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Wu XF, Xu Q, Wang A, Wang BZ, Lan XY, Li WY, Liu Y. Relationship between Indel Variants within the JAK2 Gene and Growth Traits in Goats. Animals (Basel) 2024; 14:1994. [PMID: 38998106 PMCID: PMC11240706 DOI: 10.3390/ani14131994] [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: 05/29/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
Janus kinase 2 (JAK2) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the JAK2 gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the JAK2 gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits (p < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the JAK2 gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs.
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Affiliation(s)
- Xian-Feng Wu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Qian Xu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Ao Wang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ben-Zhi Wang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xian-Yong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Wen-Yang Li
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yuan Liu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
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Fingerhut JM, Lannes R, Whitfield TW, Thiru P, Yamashita YM. Co-transcriptional splicing facilitates transcription of gigantic genes. PLoS Genet 2024; 20:e1011241. [PMID: 38870220 PMCID: PMC11207136 DOI: 10.1371/journal.pgen.1011241] [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: 04/02/2024] [Revised: 06/26/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024] Open
Abstract
Although introns are typically tens to thousands of nucleotides, there are notable exceptions. In flies as well as humans, a small number of genes contain introns that are more than 1000 times larger than typical introns, exceeding hundreds of kilobases (kb) to megabases (Mb). It remains unknown why gigantic introns exist and how cells overcome the challenges associated with their transcription and RNA processing. The Drosophila Y chromosome contains some of the largest genes identified to date: multiple genes exceed 4Mb, with introns accounting for over 99% of the gene span. Here we demonstrate that co-transcriptional splicing of these gigantic Y-linked genes is important to ensure successful transcription: perturbation of splicing led to the attenuation of transcription, leading to a failure to produce mature mRNA. Cytologically, defective splicing of the Y-linked gigantic genes resulted in disorganization of transcripts within the nucleus suggestive of entanglement of transcripts, likely resulting from unspliced long RNAs. We propose that co-transcriptional splicing maintains the length of nascent transcripts of gigantic genes under a critical threshold, preventing their entanglement and ensuring proper gene expression. Our study reveals a novel biological significance of co-transcriptional splicing.
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Affiliation(s)
- Jaclyn M. Fingerhut
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
| | - Romain Lannes
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Troy W. Whitfield
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Yukiko M. Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Koestler SA, Ball ML, Muresan L, Dinakaran V, White R. Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters. Epigenetics Chromatin 2024; 17:8. [PMID: 38528624 DOI: 10.1186/s13072-024-00535-9] [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: 03/14/2024] [Indexed: 03/27/2024] Open
Abstract
Chromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is unclear. In this study, we have used super-resolution microscopy to image the Y loops of Drosophila melanogaster primary spermatocytes, which are enormous transcriptionally active chromatin fibres, each representing single transcription units that are individually resolvable in the nuclear interior. We previously found that the Y loops consist of regular clusters of nucleosomes, with an estimated median of 54 nucleosomes per cluster with wide variation.In this study, we report that the histone modifications H3K4me3, H3K27me3, and H3K36me3 are also clustered along the Y loops, with H3K4me3 more associated with diffuse chromatin compared to H3K27me3. These histone modifications form domains that can be stretches of Y loop chromatin micrometres long, or can be in short alternating domains. The different histone modifications are associated with different sizes of chromatin clusters and unique morphologies. Strikingly, a single chromatin cluster almost always only contains only one type of the histone modifications that were labelled, suggesting exclusivity, and therefore regulation at the level of individual chromatin clusters. The active mark H3K36me3 is more associated with actively elongating RNA polymerase II than H3K27me3, with polymerase often appearing on what are assumed to be looping regions on the periphery of chromatin clusters.These results provide a foundation for understanding the relationship between chromatin state, chromatin organisation, and transcription regulation - with potential implications for pause-release dynamics, splicing complex organisation and chromatin dynamics during polymerase progression along a gene.
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Affiliation(s)
- Stefan A Koestler
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Madeleine L Ball
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Leila Muresan
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Vineet Dinakaran
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK.
