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Article ; Online: Chicken Erythrocyte: Epigenomic Regulation of Gene Activity.

Beacon, Tasnim H / Davie, James R

International journal of molecular sciences

2023 Volume 24, Issue 9

Abstract: The chicken genome is one-third the size of the human genome and has a similarity of sixty percent when it comes to gene content. Harboring similar genome sequences, chickens' gene arrangement is closer to the human genomic organization than it is to ... ...

Abstract	The chicken genome is one-third the size of the human genome and has a similarity of sixty percent when it comes to gene content. Harboring similar genome sequences, chickens' gene arrangement is closer to the human genomic organization than it is to rodents. Chickens have been used as model organisms to study evolution, epigenome, and diseases. The chicken nucleated erythrocyte's physiological function is to carry oxygen to the tissues and remove carbon dioxide. The erythrocyte also supports the innate immune response in protecting the chicken from pathogens. Among the highly studied aspects in the field of epigenetics are modifications of DNA, histones, and their variants. In understanding the organization of transcriptionally active chromatin, studies on the chicken nucleated erythrocyte have been important. Through the application of a variety of epigenomic approaches, we and others have determined the chromatin structure of expressed/poised genes involved in the physiological functions of the erythrocyte. As the chicken erythrocyte has a nucleus and is readily isolated from the animal, the chicken erythrocyte epigenome has been studied as a biomarker of an animal's long-term exposure to stress. In this review, epigenomic features that allow erythroid gene expression in a highly repressive chromatin background are presented.
MeSH term(s)	Humans ; Animals ; Chickens/genetics ; Chickens/metabolism ; Epigenomics ; Chromatin/genetics ; Histones/genetics ; Histones/metabolism ; Erythrocytes/metabolism
Chemical Substances	Chromatin ; Histones
Language	English
Publishing date	2023-05-05
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24098287
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Transcriptionally Active Chromatin-Lessons Learned from the Chicken Erythrocyte Chromatin Fractionation.

Beacon, Tasnim H / Davie, James R

Cells

2021 Volume 10, Issue 6

Abstract: The chicken erythrocyte model system has been valuable to the study of chromatin structure and function, specifically for genes involved in oxygen transport and the innate immune response. Several seminal features of transcriptionally active chromatin ... ...

Abstract	The chicken erythrocyte model system has been valuable to the study of chromatin structure and function, specifically for genes involved in oxygen transport and the innate immune response. Several seminal features of transcriptionally active chromatin were discovered in this system. Davie and colleagues capitalized on the unique features of the chicken erythrocyte to separate and isolate transcriptionally active chromatin and silenced chromatin, using a powerful native fractionation procedure. Histone modifications, histone variants, atypical nucleosomes (U-shaped nucleosomes) and other chromatin structural features (open chromatin) were identified in these studies. More recently, the transcriptionally active chromosomal domains in the chicken erythrocyte genome were mapped by combining this chromatin fractionation method with next-generation DNA and RNA sequencing. The landscape of histone modifications relative to chromatin structural features in the chicken erythrocyte genome was reported in detail, including the first ever mapping of histone H4 asymmetrically dimethylated at Arg 3 (H4R3me2a) and histone H3 symmetrically dimethylated at Arg 2 (H3R2me2s), which are products of protein arginine methyltransferases (PRMTs) 1 and 5, respectively. PRMT1 is important in the establishment and maintenance of chicken erythrocyte transcriptionally active chromatin.
MeSH term(s)	Animals ; Chickens ; Chromatin/metabolism ; Dose Fractionation, Radiation ; Erythrocytes/metabolism ; Histone Code/physiology ; Histones/metabolism ; Humans ; Methyltransferases/metabolism
Chemical Substances	Chromatin ; Histones ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2021-05-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells10061354
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Article ; Online: Introduction: Genome Biology.

Beacon, Tasnim H / Davie, James R / Hendzel, Michael J

Genome

2021 Volume 64, Issue 4, Page(s) v–vii

MeSH term(s)	Animals ; Biology ; COVID-19/genetics ; Computational Biology ; Disease/genetics ; Epigenomics ; Female ; Genome ; Humans ; Male
Language	English
Publishing date	2021-04-11
Publishing country	Canada
Document type	Journal Article
ZDB-ID	639031-6
ISSN	1480-3321 ; 0831-2796
ISSN (online)	1480-3321
ISSN	0831-2796
DOI	10.1139/gen-2021-0003
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Article ; Online: The chicken model organism for epigenomic research.

