of WBC DNA demonstrated 2349 differentially methylated cytosines (p ≤ 0.05) including 1277 hypomethylated cytosines, 1072 hypermethylated cytosines, 84 differentially methylated regions based on CpGs in promoters, and 89 DMRs in islands of TI WBC DNA compared to controls. Fetal BVDV infection during late gestation resulted in epigenomic modifications predicted to affect fetal development and immune pathways, suggesting potential consequences for postnatal growth and health of TI cattle.
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Affiliation(s)
- Hana Van Campen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
| | - Jeanette V. Bishop
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
| | - Zella Brink
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
| | - Terry E. Engle
- Department of Animal Science, Colorado State University, Fort Collins, CO 80523, USA;
| | - Carolina L. Gonzalez-Berrios
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
| | - Hanah M. Georges
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
- Currently at Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jessica N. Kincade
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
| | - Dilyara A. Murtazina
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
| | - Thomas R. Hansen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (H.V.C.); (J.V.B.); (Z.B.); (C.L.G.-B.); (H.M.G.); (J.N.K.); (D.A.M.)
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7
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Soliman HK, Coughlan JM. United by Conflict: Convergent Signatures of Parental Conflict in Angiosperms and Placental Mammals. J Hered 2024:esae009. [PMID: 38366852 DOI: 10.1093/jhered/esae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Indexed: 02/18/2024] Open
Abstract
Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: (1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? (2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? (3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? (4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.
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Affiliation(s)
- Hagar K Soliman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, United States
- Department of Biotechnology, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Jenn M Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, United States
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8
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Hou KC, Tsai MH, Akbarian S, Huang HS. Mir125b-1 is Not Imprinted in Human Brain and Shows Developmental Expression Changes in Mouse Brain. Neuroscience 2023; 529:99-106. [PMID: 37598835 DOI: 10.1016/j.neuroscience.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Genomic imprinting is a predominantly brain and placenta-specific epigenetic process that contributes to parent-of-origin-specific gene expression. While microRNAs are highly expressed in the brain, their imprinting status in this tissue remains poorly studied. Previous research demonstrated that Mir125b-2 is imprinted in the human brain and regulates hippocampal circuits and functions in mice. However, the imprinting status of another isoform of miR125b, Mir125b-1, in the human brain, as well as its spatiotemporal expression patterns in mice, have not been elucidated. Here, we show MIR125B1 is not imprinted in the human brain. Moreover, miR-125b-1 was highly expressed in the brains of mice. Furthermore, miR-125b-1 was down-regulated during brain development in mice. Specifically, miR-125b-1 displayed preferential expression in the olfactory bulb, thalamus, and hypothalamus of the mouse brain. Notably, miR-125b-1 was enriched in GABAergic neurons, particularly somatostatin-expressing GABAergic neurons, compared with glutamatergic neurons. Taken together, our findings provide the imprinting status and comprehensive spatiotemporal expression profiling of Mir125b-1 in the brain.
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Affiliation(s)
- Kuan-Chu Hou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Meng-Han Tsai
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
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9
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Higgs MJ, Webberley AE, Allan AJ, Talat M, John RM, Isles AR. The parenting hub of the hypothalamus is a focus of imprinted gene action. PLoS Genet 2023; 19:e1010961. [PMID: 37856383 PMCID: PMC10586610 DOI: 10.1371/journal.pgen.1010961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/07/2023] [Indexed: 10/21/2023] Open
Abstract
Imprinted genes are subject to germline epigenetic modification resulting in parental-specific allelic silencing. Although genomic imprinting is thought to be important for maternal behaviour, this idea is based on serendipitous findings from a small number of imprinted genes. Here, we undertook an unbiased systems biology approach, taking advantage of the recent delineation of specific neuronal populations responsible for controlling parental care, to test whether imprinted genes significantly converge to regulate parenting behaviour. Using single-cell RNA sequencing datasets, we identified a specific enrichment of imprinted gene expression in a recognised "parenting hub", the galanin-expressing neurons of the preoptic area. We tested the validity of linking enriched expression in these neurons to function by focusing on MAGE family member L2 (Magel2), an imprinted gene not previously linked to parenting behaviour. We confirmed expression of Magel2 in the preoptic area galanin expressing neurons. We then examined the parenting behaviour of Magel2-null(+/p) mice. Magel2-null mothers, fathers and virgin females demonstrated deficits in pup retrieval, nest building and pup-directed motivation, identifying a central role for this gene in parenting. Finally, we show that Magel2-null mothers and fathers have a significant reduction in POA galanin expressing cells, which in turn contributes to a reduced c-Fos response in the POA upon exposure to pups. Our findings identify a novel imprinted gene that impacts parenting behaviour and, moreover, demonstrates the utility of using single-cell RNA sequencing data to predict gene function from expression and in doing so here, have identified a purposeful role for genomic imprinting in mediating parental behaviour.
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Affiliation(s)
- Matthew J. Higgs
- Behavioural Genetics Group, Centre for Neuropsychiatric, Genetics and Genomics, Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, United Kingdom
| | - Anna E. Webberley
- Behavioural Genetics Group, Centre for Neuropsychiatric, Genetics and Genomics, Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, United Kingdom
| | | | - Moaz Talat
- The Mary Lyon Centre, MRC Harwell, Didcot, United Kingdom
| | - Rosalind M. John
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Anthony R. Isles
- Behavioural Genetics Group, Centre for Neuropsychiatric, Genetics and Genomics, Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, United Kingdom
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10
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Hoyos Sanchez MC, Bayat T, Gee RRF, Fon Tacer K. Hormonal Imbalances in Prader-Willi and Schaaf-Yang Syndromes Imply the Evolution of Specific Regulation of Hypothalamic Neuroendocrine Function in Mammals. Int J Mol Sci 2023; 24:13109. [PMID: 37685915 PMCID: PMC10487939 DOI: 10.3390/ijms241713109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
The hypothalamus regulates fundamental aspects of physiological homeostasis and behavior, including stress response, reproduction, growth, sleep, and feeding, several of which are affected in patients with Prader-Willi (PWS) and Schaaf-Yang syndrome (SYS). PWS is caused by paternal deletion, maternal uniparental disomy, or imprinting defects that lead to loss of expression of a maternally imprinted region of chromosome 15 encompassing non-coding RNAs and five protein-coding genes; SYS patients have a mutation in one of them, MAGEL2. Throughout life, PWS and SYS patients suffer from musculoskeletal deficiencies, intellectual disabilities, and hormonal abnormalities, which lead to compulsive behaviors like hyperphagia and temper outbursts. Management of PWS and SYS is mostly symptomatic and cures for these debilitating disorders do not exist, highlighting a clear, unmet medical need. Research over several decades into the molecular and cellular roles of PWS genes has uncovered that several impinge on the neuroendocrine system. In this review, we will discuss the expression and molecular functions of PWS genes, connecting them with hormonal imbalances in patients and animal models. Besides the observed hormonal imbalances, we will describe the recent findings about how the loss of individual genes, particularly MAGEL2, affects the molecular mechanisms of hormone secretion. These results suggest that MAGEL2 evolved as a mammalian-specific regulator of hypothalamic neuroendocrine function.
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Affiliation(s)
- Maria Camila Hoyos Sanchez
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
| | - Tara Bayat
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
| | - Rebecca R. Florke Gee
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
| | - Klementina Fon Tacer
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
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11
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Puzzo C, D'Angiò R, Albanese S, Orlando D, Mangili I, Capobianco M, Liberati AS, Adriani W. Inheritance of wild and truncated DAT alleles from grand-parents: Opposite transgenerational consequences on the behavioral phenotype in adolescent DAT heterozygous rats. Neurosci Lett 2023; 810:137352. [PMID: 37321389 DOI: 10.1016/j.neulet.2023.137352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/25/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
Dopamine plays important roles in implicit memory and motivation of behavior. Environmental inputs can produce transgenerational epigenetic changes. This concept also includes the uterus: experimentally, we sought to create hyper-dopaminergic uterine conditions through ineffective dopamine-transporter (DAT) protein, obtained by inserting a stop-codon into the SLC6A3 gene. By crossing WT-dam with KO-sire (or vice-versa), we obtained a 100% DAT-heterozygous (HET) offspring with known derivation of the wild allele: MAT rats are offspring of WT-female and KO-male; PAT rats are offspring of KO-female and WT-male. We reconstructed inheritance of alleles, by crossing PAT-male with MAT-female or vice-versa, obtaining GIX (PAT-male with MAT-female) and DIX (MAT-male with PAT-female) rats (such offspring present specular paths in allele inheritance from grandparents). We conducted three experiments: first, we assessed maternal behaviour (four epigenotypes: WT, MAT, PAT and WHZ=HET-pups fostered-to-a WT-dam); in the second, we analysed sleep-wake cycles of GIX and DIX epigenotypes with their WIT siblings as controls; in the third, we explored the impact of WT or MAT mother on WT or HET pups. MAT-dams (with GIX-pups) express excessive licking/grooming. However, in the mere presence of "sick" epigenotype, PAT-dams (with DIX-pups) and also WHZ (i.e., WT-dams but with HET-pups) expressed greater nest-building care towards the offspring, compared to "true-wild" litters (WT-dams with WT-pups). In Exp. 2 at adolescence, GIX epigenotype showed locomotor hyperactivity during late waking-phase, while DIX epigenotype exhibited pronounced hypoactivity compared to controls. In Exp. 3, we confirmed that HET adolescent pups receiving cares from a MAT-dam may develop additional hyperactivity when awake, but additional hypoactivity during rest-hours. Thus, behavioral changes observed in DAT-heterozygous offspring have opposite courses based on of DAT-allele inheritance from a grandparent through the sire or the dam. In conclusion, behavioural changes in the offspring have antithetic courses with respect to inheritance of DAT-allele via sperm or egg.