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4
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Krasikova A, Fishman V, Kulikova T. Lampbrush chromosome studies in the post-genomic era. Bioessays 2023; 45:e2200250. [PMID: 36855056 DOI: 10.1002/bies.202200250] [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: 12/26/2022] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 03/02/2023]
Abstract
Extraordinary extended lampbrush chromosomes with thousands of transcription loops are favorable objects in chromosome biology. Chromosomes become lampbrushy due to unusually high rate of transcription during oogenesis. However, until recently, the information on the spectrum of transcribed sequences as well as genomic context of individual chromomeres was mainly limited to tandemly repetitive elements. Here we briefly outline novel findings and future directions in lampbrush chromosome studies in the post-genomic era. We emphasize the fruitfulness of combining genome-wide approaches with microscopy imaging techniques using lampbrush chromosomes as a remarkable model object. We believe that new data on the spectrum of sequences transcribed on the lateral loops of lampbrush chromosomes and their structural organization push the boundaries in the discussion of their biological role.
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Affiliation(s)
- Alla Krasikova
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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Sun W, Dai L, Cao Y, Pan P, Zhi L, Wang X, Yuan X, Gao Z, Guo S, Liu G, Yin J, Xie L, Wang L, Wang Y, Li W, Li H, Jia Y. Monocytes reprogrammed by tumor microparticle vaccine inhibit tumorigenesis and tumor development. Cancer Nanotechnol 2023; 14:34. [PMID: 37089435 PMCID: PMC10106871 DOI: 10.1186/s12645-023-00190-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023] Open
Abstract
Tumor microparticles (T-MPs) are considered as a tumor vaccine candidate. Although some studies have analyzed the mechanism of T-MPs as tumor vaccine, we still lack understanding of how T-MPs stimulate a strong anti-tumor immune response. Here, we show that T-MPs induce macrophages to release a key chemotactic factor CCL2, which attracts monocytes to the vaccine injection site and enhances endocytosis of antigen. Monocytes subsequently enter the draining lymph node, and differentiate into monocyte-derived DCs (moDCs), which present tumor antigens to T lymphocytes and deliver a potent anti-tumor immune response. Mechanically, T-MPs activate the cGAS-STING signaling through DNA fragments, and then induce monocytes to upregulate the expression of IRF4, which is a key factor for monocyte differentiation into moDCs. More importantly, monocytes that have endocytosed T-MPs acquire the ability to treat tumors. Collectively, this work might provide novel vaccination strategy for the development of tumor vaccines and facilitate the application of T-MPs for clinic oncotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12645-023-00190-x.
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Affiliation(s)
- Weiwei Sun
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Lili Dai
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Yuqing Cao
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Pengtao Pan
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Lijuan Zhi
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Xinke Wang
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Xinzhong Yuan
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Zi Gao
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Sheng Guo
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Guoyan Liu
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Junlei Yin
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Liangliang Xie
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Liping Wang
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Yanling Wang
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Wensheng Li
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Hong Li
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
| | - Yunjie Jia
- School of Medicine, Xinxiang University, Jinsui Road 191, Xinxiang, 453003 China
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Mi F, Wu X, Wang Z, Wang R, Lan X. Relationships between the Mini-InDel Variants within the Goat CFAP43 Gene and Body Traits. Animals (Basel) 2022; 12:ani12243447. [PMID: 36552367 PMCID: PMC9774114 DOI: 10.3390/ani12243447] [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: 10/11/2022] [Revised: 11/26/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The cilia- and flagella-associated protein 43 (CFAP43) gene encodes a member of the cilia- and flagellum-associated protein family. Cilia on the cell surface influence intercellular signaling and are involved in biological processes such as osteogenesis and energy metabolism in animals. Previous studies have shown that insertion/deletion (InDel) variants in the CFAP43 gene affect litter size in Shaanbei white cashmere (SBWC) goats, and that litter size and body traits are correlated in this breed. Therefore, we hypothesized that there is a significant relationship between InDel variants within the CFAP43 gene and body traits in SBWC goats. Herein, we first investigated the association between three InDel variant loci (L-13, L-16, and L-19 loci) within CFAP43 and body traits in SBWC goats (n = 1827). Analyses revealed that the L-13, L-16, and L-19 loci were significantly associated with chest depth, four body traits, and three body traits, respectively. The results of this study are in good agreement with those previously reported and could provide useful molecular markers for the selection and breeding of goats for body traits.
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Affiliation(s)
- Fang Mi
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350000, China
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350000, China
- Correspondence: (X.W.); (X.L.)
| | - Zhen Wang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
| | - Ruolan Wang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, No. 22, Xinong Road, Xianyang 712100, China
- Correspondence: (X.W.); (X.L.)
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