Beacon, Tasnim H / Davie, James R

Genome

2020 Volume 64, Issue 4, Page(s) 476–489

Abstract: 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 ... ...

Abstract	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 in the 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.
MeSH term(s)	Animals ; Chickens/genetics ; Chromatin/chemistry ; Computational Biology ; Epigenesis, Genetic ; Epigenome ; Epigenomics/methods ; Erythrocytes ; Erythropoiesis ; Gene Expression ; Genetic Techniques ; Genome ; Genomics ; Globins ; High-Throughput Nucleotide Sequencing ; Humans ; Immunity, Innate ; Poultry/genetics ; RNA, Untranslated
Chemical Substances	Chromatin ; RNA, Untranslated ; Globins (9004-22-2)
Language	English
Publishing date	2020-11-24
Publishing country	Canada
Document type	Journal Article ; Review
ZDB-ID	639031-6
ISSN	1480-3321 ; 0831-2796
ISSN (online)	1480-3321
ISSN	0831-2796
DOI	10.1139/gen-2020-0129
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Article ; Online: Transcriptionally Active Chromatin—Lessons Learned from the Chicken Erythrocyte Chromatin Fractionation

Tasnim H. Beacon / James R. Davie

Cells, Vol 10, Iss 1354, p

2021 Volume 1354

Abstract	The chicken erythrocyte model system has been valuable to the study of chromatin structure and function, specifically for genes involved in oxygen transport and the innate immune response. Several seminal features of transcriptionally active chromatin were discovered in this system. Davie and colleagues capitalized on the unique features of the chicken erythrocyte to separate and isolate transcriptionally active chromatin and silenced chromatin, using a powerful native fractionation procedure. Histone modifications, histone variants, atypical nucleosomes (U-shaped nucleosomes) and other chromatin structural features (open chromatin) were identified in these studies. More recently, the transcriptionally active chromosomal domains in the chicken erythrocyte genome were mapped by combining this chromatin fractionation method with next-generation DNA and RNA sequencing. The landscape of histone modifications relative to chromatin structural features in the chicken erythrocyte genome was reported in detail, including the first ever mapping of histone H4 asymmetrically dimethylated at Arg 3 (H4R3me2a) and histone H3 symmetrically dimethylated at Arg 2 (H3R2me2s), which are products of protein arginine methyltransferases (PRMTs) 1 and 5, respectively. PRMT1 is important in the establishment and maintenance of chicken erythrocyte transcriptionally active chromatin.
Keywords	transcriptionally active chromatin ; compartment A and B ; phase separation ; histone modifications ; chromatin-modifying enzymes ; Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus

Beacon, Tasnim H / Delcuve, Geneviève P / Davie, James R

Genome

2020 Volume 64, Issue 4, Page(s) 386–399

Abstract: The angiotensin-converting enzyme 2 (ACE2) is the receptor for the three coronaviruses HCoV-NL63, SARS-CoV, and SARS-CoV-2. ACE2 is involved in the regulation of the renin-angiotensin system and blood pressure. ACE2 is also involved in the regulation of ... ...

Abstract	The angiotensin-converting enzyme 2 (ACE2) is the receptor for the three coronaviruses HCoV-NL63, SARS-CoV, and SARS-CoV-2. ACE2 is involved in the regulation of the renin-angiotensin system and blood pressure. ACE2 is also involved in the regulation of several signaling pathways, including integrin signaling.
MeSH term(s)	Angiotensin-Converting Enzyme 2/genetics ; COVID-19 ; Epigenesis, Genetic ; Gene Expression Regulation ; Humans ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; Receptors, Virus/genetics ; Renin-Angiotensin System ; SARS-CoV-2 ; Signal Transduction
Chemical Substances	Receptors, Virus ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-10-21
Publishing country	Canada
Document type	Journal Article ; Review
ZDB-ID	639031-6
ISSN	1480-3321 ; 0831-2796
ISSN (online)	1480-3321
ISSN	0831-2796
DOI	10.1139/gen-2020-0124
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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Genomic landscape of transcriptionally active histone arginine methylation marks, H3R2me2s and H4R3me2a, relative to nucleosome depleted regions.