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Affiliation(s)
- Concetto Puzzo
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy; Center for Behavioral Sciences and Mental Health, IstitutoSuperiore di Sanità, Rome, Italy
| | - Roberta D'Angiò
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy
| | - Sara Albanese
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy
| | - Daniela Orlando
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy
| | - Ileana Mangili
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy
| | - Micaela Capobianco
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy
| | - Anna Sara Liberati
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy; Forensic Science Academy, Via Palmiro Togliatti 11, Castel San Giorgio, Salerno, Italy
| | - Walter Adriani
- Faculty of Psychology, International Telematic University Uninettuno, Rome, Italy; Center for Behavioral Sciences and Mental Health, IstitutoSuperiore di Sanità, Rome, Italy.
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12
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Carrion SA, Michal JJ, Jiang Z. Imprinted Genes: Genomic Conservation, Transcriptomic Dynamics and Phenomic Significance in Health and Diseases. Int J Biol Sci 2023; 19:3128-3142. [PMID: 37416777 PMCID: PMC10321285 DOI: 10.7150/ijbs.83712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/25/2023] [Indexed: 07/08/2023] Open
Abstract
Since its discovery in 1991, genomic imprinting has been the subject of numerous studies into its mechanisms of establishment and regulation, evolution and function, and presence in multiple genomes. Disturbance of imprinting has been implicated in a range of diseases, ranging from debilitating syndromes to cancers to fetal deficiencies. Despite this, studies done on the prevalence and relevance of imprinting on genes have been limited in scope, tissue types available, and focus, by both availability and resources. This has left a gap in comparative studies. To address this, we assembled a collection of imprinted genes available in current literature covering five species. Here we sought to identify trends and motifs in the imprinted gene set (IGS) in three distinct arenas: evolutionary conservation, across-tissue expression, and health phenomics. Overall, we found that imprinted genes displayed less conservation and higher proportions of non-coding RNA while maintaining synteny. Maternally expressed genes (MEGs) and paternally expressed genes (PEGs) occupied distinct roles in tissue expression and biological pathway use, while imprinted genes collectively showed a broader tissue range, notable preference for tissue specific expression and limited gene pathways than comparable sex differentiation genes. Both human and murine imprinted genes showed the same clear phenotypic trends, that were distinct from those displayed by sex differentiation genes which were less involved in mental and nervous system disease. While both sets had representation across the genome, the IGS showed clearer clustering as expected, with PEGs significantly more represented than MEGs.
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Affiliation(s)
| | | | - Zhihua Jiang
- ✉ Corresponding author: Dr. Zhihua Jiang (ORCID ID: 0000-0003-1986-088X), Professor of Genome Biology. Phone: 509-335 8761;
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13
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Lu Z, Li J, Lu Y, Li L, Wang W, Zhang C, Xu L, Nie Y, Gao C, Bian X, Liu Z, Wang GZ, Sun Q. Cynomolgus-rhesus hybrid macaques serve as a platform for imprinting studies. Innovation (N Y) 2023; 4:100436. [PMID: 37215523 PMCID: PMC10196704 DOI: 10.1016/j.xinn.2023.100436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Genomic imprinting can lead to allele-specific expression (ASE), where one allele is preferentially expressed more than the other. Perturbations in genomic imprinting or ASE genes have been widely observed across various neurological disorders, notably autism spectrum disorder (ASD). In this study, we crossed rhesus cynomolgus monkeys to produce hybrid monkeys and established a framework to evaluate their allele-specific gene expression patterns using the parental genomes as a reference. Our proof-of-concept analysis of the hybrid monkeys identified 353 genes with allele-biased expression in the brain, enabling us to determine the chromosomal locations of ASE clusters. Importantly, we confirmed a significant enrichment of ASE genes associated with neuropsychiatric disorders, including ASD, highlighting the potential of hybrid monkey models in advancing our understanding of genomic imprinting.
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Affiliation(s)
- Zongyang Lu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Jie Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Lu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Wei Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chenchen Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Libing Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhong Nie
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changshan Gao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyan Bian
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
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14
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Fertan E, Gendron WH, Wong AA, Hanson GM, Brown RE, Weaver ICG. Noncanonical regulation of imprinted gene Igf2 by amyloid-beta 1-42 in Alzheimer's disease. Sci Rep 2023; 13:2043. [PMID: 36739453 PMCID: PMC9899226 DOI: 10.1038/s41598-023-29248-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Reduced insulin-like growth factor 2 (IGF2) levels in Alzheimer's disease (AD) may be the mechanism relating age-related metabolic disorders to dementia. Since Igf2 is an imprinted gene, we examined age and sex differences in the relationship between amyloid-beta 1-42 (Aβ42) accumulation and epigenetic regulation of the Igf2/H19 gene cluster in cerebrum, liver, and plasma of young and old male and female 5xFAD mice, in frontal cortex of male and female AD and non-AD patients, and in HEK293 cell cultures. We show IGF2 levels, Igf2 expression, histone acetylation, and H19 ICR methylation are lower in females than males. However, elevated Aβ42 levels are associated with Aβ42 binding to Igf2 DMR2, increased DNA and histone methylation, and a reduction in Igf2 expression and IGF2 levels in 5xFAD mice and AD patients, independent of H19 ICR methylation. Cell culture results confirmed the binding of Aβ42 to Igf2 DMR2 increased DNA and histone methylation, and reduced Igf2 expression. These results indicate an age- and sex-related causal relationship among Aβ42 levels, epigenomic state, and Igf2 expression in AD and provide a potential mechanism for Igf2 regulation in normal and pathological conditions, suggesting IGF2 levels may be a useful diagnostic biomarker for Aβ42 targeted AD therapies.
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Affiliation(s)
- Emre Fertan
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - William H Gendron
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Aimée A Wong
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Gabrielle M Hanson
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Richard E Brown
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, B3H 4R2, Canada.,Brain Repair Centre, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Ian C G Weaver
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, B3H 4R2, Canada. .,Department of Psychiatry, Dalhousie University, Halifax, NS, B3H 4R2, Canada. .,Department of Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada. .,Brain Repair Centre, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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15
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Liang D, Aygün N, Matoba N, Ideraabdullah FY, Love MI, Stein JL. Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation. Hum Mol Genet 2023; 32:402-416. [PMID: 35994039 PMCID: PMC9851749 DOI: 10.1093/hmg/ddac207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023] Open
Abstract
Genomic imprinting results in gene expression bias caused by parental chromosome of origin and occurs in genes with important roles during human brain development. However, the cell-type and temporal specificity of imprinting during human neurogenesis is generally unknown. By detecting within-donor allelic biases in chromatin accessibility and gene expression that are unrelated to cross-donor genotype, we inferred imprinting in both primary human neural progenitor cells and their differentiated neuronal progeny from up to 85 donors. We identified 43/20 putatively imprinted regulatory elements (IREs) in neurons/progenitors, and 133/79 putatively imprinted genes in neurons/progenitors. Although 10 IREs and 42 genes were shared between neurons and progenitors, most putative imprinting was only detected within specific cell types. In addition to well-known imprinted genes and their promoters, we inferred novel putative IREs and imprinted genes. Consistent with both DNA methylation-based and H3K27me3-based regulation of imprinted expression, some putative IREs also overlapped with differentially methylated or histone-marked regions. Finally, we identified a progenitor-specific putatively imprinted gene overlapping with copy number variation that is associated with uniparental disomy-like phenotypes. Our results can therefore be useful in interpreting the function of variants identified in future parent-of-origin association studies.
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Affiliation(s)
- Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Folami Y Ideraabdullah
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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16
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Sheng KY, Nakano T, Yamaguchi S. A region-dependent allele-biased expression of Dopa decarboxylase in mouse brain. Front Cell Dev Biol 2022; 10:1078927. [PMID: 36568970 PMCID: PMC9768605 DOI: 10.3389/fcell.2022.1078927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic imprinting is an epigenetic event in which genes are expressed only from either the paternal or maternal allele. Dopa decarboxylase (Ddc), is an imprinted gene that encodes an enzyme which catalyzes the conversion of L-dopa to dopamine. Although Ddc has been reported to be paternally expressed in embryonic and neonatal hearts, its expression pattern in the brain has been controversial. To visualize Ddc-expressing neurons, we established a knock-in mouse carrying a humanized Kusabira orange 1 (hKO1) reporter cassette at the Ddc locus (Ddc-hKO1). The expression of Ddc-hKO1 was detected in all known Ddc-positive cells in the brains of embryonic, neonatal, adult, and aged mice. We further developed an efficient purification method for Ddc-hKO1-positive neurons using a cell sorter. RNA sequencing analysis confirmed the enrichment of dopaminergic, serotonergic and cholinergic neurons in Ddc-hKO1-positive cell population recovered using this method. A detailed analysis of Ddc-hKO1 paternally and maternally derived heterozygous mice combined with immunostaining revealed that Ddc was preferentially expressed from the maternal allele in ventral tegmented area (VTA), substantia nigra pars compacta (SNc), and retrorubral field (RRF); while it was expressed from both alleles in dorsal raphe nucleus (DR). These results indicate that Ddc exhibit an allele-specific expression pattern in different brain regions, presumably reflecting the diverse regulatory mechanisms of imprinting.
