Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology

Zhu, Xiusheng; Huang, Qitong; Luo, Jing; Kong, Dashuai; Zhang, Yubo

doi:10.1016/j.csbj.2023.02.028

Cited by 3 publications

(3 citation statements)

References 127 publications

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“…The genetic regulatory mechanisms underlying complex traits or diseases often involve multilevel molecular regulations [56,57]. We already demonstrated the significant role played by TEs within the turquoise module in regulating skeletal muscle development.…”

Section: Construction Of Te-mediated Gene Regulatory Networkmentioning

confidence: 82%

An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits

Wang,

Lei,

Liu

2023

Animals

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The development and growth of porcine skeletal muscle determine pork quality and yield. While genetic regulation of porcine skeletal muscle development has been extensively studied using various omics data, the role of transposable elements (TEs) in this context has been less explored. To bridge this gap, we constructed a comprehensive atlas of TE expression throughout the developmental stages of porcine skeletal muscle. This was achieved by integrating porcine TE genomic coordinates with whole-transcriptome RNA-Seq data from 27 developmental stages. We discovered that in pig skeletal muscle, active Tes are closely associated with active epigenomic marks, including low levels of DNA methylation, high levels of chromatin accessibility, and active histone modifications. Moreover, these TEs include 6074 self-expressed TEs that are significantly enriched in terms of muscle cell development and myofibril assembly. Using the TE expression data, we conducted a weighted gene co-expression network analysis (WGCNA) and identified a module that is significantly associated with muscle tissue development as well as genome-wide association studies (GWAS) of the signals of pig meat and carcass traits. Within this module, we constructed a TE-mediated gene regulatory network by adopting a unique multi-omics integration approach. This network highlighted several established candidate genes associated with muscle-relevant traits, including HES6, CHRNG, ACTC1, CHRND, MAMSTR, and PER2, as well as novel genes like ENSSSCG00000005518, ENSSSCG00000033601, and PIEZO2. These novel genes hold promise for regulating muscle-related traits in pigs. In summary, our research not only enhances the TE-centered dissection of the genetic basis underlying pork production traits, but also offers a general approach for constructing TE-mediated regulatory networks to study complex traits or diseases.

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Section: Construction Of Te-mediated Gene Regulatory Networkmentioning

confidence: 82%

An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits

Wang,

Lei,

Liu

2023

Animals

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“…Gene regulatory networks help us understand the interactions between genes and their regulatory elements, such as promoters, transcription factors, silencers, epigenetic modulators, etc ., and the effect of such interactions in determining cell behaviour and responses to stimuli. 70 Several experimental and mathematical approaches have been adopted to study these gene regulatory networks. 71 Decoding gene regulatory networks is critical to the understanding of cell behavior and responses and for repairing of deregulated controls.…”

Section: Discussionmentioning

confidence: 99%

Unravelling microRNA regulation and miRNA–mRNA regulatory networks in osteogenesis driven by 3D nanotopographical cues

Balachander,

Nilawar,

Meka

et al. 2024

Biomater. Sci.

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“…3D chromatin architecture plays a pivotal role in transcriptional regulation, [ 7 ] undergoing rapid reorganizations to facilitate temporal dynamic interactions within gene regulatory networks. These networks include chromosome territories, compartments, and topologically associating domains (TADs), as well as long‐range interactions between promoters and enhancers (PEIs).…”

Section: Introductionmentioning

confidence: 99%

Building Haplotype‐Resolved 3D Genome Maps of Chicken Skeletal Muscle

Li,

Lin,

et al. 2024

Advanced Science

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Haplotype‐resolved 3D chromatin architecture related to allelic differences in avian skeletal muscle development has not been addressed so far, although chicken husbandry for meat consumption has been prevalent feature of cultures on every continent for more than thousands of years. Here, high‐resolution Hi‐C diploid maps (1.2‐kb maximum resolution) are generated for skeletal muscle tissues in chicken across three developmental stages (embryonic day 15 to day 30 post‐hatching). The sequence features governing spatial arrangement of chromosomes and characterize homolog pairing in the nucleus, are identified. Multi‐scale characterization of chromatin reorganization between stages from myogenesis in the fetus to myofiber hypertrophy after hatching show concordant changes in transcriptional regulation by relevant signaling pathways. Further interrogation of parent‐of‐origin‐specific chromatin conformation supported that genomic imprinting is absent in birds. This study also reveals promoter‐enhancer interaction (PEI) differences between broiler and layer haplotypes in skeletal muscle development‐related genes are related to genetic variation between breeds, however, only a minority of breed‐specific variations likely contribute to phenotypic divergence in skeletal muscle potentially via allelic PEI rewiring. Beyond defining the haplotype‐specific 3D chromatin architecture in chicken, this study provides a rich resource for investigating allelic regulatory divergence among chicken breeds.

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Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology

Cited by 3 publications

References 127 publications

An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits

An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits

Unravelling microRNA regulation and miRNA–mRNA regulatory networks in osteogenesis driven by 3D nanotopographical cues

Building Haplotype‐Resolved 3D Genome Maps of Chicken Skeletal Muscle

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