Beacon, Tasnim H / Xu, Wayne / Davie, James R

Gene

2020 Volume 742, Page(s) 144593

Abstract: Protein arginine methyltransferase 1 (PRMT1) and the product of this enzyme (histone H4 asymmetrically dimethylated at Arg 3; H4R3me2a) are important in the establishment and maintenance of chicken and murine erythrocyte transcriptionally active ... ...

Abstract	Protein arginine methyltransferase 1 (PRMT1) and the product of this enzyme (histone H4 asymmetrically dimethylated at Arg 3; H4R3me2a) are important in the establishment and maintenance of chicken and murine erythrocyte transcriptionally active chromatin. Silencing the expression of PRMT1 results in loss of acetylated histones H3 and H4 and methylated H3K4 and prevents erythropoiesis. Here, we show that H4R3me2a and the PRMT5-catalyzed histone H3 symmetrically dimethylated at Arg 2 (H3R2me2s) locate largely to introns of expressed genes and intergenic regions, with both marks co-localizing in the chicken polychromatic erythrocyte genome. H4R3me2a and H3R2me2s were associated with histone marks of active promoters and enhancers, as well as with the body of genes that have an atypical chromatin structure, with nucleosome depleted regions. H4R3me2a co-localized with acetylated H3K27. Previous studies have shown that PRMT1 was bound to CBP/p300, suggesting a role of PRMT1-mediated H4R3me2a in CBP/p300 recruitment and H3K27 acetylation. Moreover, PRMT1 might be a key enzyme affected when S-adenosyl methionine levels are reduced in metabolic disorders.
MeSH term(s)	Animals ; Arginine/metabolism ; Chickens ; Chromatin/metabolism ; Female ; Histone Code/genetics ; Histones/genetics ; Histones/metabolism ; Methylation ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Protein-Arginine N-Methyltransferases/metabolism ; Reticulocytes/metabolism ; Transcription, Genetic
Chemical Substances	Chromatin ; Histones ; Nucleosomes ; Arginine (94ZLA3W45F) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319)
Language	English
Publishing date	2020-03-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2020.144593
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Article ; Online: The key role of differential broad H3K4me3 and H3K4ac domains in breast cancer.

López, Camila / Barnon, Mohammad T / Beacon, Tasnim H / Nardocci, Gino / Davie, James R

Gene

2022 Volume 826, Page(s) 146463

Abstract: Epigenetic processes are radically altered in cancer cells. The altered epigenetic events may include histone post-translational modifications (PTMs), DNA modifications, and/or alterations in the levels and modifications of chromatin modifying enzymes ... ...

Abstract	Epigenetic processes are radically altered in cancer cells. The altered epigenetic events may include histone post-translational modifications (PTMs), DNA modifications, and/or alterations in the levels and modifications of chromatin modifying enzymes and chromatin remodelers. With changes in gene programming are changes in the genomic distribution of histone PTMs. Genes that are poised or transcriptionally active have histone H3 trimethylated lysine 4 (H3K4me3) located at the transcription start site and at the 5' end of the gene. However, a small population of genes that are involved in cell identity or cancer cell properties have a broad H3K4me3 domain that may stretch for several kilobases through the coding region of the gene. Each cancer cell type appears to mark a select set of cancer-related genes in this manner. In this study, we determined which genes were differentially marked with the broad H3K4me3 domain in normal-like (MCF10A), luminal-type breast cancer (MCF7), and triple-negative breast cancer (MDA-MB-231) cells. We also determined whether histone H3 acetylated lysine 4 (H3K4ac), also a mark of active promoters, had a broad domain configuration. We applied two peak callers (MACS2, PeakRanger) to analyze H3K4me3 and H3K4ac chromatin immunoprecipitation sequencing (ChIP-Seq) data. We identified genes with a broad H3K4me3 and/or H3K4ac domain specific to each cell line and show that the genes have critical roles in the breast cancer subtypes. Furthermore, we show that H3K4ac marks enhancers. The identified genes with the broad H3K4me3/H3K4ac domain have been targeted in clinical and pre-clinical studies including therapeutic treatments of breast cancer.
MeSH term(s)	Breast Neoplasms/genetics ; Chromatin ; Epigenesis, Genetic ; Female ; Histones/genetics ; Histones/metabolism ; Humans ; Lysine/genetics ; Transcription Initiation Site
Chemical Substances	Chromatin ; Histones ; histone H3 trimethyl Lys4 ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2022-03-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2022.146463
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Article: Genomic landscape of transcriptionally active histone arginine methylation marks, H3R2me2s and H4R3me2a, relative to nucleosome depleted regions