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Affiliation(s)
- Kit-Yeng Sheng
- Department of Pathology, Graduate School of Frontier Biosciences, Osaka, Japan
| | - Toru Nakano
- Department of Pathology, Graduate School of Frontier Biosciences, Osaka, Japan,Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shinpei Yamaguchi
- Graduate School of Medicine, Osaka University, Osaka, Japan,Stem Cells and Reprogramming Laboratory, Department of Biology, Faculty of Science, Toho University, Chiba, Japan,*Correspondence: Shinpei Yamaguchi,
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17
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Salminen I, Read S, Crespi B. Do the diverse phenotypes of Prader-Willi syndrome reflect extremes of covariation in typical populations? Front Genet 2022; 13:1041943. [PMID: 36506301 PMCID: PMC9731222 DOI: 10.3389/fgene.2022.1041943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
The phenotypes of human imprinted neurogenetic disorders can be hypothesized as extreme alterations of typical human phenotypes. The imprinted neurogenetic disorder Prader-Willi syndrome (PWS) features covarying phenotypes that centrally involve altered social behaviors, attachment, mood, circadian rhythms, and eating habits, that can be traced to altered functioning of the hypothalamus. Here, we conducted analyses to investigate the extent to which the behavioral variation shown in typical human populations for a set of PWAS-associated traits including autism spectrum cognition, schizotypal cognition, mood, eating, and sleeping phenotypes shows covariability that recapitulates the covariation observed in individuals with PWS. To this end, we collected data from 296 typical individuals for this set of phenotypes, and showed, using principal components analysis, evidence of a major axis reflecting key covarying PWS traits. We also reviewed the literature regarding neurogenetic syndromes that overlap in their affected traits with PWS, to determine their prevalence and properties. These findings demonstrate that a notable suite of syndromes shows phenotypic overlap with PWS, implicating a large set of imprinted and non-imprinted genes, some of which interact, in the phenotypes of this disorder. Considered together, these findings link variation in and among neurogenetic disorders with variation in typical populations, especially with regard to pleiotropic effects mediated by the hypothalamus. This work also implicates effects of imprinted gene variation on cognition and behavior in typical human populations.
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18
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Higgs MJ, Hill MJ, John RM, Isles AR. Systematic investigation of imprinted gene expression and enrichment in the mouse brain explored at single-cell resolution. BMC Genomics 2022; 23:754. [PMID: 36384442 PMCID: PMC9670596 DOI: 10.1186/s12864-022-08986-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Although a number of imprinted genes are known to be highly expressed in the brain, and in certain brain regions in particular, whether they are truly over-represented in the brain has never been formally tested. Using thirteen single-cell RNA sequencing datasets we systematically investigated imprinted gene over-representation at the organ, brain region, and cell-specific levels. RESULTS We established that imprinted genes are indeed over-represented in the adult brain, and in neurons particularly compared to other brain cell-types. We then examined brain-wide datasets to test enrichment within distinct brain regions and neuron subpopulations and demonstrated over-representation of imprinted genes in the hypothalamus, ventral midbrain, pons and medulla. Finally, using datasets focusing on these regions of enrichment, we identified hypothalamic neuroendocrine populations and the monoaminergic hindbrain neurons as specific hotspots of imprinted gene expression. CONCLUSIONS These analyses provide the first robust assessment of the neural systems on which imprinted genes converge. Moreover, the unbiased approach, with each analysis informed by the findings of the previous level, permits highly informed inferences about the functions on which imprinted gene expression converges. Our findings indicate the neuronal regulation of motivated behaviours such as feeding and sleep, alongside the regulation of pituitary function, as functional hotspots for imprinting. This adds statistical rigour to prior assumptions and provides testable predictions for novel neural and behavioural phenotypes associated with specific genes and imprinted gene networks. In turn, this work sheds further light on the potential evolutionary drivers of genomic imprinting in the brain.
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Affiliation(s)
- M J Higgs
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - M J Hill
- School of Medicine, UK Dementia Research Institute, Cardiff University, Cardiff, UK
| | - R M John
- School of Biosciences, Cardiff University, Cardiff, UK
| | - A R Isles
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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19
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Claxton M, Pulix M, Seah MKY, Bernardo R, Zhou P, Aljuraysi S, Liloglou T, Arnaud P, Kelsey G, Messerschmidt DM, Plagge A. Variable allelic expression of imprinted genes at the Peg13, Trappc9, Ago2 cluster in single neural cells. Front Cell Dev Biol 2022; 10:1022422. [PMID: 36313557 PMCID: PMC9596773 DOI: 10.3389/fcell.2022.1022422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic process through which genes are expressed in a parent-of-origin specific manner resulting in mono-allelic or strongly biased expression of one allele. For some genes, imprinted expression may be tissue-specific and reliant on CTCF-influenced enhancer-promoter interactions. The Peg13 imprinting cluster is associated with neurodevelopmental disorders and comprises canonical imprinted genes, which are conserved between mouse and human, as well as brain-specific imprinted genes in mouse. The latter consist of Trappc9, Chrac1 and Ago2, which have a maternal allelic expression bias of ∼75% in brain. Findings of such allelic expression biases on the tissue level raise the question of how they are reflected in individual cells and whether there is variability and mosaicism in allelic expression between individual cells of the tissue. Here we show that Trappc9 and Ago2 are not imprinted in hippocampus-derived neural stem cells (neurospheres), while Peg13 retains its strong bias of paternal allele expression. Upon analysis of single neural stem cells and in vitro differentiated neurons, we find not uniform, but variable states of allelic expression, especially for Trappc9 and Ago2. These ranged from mono-allelic paternal to equal bi-allelic to mono-allelic maternal, including biased bi-allelic transcriptional states. Even Peg13 expression deviated from its expected paternal allele bias in a small number of cells. Although the cell populations consisted of a mosaic of cells with different allelic expression states, as a whole they reflected bulk tissue data. Furthermore, in an attempt to identify potential brain-specific regulatory elements across the Trappc9 locus, we demonstrate tissue-specific and general silencer activities, which might contribute to the regulation of its imprinted expression bias.
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Affiliation(s)
- Michael Claxton
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Michela Pulix
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michelle K. Y. Seah
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ralph Bernardo
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Peng Zhou
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sultan Aljuraysi
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Triantafillos Liloglou
- Faculty of Health, Social Care and Medicine, Edge Hill University, Ormskirk, Lancashire, United Kingdom
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge, United Kingdom
| | - Daniel M. Messerschmidt
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Antonius Plagge
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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20
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Latchney SE, Cadney MD, Hopkins A, Garland T. DNA Methylation Analysis of Imprinted Genes in the Cortex and Hippocampus of Cross-Fostered Mice Selectively Bred for Increased Voluntary Wheel-Running. Behav Genet 2022; 52:281-297. [PMID: 35988119 PMCID: PMC9463359 DOI: 10.1007/s10519-022-10112-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/26/2022] [Indexed: 11/03/2022]
Abstract
We have previously shown that high runner (HR) mice (from a line genetically selected for increased wheel-running behavior) have distinct, genetically based, neurobiological phenotypes as compared with non-selected control (C) mice. However, developmental programming effects during early life, including maternal care and parent-of-origin-dependent expression of imprinted genes, can also contribute to variation in physical activity. Here, we used cross-fostering to address two questions. First, do HR mice have altered DNA methylation profiles of imprinted genes in the brain compared to C mice? Second, does maternal upbringing further modify the DNA methylation status of these imprinted genes? To address these questions, we cross-fostered all offspring at birth to create four experimental groups: C pups to other C dams, HR pups to other HR dams, C pups to HR dams, and HR pups to C dams. Bisulfite sequencing of 16 imprinted genes in the cortex and hippocampus revealed that the HR line had altered DNA methylation patterns of the paternally imprinted genes, Rasgrf1 and Zdbf2, as compared with the C line. Both fostering between the HR and C lines and sex modified the DNA methylation profiles for the paternally expressed genes Mest, Peg3, Igf2, Snrpn, and Impact. Ig-DMR, a gene with multiple paternal and maternal imprinted clusters, was also affected by maternal upbringing and sex. Our results suggest that differential methylation patterns of imprinted genes in the brain could contribute to evolutionary increases in wheel-running behavior and are also dependent on maternal upbringing and sex.
