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Comprehensive Identification of the Bovine KLF Gene Family and Its Functional Regulation in Muscle Development: Insights from Single-Nuclei Transcriptomics.

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Title: Comprehensive Identification of the Bovine KLF Gene Family and Its Functional Regulation in Muscle Development: Insights from Single-Nuclei Transcriptomics.
Authors: Ma, Fengying, Zhou, Le, Guo, Lili, Chang, Chencheng, Dan, Dan, Bao, Yanchun, Han, Guiting, Gu, Mingjuan, Zhu, Lin, Na, Risu, Shi, Caixia, Zhang, Jiaxin, Zhang, Wenguang
Source: Animals (2076-2615); Oct2025, Vol. 15 Issue 19, p2930, 18p
Subject Terms: MUSCLE growth, KRUPPEL-like factors, RNA sequencing, ANIMAL breeding, BEEF industry, BOS, HEREDITY, TRANSCRIPTOMES
Abstract: Simple Summary: Beef production is important for global food security. Understanding the genetic factors that control muscle growth and meat quality in cattle is key to improving breeding strategies. This study focused on a family of genes called KLF transcription factors, which are known to be master regulators of growth and metabolism. We systematically identified 14 KLF genes in the cattle genome. Using advanced single-nuclei RNA sequencing technology, we mapped the activity of these genes across different cell types (such as muscle fibers, fat cells, and immune cells) in the muscle tissue of two cattle breeds: Angus (beef breed) and Holstein (dairy breed). We discovered that the activity of these KLF genes varies greatly between cell types and between breeds. Using a machine learning approach, we identified KLF6, KLF9, KLF10, and KLF12 as key genes that may drive the differences in muscle development between the two breeds. Our findings provide valuable genetic targets for future breeding programs aimed at enhancing beef quality and yield. The Krüppel-like factor (KLF) family of transcription regulators plays pivotal roles in adipogenesis, myogenesis, and metabolism. While comprehensively studied in humans and mice, its characterization in cattle remains limited, especially within the skeletal muscle niche. This study aimed to systematically characterize the KLF family in Bos taurus and elucidate its role in breed-specific muscular development. We employed an integrated approach of comparative genomics and single-nucleus RNA sequencing (snRNA-seq) on longissimus dorsi muscle from Angus (ANG, beef breed) and Holstein (HST, dairy breed) cattle. Phylogenomic analysis identified 14 KLF genes, revealing evolutionary conservation and potential functional divergence. snRNA-seq delineated 11 distinct cell populations and uncovered cell-type-specific expression patterns of KLFs. Further machine learning based analysis pinpointed KLF6, KLF9, KLF10, and KLF12 as key global drivers of transcriptional differences between breeds, while KLF6 was identified as a major cell-type-specific contributor in lymphatic endothelial cells. Our work provides a foundational resource for understanding the KLF family in cattle and identifies promising candidate genes for improving meat production traits through molecular breeding. [ABSTRACT FROM AUTHOR]
Copyright of Animals (2076-2615) is the property of MDPI and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Comprehensive Identification of the Bovine KLF Gene Family and Its Functional Regulation in Muscle Development: Insights from Single-Nuclei Transcriptomics.
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  Data: Animals (2076-2615); Oct2025, Vol. 15 Issue 19, p2930, 18p
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  Data: <searchLink fieldCode="DE" term="%22MUSCLE+growth%22">MUSCLE growth</searchLink><br /><searchLink fieldCode="DE" term="%22KRUPPEL-like+factors%22">KRUPPEL-like factors</searchLink><br /><searchLink fieldCode="DE" term="%22RNA+sequencing%22">RNA sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22ANIMAL+breeding%22">ANIMAL breeding</searchLink><br /><searchLink fieldCode="DE" term="%22BEEF+industry%22">BEEF industry</searchLink><br /><searchLink fieldCode="DE" term="%22BOS%22">BOS</searchLink><br /><searchLink fieldCode="DE" term="%22HEREDITY%22">HEREDITY</searchLink><br /><searchLink fieldCode="DE" term="%22TRANSCRIPTOMES%22">TRANSCRIPTOMES</searchLink>
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  Data: Simple Summary: Beef production is important for global food security. Understanding the genetic factors that control muscle growth and meat quality in cattle is key to improving breeding strategies. This study focused on a family of genes called KLF transcription factors, which are known to be master regulators of growth and metabolism. We systematically identified 14 KLF genes in the cattle genome. Using advanced single-nuclei RNA sequencing technology, we mapped the activity of these genes across different cell types (such as muscle fibers, fat cells, and immune cells) in the muscle tissue of two cattle breeds: Angus (beef breed) and Holstein (dairy breed). We discovered that the activity of these KLF genes varies greatly between cell types and between breeds. Using a machine learning approach, we identified KLF6, KLF9, KLF10, and KLF12 as key genes that may drive the differences in muscle development between the two breeds. Our findings provide valuable genetic targets for future breeding programs aimed at enhancing beef quality and yield. The Krüppel-like factor (KLF) family of transcription regulators plays pivotal roles in adipogenesis, myogenesis, and metabolism. While comprehensively studied in humans and mice, its characterization in cattle remains limited, especially within the skeletal muscle niche. This study aimed to systematically characterize the KLF family in Bos taurus and elucidate its role in breed-specific muscular development. We employed an integrated approach of comparative genomics and single-nucleus RNA sequencing (snRNA-seq) on longissimus dorsi muscle from Angus (ANG, beef breed) and Holstein (HST, dairy breed) cattle. Phylogenomic analysis identified 14 KLF genes, revealing evolutionary conservation and potential functional divergence. snRNA-seq delineated 11 distinct cell populations and uncovered cell-type-specific expression patterns of KLFs. Further machine learning based analysis pinpointed KLF6, KLF9, KLF10, and KLF12 as key global drivers of transcriptional differences between breeds, while KLF6 was identified as a major cell-type-specific contributor in lymphatic endothelial cells. Our work provides a foundational resource for understanding the KLF family in cattle and identifies promising candidate genes for improving meat production traits through molecular breeding. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label:
  Group: Ab
  Data: <i>Copyright of Animals (2076-2615) is the property of MDPI and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.3390/ani15192930
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 18
        StartPage: 2930
    Subjects:
      – SubjectFull: MUSCLE growth
        Type: general
      – SubjectFull: KRUPPEL-like factors
        Type: general
      – SubjectFull: RNA sequencing
        Type: general
      – SubjectFull: ANIMAL breeding
        Type: general
      – SubjectFull: BEEF industry
        Type: general
      – SubjectFull: BOS
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      – SubjectFull: HEREDITY
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      – SubjectFull: TRANSCRIPTOMES
        Type: general
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      – TitleFull: Comprehensive Identification of the Bovine KLF Gene Family and Its Functional Regulation in Muscle Development: Insights from Single-Nuclei Transcriptomics.
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            – D: 01
              M: 10
              Text: Oct2025
              Type: published
              Y: 2025
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