Beacon, Tasnim H / Xu, Wayne / Davie, James R

Gene. 2020 June 05, v. 742

2020

Abstract	Protein arginine methyltransferase 1 (PRMT1) and the product of this enzyme (histone H4 asymmetrically dimethylated at Arg 3; H4R3me2a) are important in the establishment and maintenance of chicken and murine erythrocyte transcriptionally active chromatin. Silencing the expression of PRMT1 results in loss of acetylated histones H3 and H4 and methylated H3K4 and prevents erythropoiesis. Here, we show that H4R3me2a and the PRMT5-catalyzed histone H3 symmetrically dimethylated at Arg 2 (H3R2me2s) locate largely to introns of expressed genes and intergenic regions, with both marks co-localizing in the chicken polychromatic erythrocyte genome. H4R3me2a and H3R2me2s were associated with histone marks of active promoters and enhancers, as well as with the body of genes that have an atypical chromatin structure, with nucleosome depleted regions. H4R3me2a co-localized with acetylated H3K27. Previous studies have shown that PRMT1 was bound to CBP/p300, suggesting a role of PRMT1-mediated H4R3me2a in CBP/p300 recruitment and H3K27 acetylation. Moreover, PRMT1 might be a key enzyme affected when S-adenosyl methionine levels are reduced in metabolic disorders.
Keywords	acetylation ; arginine ; chickens ; erythrocytes ; erythropoiesis ; histones ; introns ; methionine ; methylation ; mice ; nucleosomes ; transcription (genetics) ; type I protein arginine methyltransferase
Language	English
Dates of publication	2020-0605
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2020.144593
Database	NAL-Catalogue (AGRICOLA)

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Article: The key role of differential broad H3K4me3 and H3K4ac domains in breast cancer

López, Camila / Barnon, Mohammad T. / Beacon, Tasnim H. / Nardocci, Gino / Davie, James R.

Gene. 2022 June 05, v. 826

2022

Abstract	Epigenetic processes are radically altered in cancer cells. The altered epigenetic events may include histone post-translational modifications (PTMs), DNA modifications, and/or alterations in the levels and modifications of chromatin modifying enzymes and chromatin remodelers. With changes in gene programming are changes in the genomic distribution of histone PTMs. Genes that are poised or transcriptionally active have histone H3 trimethylated lysine 4 (H3K4me3) located at the transcription start site and at the 5′ end of the gene. However, a small population of genes that are involved in cell identity or cancer cell properties have a broad H3K4me3 domain that may stretch for several kilobases through the coding region of the gene. Each cancer cell type appears to mark a select set of cancer-related genes in this manner. In this study, we determined which genes were differentially marked with the broad H3K4me3 domain in normal-like (MCF10A), luminal-type breast cancer (MCF7), and triple-negative breast cancer (MDA-MB-231) cells. We also determined whether histone H3 acetylated lysine 4 (H3K4ac), also a mark of active promoters, had a broad domain configuration. We applied two peak callers (MACS2, PeakRanger) to analyze H3K4me3 and H3K4ac chromatin immunoprecipitation sequencing (ChIP-Seq) data. We identified genes with a broad H3K4me3 and/or H3K4ac domain specific to each cell line and show that the genes have critical roles in the breast cancer subtypes. Furthermore, we show that H3K4ac marks enhancers. The identified genes with the broad H3K4me3/H3K4ac domain have been targeted in clinical and pre-clinical studies including therapeutic treatments of breast cancer.
Keywords	DNA ; breast neoplasms ; cell lines ; chromatin ; chromatin immunoprecipitation ; epigenetics ; genomics ; histones ; lysine ; neoplasm cells ; therapeutics ; transcription (genetics) ; transcription initiation site
Language	English
Dates of publication	2022-0605
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2022.146463
Database	NAL-Catalogue (AGRICOLA)

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