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Affiliation(s)
- Sarah E Latchney
- Department of Biology, St. Mary's College of Maryland, 18952 E. Fisher Rd, Saint Mary's City, MD, 20686, USA.
| | - Marcell D Cadney
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | | | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
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21
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Kenny D, Sleator RD, Murphy CP, Evans RD, Berry DP. Detection of Genomic Imprinting for Carcass Traits in Cattle Using Imputed High-Density Genotype Data. Front Genet 2022; 13:951087. [PMID: 35910233 PMCID: PMC9334527 DOI: 10.3389/fgene.2022.951087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/16/2022] [Indexed: 12/03/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon defined as the silencing of an allele, at least partially, at a given locus based on the sex of the transmitting parent. The objective of the present study was to detect the presence of SNP-phenotype imprinting associations for carcass weight (CW), carcass conformation (CC) and carcass fat (CF) in cattle. The data used comprised carcass data, along with imputed, high-density genotype data on 618,837 single nucleotide polymorphisms (SNPs) from 23,687 cattle; all animal genotypes were phased with respect to parent of origin. Based on the phased genotypes and a series of single-locus linear models, 24, 339, and 316 SNPs demonstrated imprinting associations with CW, CC, and CF, respectively. Regardless of the trait in question, no known imprinted gene was located within 0.5 Mb of the SNPs demonstrating imprinting associations in the present study. Since all imprinting associations detected herein were at novel loci, further investigation of these regions may be warranted. Nonetheless, knowledge of these associations might be useful for improving the accuracy of genomic evaluations for these traits, as well as mate allocations systems to exploit the effects of genomic imprinting.
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Affiliation(s)
- David Kenny
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Co. Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Co. Cork, Ireland
| | - Roy D. Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Co. Cork, Ireland
| | - Craig P. Murphy
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Co. Cork, Ireland
| | - Ross D. Evans
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - Donagh P. Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Co. Cork, Ireland
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22
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Li X, Wang M, Liu S, Chen X, Qiao Y, Yang X, Yao J, Wu S. Paternal transgenerational nutritional epigenetic effect: A new insight into nutritional manipulation to reduce the use of antibiotics in animal feeding. ANIMAL NUTRITION 2022; 11:142-151. [PMID: 36204282 PMCID: PMC9527621 DOI: 10.1016/j.aninu.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 11/15/2022]
Abstract
The use of antibiotics in animal feeding has been banned in many countries because of increasing concerns about the development of bacterial resistance to antibiotics and potential issues on food safety. Searching for antibiotic substitutes is essential. Applying transgenerational epigenetic technology to animal production could be an alternative. Some environmental changes can be transferred to memory-like responses in the offspring through epigenetic mechanisms without changing the DNA sequence. In this paper, we reviewed those nutrients and non-nutritional additives that have transgenerational epigenetic effects, including some amino acids, vitamins, and polysaccharides. The paternal transgenerational nutritional epigenetic regulation was particularly focused on mechanism of the substantial contribution of male stud animals to the animal industries. We illustrated the effects of paternal transgenerational epigenetics on the metabolism and immunity in farming animals and proposed strategies to modulate male breeding livestock or poultry.
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Affiliation(s)
- Xinyi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Medicine, Karolinska Institutet, Solna, Stockholm 17165, Sweden
| | - Mengya Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shimin Liu
- Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
| | - Xiaodong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Qiao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Animal Engineering, Yangling Vocational and Technical College, Yangling, Shaanxi 712100, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Corresponding authors.
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Corresponding authors.
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23
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Behavioral Phenotype in Heterozygous DAT Rats: Transgenerational Transmission of Maternal Impact and the Role of Genetic Asset. Brain Sci 2022; 12:brainsci12040469. [PMID: 35448000 PMCID: PMC9032929 DOI: 10.3390/brainsci12040469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 11/17/2022] Open
Abstract
Dopamine transporter (DAT) is involved in dopamine (DA) reuptake in presynaptic terminals. Deletion of DAT results in a hyperdopaminergic KO-rat phenotype. To conduct our studies in heterozygous DAT rats, several pedigree lines were created, with known derivation of the allele (i.e., maternal or paternal). Our purpose was to elucidate the role of parental origin rather than maternal care, assessing if maternal maltreatments generated sequelae in female offspring. In the first experiment, female rats and their pups were observed during postnatal lactation. Control dams were WT and heterozygous ones were MAT (but K-MAT, with previous experience of early maltreatment by their KO adoptive dams). WT dams were highly attracted to their offspring (predictably, they spent a lot of time licking their pups); in contrast, K-MAT dams showed strangely comparable levels of caring for their pups and exploring the environment. Subsequently, peculiar features of the circadian cycle were found in adolescent rats with different epigenotypes (WT, MUX = offspring of MAT father, MIK = offspring of K-MAT dam). The MIK epigenotype produced locomotor hyperactivity also during resting hours, well above typical values. The MUX epigenotype, on the other hand, was less active and presented a depression-like profile. This study is unique: maltreatment was generated in a spontaneous way from a DAT-KO mother to offspring. We highlight how future studies will address separate contributions by genotype and upbringing. In conclusion, paternal-allele asset generates sequelae diametrically opposed to the inheritance of early maternal trauma.
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24
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Martini P, Sales G, Diamante L, Perrera V, Colantuono C, Riccardo S, Cacchiarelli D, Romualdi C, Martello G. BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes. Commun Biol 2022; 5:146. [PMID: 35177756 PMCID: PMC8854590 DOI: 10.1038/s42003-022-03087-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic imprinting and X chromosome inactivation (XCI) are two prototypical epigenetic mechanisms whereby a set of genes is expressed mono-allelically in order to fine-tune their expression levels. Defects in genomic imprinting have been observed in several neurodevelopmental disorders, in a wide range of tumours and in induced pluripotent stem cells (iPSCs). Single Nucleotide Variants (SNVs) are readily detectable by RNA-sequencing allowing the determination of whether imprinted or X-linked genes are aberrantly expressed from both alleles, although standardised analysis methods are still missing. We have developed a tool, named BrewerIX, that provides comprehensive information about the allelic expression of a large, manually-curated set of imprinted and X-linked genes. BrewerIX does not require programming skills, runs on a standard personal computer, and can analyze both bulk and single-cell transcriptomes of human and mouse cells directly from raw sequencing data. BrewerIX confirmed previous observations regarding the bi-allelic expression of some imprinted genes in naive pluripotent cells and extended them to preimplantation embryos. BrewerIX also identified misregulated imprinted genes in breast cancer cells and in human organoids and identified genes escaping XCI in human somatic cells. We believe BrewerIX will be useful for the study of genomic imprinting and XCI during development and reprogramming, and for detecting aberrations in cancer, iPSCs and organoids. Due to its ease of use to non-computational biologists, its implementation could become standard practice during sample assessment, thus raising the robustness and reproducibility of future studies.
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Affiliation(s)
- Paolo Martini
- Department of Biology, University of Padova, Padua, Italy
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, Padua, Italy
| | - Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padova, Padua, Italy
| | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padova, Padua, Italy
- International School for Advanced Studies (SISSA/ISAS), Trieste, 34136, Italy
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Sara Riccardo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
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25
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Pepe M, Calcaprina B, Vaquer F, Laviola G, Adriani W. DAT-truncated epigenetics: heterozigosity of the grand-mother rat temperates the vulnerable phenotype in second-generation offspring. Int J Dev Neurosci 2022; 82:168-179. [PMID: 35156234 DOI: 10.1002/jdn.10172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 11/07/2022] Open
Abstract
Behavioral phenotype differs among epigenotypes of dopamine-transporter heterozygous (DAT-HET) rats. Epigenetic regulations act through trans-generational effects, referring to phenotypic variations emerging at second or third generation. To investigate trans-generational influences exerted by maternal grandmothers, we developed breeding schemes where only the genotype of maternal grandmothers varied. Heterozygous females, to serve as MAT vs MIX mothers, were generated, respectively, from WTxKO=MAT and MATxKO=MIX breeding, with KO males acting as grandfather. The HET experimental groups, generated from either MAT or MIX mothers, were called MIX-by-MAT and MIX2 (male-fathers KO; asset-M: wild\healthy-allele from dam); or SOT and SIX (male-fathers WT; asset-P: mutated-allele from dam). Thus, sequelae of first-encounter between wild\healthy and mutated DAT-alleles (in maternal-lineage) were compared at first- (MAT-dam, WT-grandmother) vs. at second- (MIX-dam, HET-grandmother) generation. We characterized, within these epigenotypes, (1) circadian home-cage activity; (2) preference for social stimuli. Marked alterations of circadian activity appeared in HETs, if offspring of MAT-dams, compared to MIX2 (HET offspring of MIX-dams) which, in turn, were undistinguishable from WT-controls. A clear-cut social preference by WT-rats was expressed towards SIX compared to SOT stimulus-rats, confirming reduced social motivations. In conclusion, significant epigenetic modulations took place in DAT-HET rats, as a function of maternal grandmother's genotype.
