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The FvABF3-FvALKBH10B-FvSEP3 cascade regulates fruit ripening in strawberry.
Nat Commun
December 2024
State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
Fruit ripening is a highly-orchestrated process that requires the fine-tuning and precise control of gene expression, which is mainly governed by phytohormones, epigenetic modifiers, and transcription factors. How these intrinsic regulators coordinately modulate the ripening remains elusive. Here we report the identification and characterization of FvALKBH10B as an N-methyladenosine (mA) RNA demethylase necessary for the normal ripening of strawberry (Fragaria vesca) fruit.
View Article and Find Full Text PDFElevated EBF2 in mouse but not pig drives the progressive brown fat lineage specification via chromatin activation.
J Adv Res
December 2024
College of Animal Science, Shandong Provincial Key Laboratory for Livestock Germplasm Innovation & Utilization, Shandong Agricultural University, Taian, China; College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China. Electronic address:
Brown adipose tissue (BAT) is responsible for non-shivering thermogenesis, but it is absent in some mammals, including pigs. During development, BAT progenitors are derived from paired box 7 (Pax7)-expressing somitic mesodermal stem cells, which also give rise to skeletal muscle. However, the intrinsic mechanisms underlying the fate decisions between brown fat and muscle progenitors remain elusive.
View Article and Find Full Text PDFRevealing long-range heterogeneous organization of nucleoproteins with N-methyladenine footprinting.
bioRxiv
December 2024
Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
A major challenge in epigenetics is uncovering the dynamic distribution of nucleosomes and other DNA-binding proteins, which plays a crucial role in regulating cellular functions. Established approaches such as ATAC-seq, ChIP-seq, and CUT&RUN provide valuable insights but are limited by the ensemble nature of their data, masking the cellular and molecular heterogeneity that is often functionally significant. Recently, long-read sequencing technologies, particularly Single Molecule, Real-Time (SMRT/PacBio) sequencing, have introduced transformative capabilities, such as N-methyladenine (6mA) footprinting.
View Article and Find Full Text PDFHigher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome.
Brief Bioinform
November 2024
Division of Developmental Biology & Medicine, Faculty of Biology, Medicine, and Health, School of Biological Sciences, The University of Manchester, Manchester, UK.
Complex direct and indirect relationships between multiple variables, termed higher order interactions (HOIs), are characteristics of all natural systems. Traditional differential and network analyses fail to account for the omic datasets richness and miss HOIs. We investigated peripheral blood DNA methylation data from Kabuki syndrome type 1 (KS1) and control individuals, identified 2,002 differentially methylated points (DMPs), and inferred 17 differentially methylated regions, which represent only 189 DMPs.
View Article and Find Full Text PDFEpigenetic regulation of complement C1Q gene expression.
Front Immunol
December 2024
Department of Life Sciences, University of Trieste, Trieste, ;Italy.
Human C1q is a multifaceted complement protein whose functions range from activating the complement classical pathway to immunomodulation and promoting placental development and tumorigenesis. It is encoded by the , , and genes located on chromosome 1. C1q, unlike most complement components, has extrahepatic expression by a range of cells including macrophages, monocytes and immature dendritic cells.
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