Chromatin organization of transcribed genes in chicken polychromatic erythrocytes

Jahan, Sanzida; Beacon, Tasnim H.; He, Shihua; González, Carolina; Xu, Wayne; Delcuve, Geneviève P.; Jia, Shuo; Hu, Pingzhao; Davie, James R.

doi:10.1016/j.gene.2019.03.001

Cited by 8 publications

(14 citation statements)

References 36 publications

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“…where the orientation of single guide RNA relative to the TSS of gene is a crucial step in the experiment (Baliou et al 2018). Our FAIRE-seq studies in chicken polychromatic erythrocytes provided an experimental approach to accurately identify TSS of expressed genes (Jahan et al 2019b). FAIRE-seq was applied to map out the position of the nucleosome-free, regulatory regions in relation to the active histone marks.…”

Section: Chicken Promoter Organizationmentioning

confidence: 99%

“…In recent studies, the sequences were aligned with the most updated chicken genome assembly, galGal6. Although most H3K4me3 aligned with expressed genes that have been annotated, there were H3K4me3 marks that located to sites in which there was no known gene, suggesting that there are still genes and their promoters yet to be annotated (Jahan et al 2019b).…”

Section: Chicken Promoter Organizationmentioning

confidence: 99%

“…The characterization of the chicken erythroid chromatin structure has been further advanced with the advent of high throughput sequencing technologies (Jahan et al 2016a(Jahan et al , 2019a(Jahan et al , 2020aFishman et al 2019b;Beacon et al 2020a); studies which have increased our understanding of the regulation of the vertebrate epigenome.…”

Section: Erythropoiesismentioning

confidence: 99%

“…Polychromatic erythrocytes express the adult βᴬ-globin gene as do 15-day chicken embryo erythrocytes, but do not express the βᴴ-globin gene as do cells of late embryos and newly hatched chickens. Within the polychromatic erythrocyte LCR, the location of the hypersensitive sites was identified by FAIRE-seq suggesting the nucleosome depleted regions were likely the binding sites for transcription factors (Jahan et al 2019b). Several investigators have used this nucleated, nonreplicating G0-phase cells to investigate the globin genes.…”

Section: β-Globin Domainmentioning

confidence: 99%

“…Davie and his team successfully combined a variety of genomic approaches to determine the composition and structure of transcriptionally active chromatin in chicken polychromatic erythrocytes (non-replicating, transcriptionally active nucleated cells) (Delcuve and Davie 1989;Jahan et al 2016bJahan et al , 2019bBeacon et al 2020b). Fractionation of 0.15 M NaCl soluble chromatin coupled with acetic acid-urea-Triton-X100 (AUT) electrophoresis and western blotting were applied to isolate and characterize active gene enriched chromatin fractions (Delcuve and Davie 1992).…”

Section: Chicken Erythrocyte Chromatin Structurementioning

confidence: 99%

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The chicken model organism for epigenomic research

Beacon

Davie

2021

Genome

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The chicken model organism has advanced the areas of developmental biology, virology, immunology, oncology, epigenetic regulation of gene expression, conservation biology, and genomics of domestication. Further, the chicken model organism has aided in our understanding of human disease. Through the recent advances in high-throughput sequencing and bioinformatic tools, researchers have successfully identified sequences in the chicken genome that have human orthologs, improving mammalian genome annotation. In this review, we highlight the importance of chicken as an animal model in basic and pre-clinical research. We will present the importance of chicken in poultry epigenetics and in genomic studies that trace back to their ancestor, the last link between human and chicken tree of life. There are still many genes of unknown function in the chicken genome yet to be characterized. By taking advantage of recent sequencing technologies, it is possible to gain further insight into the chicken epigenome.

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Section: Chicken Promoter Organizationmentioning

confidence: 99%

Section: Chicken Promoter Organizationmentioning

confidence: 99%

Section: Erythropoiesismentioning

confidence: 99%

Section: β-Globin Domainmentioning

confidence: 99%

Section: Chicken Erythrocyte Chromatin Structurementioning

confidence: 99%

See 3 more Smart Citations

The chicken model organism for epigenomic research

Beacon

Davie

2021

Genome

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SARS‐CoV‐2 multifaceted interaction with the human host. Part II: Innate immunity response, immunopathology, and epigenetics

Beacon

Su²,

Lakowski

et al. 2020

IUBMB Life

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The SARS-CoV-2 makes its way into the cell via the ACE2 receptor and the proteolytic action of TMPRSS2. In response to the SARS-CoV-2 infection, the innate immune response is the first line of defense, triggering multiple signaling pathways to produce interferons, pro-inflammatory cytokines and chemokines, and initiating the adaptive immune response against the virus. Unsurprisingly, the virus has developed strategies to evade detection, which can result in delayed, excessive activation of the innate immune system. The response elicited by the host depends on multiple factors, including health status, age, and sex. An overactive innate immune response can lead to a cytokine storm, inflammation, and vascular disruption, leading to the vast array of symptoms exhibited by COVID-19 patients. What is known about the expression and epigenetic regulation of the ACE2 gene and the various players in the host response are explored in this review.

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Genomic landscape of transcriptionally active histone arginine methylation marks, H3R2me2s and H4R3me2a, relative to nucleosome depleted regions

Beacon

Davie

2020

Gene

View full text Add to dashboard Cite

Chromatin organization of transcribed genes in chicken polychromatic erythrocytes

Cited by 8 publications

References 36 publications

The chicken model organism for epigenomic research

The chicken model organism for epigenomic research

SARS‐CoV‐2 multifaceted interaction with the human host. Part II: Innate immunity response, immunopathology, and epigenetics

Genomic landscape of transcriptionally active histone arginine methylation marks, H3R2me2s and H4R3me2a, relative to nucleosome depleted regions

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