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Affiliation(s)
- Martina Pepe
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Barbara Calcaprina
- Faculty of Psychology, Università Telematica Internazionale "Uninettuno", Rome, Italy
| | - Francesca Vaquer
- Faculty of Psychology, Università Telematica Internazionale "Uninettuno", Rome, Italy
| | - Giovanni Laviola
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Walter Adriani
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy.,Faculty of Psychology, Università Telematica Internazionale "Uninettuno", Rome, Italy
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26
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Liberati AS, Calcaprina B, Adriani W. Keeping Track of the Genealogy of Heterozygotes Using Epigenetic Reference Codes and Breeding Tables. Front Behav Neurosci 2022; 15:781235. [PMID: 35221940 PMCID: PMC8874286 DOI: 10.3389/fnbeh.2021.781235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Studying neurobehavioral consequences of the hypofunctional dopamine transporter (DAT) across several generations entails the need to monitor allelic transmission to offspring, taking into account both maternal and paternal inheritance. Since each type of heterozygote expresses differential phenotypes, based on lineage of inheritance for wild and mutated alleles (from male or female ancestors), it is important to track transgenerational epigenetic effects. We deemed it essential to assign specific abbreviations identifying their characteristics. Therefore, we devised a Mendelian-inspired table to keep track of these. Starting from two progenitors (WT and KO) we named resulting heterozygous progenies MAT and PAT to differentiate them based on inheritance of the wild allele (from the mother or father). Tracing subsequent generations, similar logic has been followed: if coupling HET dams with KO males, initials “M” [(grand)maternal] and “P” [(grand)paternal] are kept, but “AT” is turned into “IX” (MIX and PIX), while if breeding HETs with WTs, “M” is changed to “W” resembling an upside down “M” and “P” to “S” for “sperm” (WAT and SOT). To underline the development within “hyperdopaminergic-uterus” a central letter “U” is added (MUX, PUX, and QULL), while a Greek initial (μAT, μIX, and νIX) underlines the uterine-worsened origin of the allele. In HET × HET breeding (GIX and DIX), the mutated allele can be inherited from both sides of the genealogical line. However, when the mother is MAT, wild and mutated alleles encounter for the first time, causing putative anomalies in the progeny. Replacing dam with a second-generation female (MIX and MUX) may mitigate epigenetic effects on third-generation offspring; therefore suffixes (“-f,” “-fu,” “-ϕ,” and “-ϕu”) emphasize that subsequent-generation dams imply that the alleles already encountered in HET (rather than WT) grand-dams.
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Affiliation(s)
- Anna Sara Liberati
- Faculty of Psychology, Università Telematica Internazionale “Uninettuno,” Rome, Italy
| | - Barbara Calcaprina
- Faculty of Psychology, Università Telematica Internazionale “Uninettuno,” Rome, Italy
| | - Walter Adriani
- Faculty of Psychology, Università Telematica Internazionale “Uninettuno,” Rome, Italy
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Walter Adriani,
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27
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Oggiano M, Buccheri C, Alleva E, Adriani W. Dopaminergic modulation of the circadian activity and sociability: Dissecting parental inheritance versus maternal styles as determinants of epigenetic influence. Behav Brain Res 2022; 417:113623. [PMID: 34624423 DOI: 10.1016/j.bbr.2021.113623] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/15/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022]
Abstract
In mammalians, social life and circadian rhythms find their neurobiological basis in a network that includes the dopaminergic system. The malfunctioning of dopamine pathways can lead to various disorders such as Attention-Deficit/Hyperactivity and Obsessive/compulsive disorders. A useful research approach is to exploit animal models that carry a functional silencing of SLC6A3 gene, encoding the dopamine transporter (DAT). Hyperactivity, working memory deficits, and asocial tendencies are core features in truncated-DAT rats, for example. We investigated how inheritance and maternal caring style influence circadian rhythms and social behaviours in DAT heterozygous (HET) rats, belonging to four groups: Mat-P, Mat-M, Mix-P, and Mix-M (Mat label stands for care from wild-type dam, Mix label stands for care by heterozygous dam; M label stands for maternal wild-DAT and P label stands for paternal wild-DAT). In Experiment 1, we monitored 24/7 the spontaneous locomotor activity of peri-adolescent subjects. Hyperactivity occurred only in P-asset subjects (with maternal-origin truncated-DAT allele) at specific bins of the day. In Experiment 2, we observed social interactions of the same rats. Mix-M subjects (raised by HET dams and/or inheriting the wild-DAT allele from mothers) tend to interact with all rats; Mat-P (cared by WT dams and/or inheriting the truncated-DAT allele from mothers) seem to be ignored, when acting as stimulus subjects. Overall, results confirm complex modulations for circadian cycle and social life: flexible DAT expression in HET subjects depends on epigenetic combinations of parental inheritance and early experiential factors. Once confirmed, these data could shed light on trans-generational contributions to dopaminergic-related disorders.
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Affiliation(s)
- Maurizio Oggiano
- European Mind and Metabolism Association, Via Valtellina 108, Rome, Italy
| | - Clelia Buccheri
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Enrico Alleva
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Walter Adriani
- European Mind and Metabolism Association, Via Valtellina 108, Rome, Italy; Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy.
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Glaser J, Iranzo J, Borensztein M, Marinucci M, Gualtieri A, Jouhanneau C, Teissandier A, Gaston-Massuet C, Bourc'his D. The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates. eLife 2022; 11:e65641. [PMID: 35049495 PMCID: PMC8809892 DOI: 10.7554/elife.65641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Genomic imprinting refers to the mono-allelic and parent-specific expression of a subset of genes. While long recognized for their role in embryonic development, imprinted genes have recently emerged as important modulators of postnatal physiology, notably through hypothalamus-driven functions. Here, using mouse models of loss, gain and parental inversion of expression, we report that the paternally expressed Zdbf2 gene controls neonatal growth in mice, in a dose-sensitive but parent-of-origin-independent manner. We further found that Zdbf2-KO neonates failed to fully activate hypothalamic circuits that stimulate appetite, and suffered milk deprivation and diminished circulating Insulin Growth Factor 1 (IGF-1). Consequently, only half of Zdbf2-KO pups survived the first days after birth and those surviving were smaller. This study demonstrates that precise imprinted gene dosage is essential for vital physiological functions at the transition from intra- to extra-uterine life, here the adaptation to oral feeding and optimized body weight gain.
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Affiliation(s)
- Juliane Glaser
- Institut Curie, PSL Research University, INSERM, CNRSParisFrance
| | - Julian Iranzo
- Institut Curie, PSL Research University, INSERM, CNRSParisFrance
| | - Maud Borensztein
- Institut Curie, PSL Research University, INSERM, CNRSParisFrance
| | - Mattia Marinucci
- Institut Curie, PSL Research University, INSERM, CNRSParisFrance
| | - Angelica Gualtieri
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | - Colin Jouhanneau
- Institut Curie, PSL Research University, Animal Transgenesis PlatformParisFrance
| | | | - Carles Gaston-Massuet
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
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Kobayashi EH, Shibata S, Oike A, Kobayashi N, Hamada H, Okae H, Arima T. Genomic imprinting in human placentation. Reprod Med Biol 2022; 21:e12490. [PMID: 36465588 PMCID: PMC9713850 DOI: 10.1002/rmb2.12490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Background Genomic imprinting (GI) is a mammalian-specific epigenetic phenomenon that has been implicated in the evolution of the placenta in mammals. Methods Embryo transfer procedures and trophoblast stem (TS) cells were used to re-examine mouse placenta-specific GI genes. For the analysis of human GI genes, cytotrophoblast cells isolated from human placental tissues were used. Using human TS cells, the biological roles of human GI genes were examined. Main findings (1) Many previously identified mouse GI genes were likely to be falsely identified due to contaminating maternal cells. (2) Human placenta-specific GI genes were comprehensively determined, highlighting incomplete erasure of germline DNA methylation in the human placenta. (3) Human TS cells retained normal GI patterns. (4) Complete hydatidiform mole-derived TS cells were characterized by aberrant GI and enhanced trophoblastic proliferation. The maternally expressed imprinted gene p57KIP2 may be responsible for the enhanced proliferation. (5) The primate-specific microRNA cluster on chromosome 19, which is a placenta-specific GI gene, is essential for self-renewal and differentiation of human TS cells. Conclusion Genomic imprinting plays diverse and important roles in human placentation. Experimental analyses using TS cells suggest that the GI maintenance is necessary for normal placental development in humans.
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Affiliation(s)
- Eri H. Kobayashi
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Shun Shibata
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Akira Oike
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Norio Kobayashi
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Hirotaka Hamada
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Hiroaki Okae
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
| | - Takahiro Arima
- Department of Informative GeneticsTohoku University School of MedicineSendaiJapan
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Erickson A, Zhou S, Luo J, Li L, Huang X, Even Z, Huang H, Xu HM, Peng J, Lu L, Wang X. Genetic architecture of protein expression and its regulation in the mouse brain. BMC Genomics 2021; 22:875. [PMID: 34863093 PMCID: PMC8642946 DOI: 10.1186/s12864-021-08168-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged considerably behind. Here we investigate genetic architecture of protein expression by profiling a deep mouse brain proteome of two inbred strains, C57BL/6 J (B6) and DBA/2 J (D2), and their reciprocal F1 hybrids using two-dimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) technology. RESULTS By comparing protein expression levels in the four mouse strains, we observed 329 statistically significant differentially expressed proteins between the two parental strains and characterized the genetic basis of protein expression. We further applied a proteogenomic approach to detect variant peptides and define protein allele-specific expression (pASE), identifying 33 variant peptides with cis-effects and 17 variant peptides showing trans-effects. Comparison of regulation at transcript and protein levels show a significant divergence. CONCLUSIONS The results provide a comprehensive analysis of genetic architecture of protein expression and the contribution of cis- and trans-acting regulatory differences to protein expression.
