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Chen S, Jiang J, Liang W, Tang Y, Lyu R, Hu Y, Cai D, Luo X, Sun M. Comprehensive Annotation and Expression Profiling of C2H2 Zinc Finger Transcription Factors across Chicken Tissues. Int J Mol Sci 2024; 25:10525. [PMID: 39408854 PMCID: PMC11476951 DOI: 10.3390/ijms251910525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 09/27/2024] [Accepted: 09/28/2024] [Indexed: 10/20/2024] Open
Abstract
As the most abundant class of transcription factors in eukaryotes, C2H2-type zinc finger proteins (C2H2-ZFPs) play critical roles in various biological processes. Despite being extensively studied in mammals, C2H2-ZFPs remain poorly characterized in birds. Recent accumulation of multi-omics data for chicken enables the genome-wide investigation of C2H2-ZFPs in birds. The purpose of this study is to reveal the genomic occurrence and evolutionary signature of chicken C2H2-ZFPs, and further depict their expression profiles across diverse chicken tissues. Here, we annotated 301 C2H2-ZFPs in chicken genome, which are associated with different effector domains, including KRAB, BTB, HOMEO, PHD, SCAN, and SET. Among them, most KRAB-ZFPs lack orthologues in mammals and tend to form clusters by duplication, supporting their fast evolution in chicken. We also annotated a unique and previously unidentified SCAN-ZFP, which is lineage-specific and highly expressed in ovary and testis. By integrating 101 RNA-seq datasets for 32 tissues, we found that most C2H2-ZFPs have tissue-specific expression. Particularly, 74 C2H2-ZFPs-including 27 KRAB-ZFPs-show blastoderm-enriched expression, indicating their association with early embryo development. Overall, this study performs comprehensive annotation and expression profiling of C2H2 ZFPs in diverse chicken tissues, which gives new insights into the evolution and potential function of C2H2-ZFPs in avian species.
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Affiliation(s)
- Shuai Chen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (S.C.); (J.J.); (W.L.); (Y.T.); (R.L.)
| | - Jiayao Jiang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (S.C.); (J.J.); (W.L.); (Y.T.); (R.L.)
| | - Wenxiu Liang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (S.C.); (J.J.); (W.L.); (Y.T.); (R.L.)
| | - Yuchen Tang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (S.C.); (J.J.); (W.L.); (Y.T.); (R.L.)
| | - Renzhe Lyu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (S.C.); (J.J.); (W.L.); (Y.T.); (R.L.)
| | - Yun Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.H.); (D.C.)
| | - Demin Cai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.H.); (D.C.)
| | - Xugang Luo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.H.); (D.C.)
| | - Mingan Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (S.C.); (J.J.); (W.L.); (Y.T.); (R.L.)
- Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Oomen ME, Torres-Padilla ME. Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. EMBO Rep 2024; 25:1721-1733. [PMID: 38528171 PMCID: PMC11015026 DOI: 10.1038/s44319-024-00118-5] [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: 12/07/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish elements and acting as a source of genome instability, several of these elements have been co-opted as part of a complex system of genome regulation. Many TEs have lost transposition ability and their transcriptional potential has been tampered as a result of interactions with the host throughout evolutionary time. It has been proposed that TEs have been ultimately repurposed to function as gene regulatory hubs scattered throughout our genomes. In the early embryo in particular, TEs find a perfect environment of naïve chromatin to escape transcriptional repression by the host. As a consequence, it is thought that hosts found ways to co-opt TE sequences to regulate large-scale changes in chromatin and transcription state of their genomes. In this review, we discuss several examples of TEs expressed during embryo development, their potential for co-option in genome regulation and the evolutionary pressures on TEs and on our genomes.
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Affiliation(s)
- Marlies E Oomen
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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