The chicken model organism for epigenomic research

Beacon, Tasnim H.; Davie, James R.

doi:10.1139/gen-2020-0129

Cited by 19 publications

(14 citation statements)

References 86 publications

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“…Chicken has been widely accepted as a crucial research model organism for implications on phylogenetics and embryology, along with agriculture and biology, such as adipogenesis, development, immune, medicine, and cancer, owing to its convenience for operation and the extensive conservation of synteny between chicken and mammals ( Burt, 2007 ; Beacon and Davie, 2021 ). Both muscle development and IMF deposition are complex and precisely orchestrated processes mediated by a network of regulatory factors directly and indirectly related to growth development and lipid metabolism.…”

Section: Discussionmentioning

confidence: 99%

Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler

Tian

Wang

et al. 2021

Front. Cell Dev. Biol.

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Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.

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Section: Discussionmentioning

confidence: 99%

Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler

Tian

Wang

et al. 2021

Front. Cell Dev. Biol.

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“…USP3 can dampen type I interferon production by removing K63-linked polyubiquitin chains of RIG-I because the activation of RIG-I signaling requires both RNA binding and the polyubiquitin chains ( Cui et al, 2014 ). Chicken expresses 2 members of the RIG-I-like receptor ( RLR ) family, MDA5 and LGP2 ( Beacon and Davie, 2021 ). MDA5 shares the same domain architecture with RIG-I ( Rehwinkel and Gack, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

“…Avian innate immunity is considered similar to the mammalian system in terms of structure and function. Characterizing the avian immunity genes would allow targeting of crucial regulators in both avian and mammal infections ( Beacon and Davie, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Research Note: IsomiRs of chicken miR-146b-5p are activated upon Salmonella enterica serovar Enteritidis infection

Liu

Miao

et al. 2022

Poultry Science

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“…In fact, chicken RBC undergo a dramatic drop in RNA synthesis and are regarded as transcriptionally inert cells [10][11][12] , although the exact extent of this repression has not been studied. The chicken nucleated erythrocyte has been useful in the study of chromatin structure and transcriptional regulation 13 . However, the molecular mechanisms that mediate the extensive silencing of the erythroid genome are largely unknown and a study at high resolution of the remodeling of the chromatin and genome organization during this process is still lacking.…”

Section: Introductionmentioning

confidence: 99%

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

Penagos-Puig

Claudio-Galeana

Stephenson-Gussinye

et al. 2022

Preprint

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Chicken erythrocytes are nucleated cells often referred to as transcriptionally inactive, although the epigenetic changes and chromatin remodeling that mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here we characterized the changes in gene expression, chromatin accessibility, genome organization, and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and found a complex chromatin reorganization at different genomic scales. We identified a robust decrease in transcription in erythrocytes. Nevertheless, a set of genes maintains their expression in erythrocytes, including genes involved in RNA pol II promoter-proximal pausing. Erythrocytes exhibit an inverted nuclear architecture and reposition euchromatin towards the nuclear periphery together with the paused RNA polymerase. In erythrocytes, chromatin domains are partially lost genome-wide except at mini domains retained around paused promoters. Our results suggest that promoter-proximal pausing of the RNA pol II participates in the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.

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The chicken model organism for epigenomic research

Cited by 19 publications

References 86 publications

Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler

Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler

Research Note: IsomiRs of chicken miR-146b-5p are activated upon Salmonella enterica serovar Enteritidis infection

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

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