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Affiliation(s)
- Alyssa Erickson
- Department of Biology, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38163, USA
| | - Jie Luo
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ling Li
- Department of Biology, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Xin Huang
- Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zachary Even
- Department of Biology, University of North Dakota, Grand Forks, ND, 58202, USA
| | - He Huang
- Department of Biology, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Hai-Ming Xu
- Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38163, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Xusheng Wang
- Department of Biology, University of North Dakota, Grand Forks, ND, 58202, USA.
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Zhang Z, Yu S, Li J, Zhu Y, Jiang S, Xia H, Zhou Y, Sun D, Liu M, Li C, Zhu Y, Ruan Y, Dong X. Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm. BMC PLANT BIOLOGY 2021; 21:570. [PMID: 34863098 PMCID: PMC8642925 DOI: 10.1186/s12870-021-03344-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/26/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. RESULTS Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. CONCLUSION Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.
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Affiliation(s)
- Zhichao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Jing Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yanbin Zhu
- State Key Laboratory of Maize Bio-Breeding, Shenyang, China
- State Key Laboratory of the Northeast Crop Genetics and Breeding, Shenyang, China
| | - Siqi Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Haoran Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yue Zhou
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Daqiu Sun
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yanshu Zhu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China.
- State Key Laboratory of Maize Bio-Breeding, Shenyang, China.
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Sherbina K, León-Novelo LG, Nuzhdin SV, McIntyre LM, Marroni F. Power calculator for detecting allelic imbalance using hierarchical Bayesian model. BMC Res Notes 2021; 14:436. [PMID: 34838135 PMCID: PMC8626927 DOI: 10.1186/s13104-021-05851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Allelic imbalance (AI) is the differential expression of the two alleles in a diploid. AI can vary between tissues, treatments, and environments. Methods for testing AI exist, but methods are needed to estimate type I error and power for detecting AI and difference of AI between conditions. As the costs of the technology plummet, what is more important: reads or replicates? RESULTS We find that a minimum of 2400, 480, and 240 allele specific reads divided equally among 12, 5, and 3 replicates is needed to detect a 10, 20, and 30%, respectively, deviation from allelic balance in a condition with power > 80%. A minimum of 960 and 240 allele specific reads divided equally among 8 replicates is needed to detect a 20 or 30% difference in AI between conditions with comparable power. Higher numbers of replicates increase power more than adding coverage without affecting type I error. We provide a Python package that enables simulation of AI scenarios and enables individuals to estimate type I error and power in detecting AI and differences in AI between conditions.
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Affiliation(s)
- Katrina Sherbina
- Quantitative and Computational Biology Section, University of Southern California, Los Angeles, CA, 90046, USA
| | - Luis G León-Novelo
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston-School of Public Health, Houston, TX, 77030, USA
| | - Sergey V Nuzhdin
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA, 90046, USA
| | - Lauren M McIntyre
- Genetics Institute and Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32603, USA
| | - Fabio Marroni
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, Università di Udine, 33100, Udine, Italy.
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McCarthy DM, Bhide PG. Heritable consequences of paternal nicotine exposure: from phenomena to mechanisms†. Biol Reprod 2021; 105:632-643. [PMID: 34126634 PMCID: PMC8444703 DOI: 10.1093/biolre/ioab116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/14/2021] [Accepted: 06/07/2021] [Indexed: 12/25/2022] Open
Abstract
Our understanding of the interactions between genetic and environmental factors in shaping behavioral phenotypes has expanded to include environment-induced epigenetic modifications and the intriguing possibility of their association with heritable behavioral phenotypes. The molecular basis of heritability of phenotypes arising from environment-induced epigenetic modifications is not well defined yet. However, phenomenological evidence in favor of it is accumulating rapidly. The resurgence of interest has led to focus on epigenetic modification of germ cells as a plausible mechanism of heritability. Perhaps partly because of practical reasons such as ease of access to male germ cells compared to female germ cells, attention has turned toward heritable effects of environmental influences on male founders. Public health implications of heritable effects of paternal exposures to addictive substances or to psycho-social factors may be enormous. Considering nicotine alone, over a billion people worldwide use nicotine-containing products, and the majority are men. Historically, the adverse effects of nicotine use by pregnant women received much attention by scientists and public policy experts alike. The implications of nicotine use by men for the physical and mental well-being of their children were not at the forefront of research until recently. Here, we review progress in the emerging field of heritable effects of paternal nicotine exposure and its implications for behavioral health of individuals in multiple generations.
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Affiliation(s)
- Deirdre M McCarthy
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, USA
| | - Pradeep G Bhide
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, 32306, USA
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Kozlova A, Butler RR, Zhang S, Ujas T, Zhang H, Steidl S, Sanders AR, Pang ZP, Vezina P, Duan J. Sex-specific nicotine sensitization and imprinting of self-administration in rats inform GWAS findings on human addiction phenotypes. Neuropsychopharmacology 2021; 46:1746-1756. [PMID: 34007041 PMCID: PMC8358005 DOI: 10.1038/s41386-021-01027-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/26/2021] [Accepted: 04/22/2021] [Indexed: 02/04/2023]
Abstract
Repeated nicotine exposure leads to sensitization (SST) and enhances self-administration (SA) in rodents. However, the molecular basis of nicotine SST and SA and their biological relevance to the mounting genome-wide association study (GWAS) loci of human addictive behaviors are poorly understood. Considering a gateway drug role of nicotine, we modeled nicotine SST and SA in F1 progeny of inbred rats (F344/BN) and conducted integrative genomics analyses. We unexpectedly observed male-specific nicotine SST and a parental effect of SA only present in paternal F344 crosses. Transcriptional profiling in the ventral tegmental area (VTA) and nucleus accumbens (NAc) core and shell further revealed sex- and brain region-specific transcriptomic signatures of SST and SA. We found that genes associated with SST and SA were enriched for those related to synaptic processes, myelin sheath, and tobacco use disorder or chemdependency. Interestingly, SST-associated genes were often downregulated in male VTA but upregulated in female VTA, and strongly enriched for smoking GWAS risk variants, possibly explaining the male-specific SST. For SA, we found widespread region-specific allelic imbalance of expression (AIE), of which genes showing AIE bias toward paternal F344 alleles in NAc core were strongly enriched for SA-associated genes and for GWAS risk variants of smoking initiation, likely contributing to the parental effect of SA. Our study suggests a mechanistic link between transcriptional changes underlying the NIC SST and SA and human nicotine addiction, providing a resource for understanding the neurobiology basis of the GWAS findings on human smoking and other addictive phenotypes.
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Affiliation(s)
- Alena Kozlova
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Robert R. Butler
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Siwei Zhang
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Thomas Ujas
- grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Hanwen Zhang
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA
| | - Stephan Steidl
- grid.164971.c0000 0001 1089 6558Department of Psychology, Loyola University Chicago, Chicago, IL USA
| | - Alan R. Sanders
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL USA
| | - Zhiping P. Pang
- grid.430387.b0000 0004 1936 8796Department of Neuroscience and Cell Biology and Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Paul Vezina
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA.
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL, USA. .,Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA.
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Sun X, Chen Z. Cancer-associated fibroblast-derived CCL5 contributes to cisplatin resistance in A549 NSCLC cells partially through upregulation of lncRNA HOTAIR expression. Oncol Lett 2021; 22:696. [PMID: 34457051 PMCID: PMC8358620 DOI: 10.3892/ol.2021.12957] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/28/2021] [Indexed: 12/20/2022] Open
Abstract
Aberrant C-C motif chemokine ligand 5 (CCL5) is associated with disease progression, poor prognosis and chemotherapy resistance in human malignancy. The tumor microenvironment (TME) contributes to chemotherapy resistance. However, the role of cancer-associated fibroblasts (CAFs)-derived CCL5 is not well documented. Hence, the present study aimed to investigate the effects of CAFs on chemotherapy resistance in A549 non-small cell lung cancer (NSCLC) cells and the underlying mechanism. Primary CAFs isolated from patients with NSCLC were found to express and secrete elevated levels of CCL5, which attenuated cisplatin (DDP)-induced apoptosis, as indicated by flow cytometry analysis. In addition, CCL5 upregulated the expression levels of long non-coding RNA (lncRNA) HOX transcript antisense RNA (HOTAIR) in the tumor cells, and silencing HOTAIR in tumor cells enhanced the cytotoxic effect of cisplatin, characterized by decreased cell viability and increased apoptotic rate. Mechanistically, HOTAIR was found to inactivate the caspase-3/BCL-2 signaling pathway in A549 NSCLC cells. Collectively, the current study demonstrated that CAFs in the TME may serve a crucial role in the higher expression levels of CCL5 in tumors and that CAF-derived CCL5 may promote cisplatin resistance via upregulating lncRNA HOTAIR expression.
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Affiliation(s)
- Xiangjun Sun
- Department of Respiratory and Critical Care Medicine, Hanchuan People's Hospital, Hanchuan, Hubei 431600, P.R. China
| | - Zhijie Chen
- Department of General Surgery, Hanchuan People's Hospital, Hanchuan, Hubei 431600, P.R. China
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Prickett AR, Montibus B, Barkas N, Amante SM, Franco MM, Cowley M, Puszyk W, Shannon MF, Irving MD, Madon-Simon M, Ward A, Schulz R, Baldwin HS, Oakey RJ. Imprinted Gene Expression and Function of the Dopa Decarboxylase Gene in the Developing Heart. Front Cell Dev Biol 2021; 9:676543. [PMID: 34239874 PMCID: PMC8258389 DOI: 10.3389/fcell.2021.676543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Dopa decarboxylase (DDC) synthesizes serotonin in the developing mouse heart where it is encoded by Ddc_exon1a, a tissue-specific paternally expressed imprinted gene. Ddc_exon1a shares an imprinting control region (ICR) with the imprinted, maternally expressed (outside of the central nervous system) Grb10 gene on mouse chromosome 11, but little else is known about the tissue-specific imprinted expression of Ddc_exon1a. Fluorescent immunostaining localizes DDC to the developing myocardium in the pre-natal mouse heart, in a region susceptible to abnormal development and implicated in congenital heart defects in human. Ddc_exon1a and Grb10 are not co-expressed in heart nor in brain where Grb10 is also paternally expressed, despite sharing an ICR, indicating they are mechanistically linked by their shared ICR but not by Grb10 gene expression. Evidence from a Ddc_exon1a gene knockout mouse model suggests that it mediates the growth of the developing myocardium and a thinning of the myocardium is observed in a small number of mutant mice examined, with changes in gene expression detected by microarray analysis. Comparative studies in the human developing heart reveal a paternal expression bias with polymorphic imprinting patterns between individual human hearts at DDC_EXON1a, a finding consistent with other imprinted genes in human.
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Affiliation(s)
- Adam R. Prickett
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Bertille Montibus
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Nikolaos Barkas
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Samuele M. Amante
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Maurício M. Franco
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Michael Cowley
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - William Puszyk
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Matthew F. Shannon
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Melita D. Irving
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- Department of Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Marta Madon-Simon
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Andrew Ward
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - H. Scott Baldwin
- Department of Pediatrics (Cardiology), Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rebecca J. Oakey
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
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Srancikova A, Bacova Z, Bakos J. The epigenetic regulation of synaptic genes contributes to the etiology of autism. Rev Neurosci 2021; 32:791-802. [PMID: 33939901 DOI: 10.1515/revneuro-2021-0014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/12/2021] [Indexed: 12/30/2022]
Abstract
Epigenetic mechanisms greatly affect the developing brain, as well as the maturation of synapses with pervasive, long-lasting consequences on behavior in adults. Substantial evidence exists that implicates dysregulation of epigenetic mechanisms in the etiology of neurodevelopmental disorders. Therefore, this review explains the role of enzymes involved in DNA methylation and demethylation in neurodevelopment by emphasizing changes of synaptic genes and proteins. Epigenetic causes of sex-dependent differences in the brain are analyzed in conjunction with the pathophysiology of autism spectrum disorders. Special attention is devoted to the epigenetic regulation of the melanoma-associated antigen-like gene 2 (MAGEL2) found in Prader-Willi syndrome, which is known to be accompanied by autistic symptoms.
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Affiliation(s)
- Annamaria Srancikova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Zuzana Bacova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
| | - Jan Bakos
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University, Bratislava, Slovakia
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Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HES, Loux SC, Esteller-Vico A, Norris JK, Anand L, Scoggin KE, Rodriguez Lopez CM, Breen J, Bailey E, Daels P, Ball BA. Parental bias in expression and interaction of genes in the equine placenta. Proc Natl Acad Sci U S A 2021; 118:e2006474118. [PMID: 33853939 PMCID: PMC8072238 DOI: 10.1073/pnas.2006474118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a workflow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.
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Affiliation(s)
- Pouya Dini
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Theodore Kalbfleisch
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202
| | - José M Uribe-Salazar
- Department of Biochemistry and Molecular Medicine, Genome Center, Medical Investigation of Neurodevelopmental Disorders Institute, University of California, Davis, CA 95616
| | - Mariano Carossino
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, 35516, Egypt
| | - Shavahn C Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Alejandro Esteller-Vico
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Jamie K Norris
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Ernest Bailey
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Peter Daels
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Barry A Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503;
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Cornish A, Roychoudhury S, Sarma K, Pramanik S, Bhakat K, Dudley A, Mishra NK, Guda C. Red panda: a novel method for detecting variants in single-cell RNA sequencing. BMC Genomics 2020; 21:830. [PMID: 33372593 PMCID: PMC7771073 DOI: 10.1186/s12864-020-07224-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at identifying single nucleotide variations or micro (1-50 bp) insertions and deletions in single-cell RNA sequencing (scRNA-seq) data. Generating high-quality variant data is vital to the study of the aforementioned diseases, among others. RESULTS In this study, we report the design and implementation of Red Panda, a novel method to accurately identify variants in scRNA-seq data. Variants were called on scRNA-seq data from human articular chondrocytes, mouse embryonic fibroblasts (MEFs), and simulated data stemming from the MEF alignments. Red Panda had the highest Positive Predictive Value at 45.0%, while other tools-FreeBayes, GATK HaplotypeCaller, GATK UnifiedGenotyper, Monovar, and Platypus-ranged from 5.8-41.53%. From the simulated data, Red Panda had the highest sensitivity at 72.44%. CONCLUSIONS We show that our method provides a novel and improved mechanism to identify variants in scRNA-seq as compared to currently existing software. However, methods for identification of genomic variants using scRNA-seq data can be still improved.
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Affiliation(s)
- Adam Cornish
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Shrabasti Roychoudhury
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Krishna Sarma
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Suravi Pramanik
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kishor Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Andrew Dudley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nitish K Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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40
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Li J, Zhang C, Si H, Gu S, Liu X, Li D, Meng S, Yang X, Li S. Brain-specific monoallelic expression of bovine UBE3A is associated with genomic position. Anim Genet 2020; 52:47-54. [PMID: 33200847 DOI: 10.1111/age.13023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2020] [Indexed: 11/30/2022]
Abstract
Genomic imprinting is a rare epigenetic process in mammalian cells that leads to monoallelic expression of a gene with a parent-specific pattern. The UBE3A (ubiquitin protein ligase E3A) gene is imprinted with maternal allelic expression in the brain but biallelically expressed in all other tissues in humans. The silencing of the paternal UBE3A allele is thought to be caused by the paternally expressed antisense RNA transcript of UBE3A-ATS. The aberrant imprinted expression of the UBE3A is associated with several neurodevelopmental syndromes and psychological disorders. Cattle are a valuable model species in determining the genetic etiology of sporadic human disorder, and maternal expression of UEB3A has been revealed by next-generation sequencing study in the bovine conceptus. In this study, we investigated the allelic expression of UBE3A and UBE3A-ATS in adult bovine somatic tissues. To confirm the splicing pattern of bovine UBE3A, five 5' alternative transcripts (MT210534-MT210538) were first obtained from bovine brain tissue by RT-PCR. Based on 10 SNP genotypes, we found that the brain-specific monoallelic expression of bovine UBE3A did not occur along the entire locus, and there was a shift from biallelic expression to monoallelic expression in exon 14 of the UBE3A gene. However, the brain-specific monoallelic expression of bovine UBE3A-ATS occurred in the entire gene. These observations demonstrated that the monoallelic expression did not occur along the bovine UBE3A entire locus and was associated with the genomic position.
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Affiliation(s)
- J Li
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - C Zhang
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - H Si
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - S Gu
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - X Liu
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - D Li
- College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, China
| | - S Meng
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - X Yang
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - S Li
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
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41
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Howe J, Schiøtt M, Li Q, Wang Z, Zhang G, Boomsma JJ. A novel method for using RNA-seq data to identify imprinted genes in social Hymenoptera with multiply mated queens. J Evol Biol 2020; 33:1770-1782. [PMID: 33030255 DOI: 10.1111/jeb.13716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/13/2020] [Accepted: 09/21/2020] [Indexed: 11/30/2022]
Abstract
Genomic imprinting results in parent-of-origin-dependent gene expression biased towards either the maternally or paternally derived allele at the imprinted locus. The kinship theory of genomic imprinting argues that this unusual expression pattern can be a manifestation of intra-genomic conflict between the maternally and paternally derived halves of the genome that arises because they are not equally related to the genomes of social partners. The theory thus predicts that imprinting may evolve wherever there are close interactions among asymmetrically related kin. The social Hymenoptera with permanent caste differentiation are suitable candidates for testing the kinship theory because haplodiploid sex determination creates strong relatedness asymmetries and nursing workers interact closely with kin. However, progress in the search for imprinted genes in the social Hymenoptera has been slow, in part because tests for imprinting rely on reciprocal crosses that are impossible in most species. Here, we develop a method to systematically search for imprinting in haplodiploid social insects without crosses, using instead samples of pooled individuals collected from natural colonies. We tested this protocol using data available for the leaf-cutting ant Acromyrmex echinatior, providing the first genome-wide search for imprinting in any ant. Although we identified several genes as potentially imprinted, none of the four genes tested could be verified as imprinted using digital droplet PCR, highlighting the need for higher quality genomic assemblies that accurately map duplicated genes.
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Affiliation(s)
- Jack Howe
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Morten Schiøtt
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Qiye Li
- BGI-Shenzhen, Shenzhen, China
| | | | - Guojie Zhang
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, China
| | - Jacobus J Boomsma
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Copenhagen, Denmark
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42
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Laukoter S, Pauler FM, Beattie R, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex. Neuron 2020; 107:1160-1179.e9. [PMID: 32707083 PMCID: PMC7523403 DOI: 10.1016/j.neuron.2020.06.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/20/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.
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Affiliation(s)
- Susanne Laukoter
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Florian M Pauler
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Robert Beattie
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nicole Amberg
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Andi H Hansen
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Carmen Streicher
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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Klobučar T, Kreibich E, Krueger F, Arez M, Pólvora-Brandão D, von Meyenn F, da Rocha ST, Eckersley-Maslin M. IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions. Nucleic Acids Res 2020; 48:e92. [PMID: 32621604 PMCID: PMC7498334 DOI: 10.1093/nar/gkaa567] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/16/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold coverage. We adapted amplicon bisulfite-sequencing protocols to design IMPLICON for ICRs in adult tissues of inbred mice, validating it in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles. Lastly, we developed a human version of IMPLICON and detected imprinting errors in embryonic and induced pluripotent stem cells. We also provide rules and guidelines to adapt this method for investigating the DNA methylation landscape of any set of genomic regions. In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.
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Affiliation(s)
- Tajda Klobučar
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Elisa Kreibich
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Maria Arez
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Duarte Pólvora-Brandão
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | | - Simão Teixeira da Rocha
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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Varrault A, Dubois E, Le Digarcher A, Bouschet T. Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain. EPIGENOMES 2020; 4:21. [PMID: 34968292 PMCID: PMC8594728 DOI: 10.3390/epigenomes4030021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Imprinted genes are a group of ~150 genes that are preferentially expressed from one parental allele owing to epigenetic marks asymmetrically distributed on inherited maternal and paternal chromosomes. Altered imprinted gene expression causes human brain disorders such as Prader-Willi and Angelman syndromes and additional rare brain diseases. Research data principally obtained from the mouse model revealed how imprinted genes act in the normal and pathological brain. However, a better understanding of imprinted gene functions calls for building detailed maps of their parent-of-origin-dependent expression and of associated epigenetic signatures. Here we review current methods for quantifying genomic imprinting at tissue and cell resolutions, with a special emphasis on methods to detect parent-of-origin dependent expression and their applications to the brain. We first focus on bulk RNA-sequencing, the main method to detect parent-of-origin-dependent expression transcriptome-wide. We discuss the benefits and caveats of bulk RNA-sequencing and provide a guideline to use it on F1 hybrid mice. We then review methods for detecting parent-of-origin-dependent expression at cell resolution, including single-cell RNA-seq, genetic reporters, and molecular probes. Finally, we provide an overview of single-cell epigenomics technologies that profile additional features of genomic imprinting, including DNA methylation, histone modifications and chromatin conformation and their combination into sc-multimodal omics approaches, which are expected to yield important insights into genomic imprinting in individual brain cells.
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Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Emeric Dubois
- Montpellier GenomiX (MGX), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
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Liang ZS, Cimino I, Yalcin B, Raghupathy N, Vancollie VE, Ibarra-Soria X, Firth HV, Rimmington D, Farooqi IS, Lelliott CJ, Munger SC, O’Rahilly S, Ferguson-Smith AC, Coll AP, Logan DW. Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity. PLoS Genet 2020; 16:e1008916. [PMID: 32877400 PMCID: PMC7467316 DOI: 10.1371/journal.pgen.1008916] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 11/30/2022] Open
Abstract
Some imprinted genes exhibit parental origin specific expression bias rather than being transcribed exclusively from one copy. The physiological relevance of this remains poorly understood. In an analysis of brain-specific allele-biased expression, we identified that Trappc9, a cellular trafficking factor, was expressed predominantly (~70%) from the maternally inherited allele. Loss-of-function mutations in human TRAPPC9 cause a rare neurodevelopmental syndrome characterized by microcephaly and obesity. By studying Trappc9 null mice we discovered that homozygous mutant mice showed a reduction in brain size, exploratory activity and social memory, as well as a marked increase in body weight. A role for Trappc9 in energy balance was further supported by increased ad libitum food intake in a child with TRAPPC9 deficiency. Strikingly, heterozygous mice lacking the maternal allele (70% reduced expression) had pathology similar to homozygous mutants, whereas mice lacking the paternal allele (30% reduction) were phenotypically normal. Taken together, we conclude that Trappc9 deficient mice recapitulate key pathological features of TRAPPC9 mutations in humans and identify a role for Trappc9 and its imprinting in controlling brain development and metabolism.
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Affiliation(s)
- Zhengzheng S. Liang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Irene Cimino
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Binnaz Yalcin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, France
| | | | | | - Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Helen V. Firth
- Department of Clinical Genetics, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Debra Rimmington
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Stephen O’Rahilly
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | | | - Anthony P. Coll
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Darren W. Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
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46
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Botet R, Keurentjes JJB. The Role of Transcriptional Regulation in Hybrid Vigor. FRONTIERS IN PLANT SCIENCE 2020; 11:410. [PMID: 32351526 PMCID: PMC7174566 DOI: 10.3389/fpls.2020.00410] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
The genetic basis of hybrid vigor in plants remains largely unsolved but strong evidence suggests that variation in transcriptional regulation can explain many aspects of this phenomenon. Natural variation in transcriptional regulation is highly abundant in virtually all species and thus a potential source of heterotic variability. Allele Specific Expression (ASE), which is tightly linked to parent of origin effects and modulated by complex interactions in cis and in trans, is generally considered to play a key role in explaining the differences between hybrids and parental lines. Here we discuss the recent developments in elucidating the role of transcriptional variation in a number of aspects of hybrid vigor, thereby bridging old paradigms and hypotheses with contemporary research in various species.
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Affiliation(s)
- Ramon Botet
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
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47
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48
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Thamban T, Agarwaal V, Khosla S. Role of genomic imprinting in mammalian development. J Biosci 2020; 45:20. [PMID: 31965998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-mendelian inheritance refers to the group of phenomena and observations related to the inheritance of genetic information that cannot be merely explained by Mendel's laws of inheritance. Phenomenon including Genomic imprinting, X-chromosome Inactivation, Paramutations are some of the best studied examples of non-mendelian inheritance. Genomic imprinting is a process that reversibly marks one of the two homologous loci, chromosome or chromosomal sets during development, resulting in functional non-equivalence of gene expression. Genomic imprinting is known to occur in a few insect species, plants, and placental mammals. Over the years, studies on imprinted genes have contributed immensely to highlighting the role of epigenetic modifications and the epigenetic circuitry during gene expression and development. In this review, we discuss the phenomenon of genomic imprinting in mammals and the role it plays especially during fetoplacental growth and early development.
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Affiliation(s)
- Thushara Thamban
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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49
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Wada T, Wallerich S, Becskei A. Stochastic Gene Choice during Cellular Differentiation. Cell Rep 2019; 24:3503-3512. [PMID: 30257211 DOI: 10.1016/j.celrep.2018.08.074] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/02/2018] [Accepted: 08/24/2018] [Indexed: 01/06/2023] Open
Abstract
Genes in higher eukaryotes are regulated by long-range interactions, which can determine what combination of genes is expressed in a chromosomal segment. The choice of the genes can display exclusivity, independence, or co-occurrence. We introduced a simple measure to quantify this interdependence in gene expression and differentiated mouse embryonic stem cells to neurons to measure the single-cell expression of the gene isoforms in the protocadherin (Pcdh) cluster, a key component of neuronal diversity. As the neuronal progenitors mature into neurons, expression of the gene isoforms in the Pcdh array is initially concurrent. Even though the number of the expressed genes is increasing during differentiation, the expression shifts toward exclusivity. The expression frequency correlates highly with CTCF binding to the promoters and follows dynamically the changes in the binding during the differentiation. These findings aid in understanding the interplay between cellular differentiation and stochastic gene choice.
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Affiliation(s)
- Takeo Wada
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel 4056, Switzerland
| | - Sandrine Wallerich
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel 4056, Switzerland
| | - Attila Becskei
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel 4056, Switzerland.
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Han Q, Bartels A, Cheng X, Meyer A, An YQC, Hsieh TF, Xiao W. Epigenetics Regulates Reproductive Development in Plants. PLANTS 2019; 8:plants8120564. [PMID: 31810261 PMCID: PMC6963493 DOI: 10.3390/plants8120564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Xi Cheng
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Angela Meyer
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, MO 63132, USA;
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Correspondence: ; Tel.: +1-314-977-2547
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