DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES

Karla O'Neill, Rachelle E Irwin, Sarah-Jayne Mackin, Avinash Thakur, Sara-Jayne Thursby, Ciske Bertens, Laura Masala, Jayne E.P. Loughery, Darragh G McArt, CP Walsh

Research output: Contribution to conferenceAbstract

Abstract

DNA methylation is a critical mechanism for regulating gene expression and ensuring genomic stability. However, loss of function mutations of methyltransferase enzymes such as DNMT1 in normal differentiated cells result in a lethal phenotype. Consequently, existing investigations have only assessed DNMT1 knockdowns in embryonic stem cells or cancer cell lines. Here, isogenic lines of hypomorphic, normal, immortalised fibroblasts have instead been generated via stable integration with short hairpin RNA. Enrichment analysis of epigenome-wide methylation arrays indicated widespread demethylation within promoter and gene body regions. In addition, four specific gene categories were highlighted as most affected; protocadherins, genes regulating body mass, olfactory receptors and cancer/testis antigens. Comparison of short-term siRNA and long-term shRNA-mediated depletion of DNMT1 indicated that many regions recover methylation as shRNA-containing cell lines adapt to lowered levels of DNMT1. Interestingly, polycomb-regulated genes are refractory to de novo DNA methylation in these cells following recovery, reinforcing the concept of mutually-exclusive domains that are regulated by these two major epigenetic mechanisms.

Conference

Conference20th Meeting of the Irish Society of Human Genetics
CountryIreland
CityDublin
Period15/09/1715/09/18
Internet address

Fingerprint

Small Interfering RNA
DNA Methylation
Methylation
Genes
Odorant Receptors
Cell Line
Body Regions
Genomic Instability
Testicular Neoplasms
Methyltransferases
Embryonic Stem Cells
Epigenomics
Fibroblasts
Phenotype
Gene Expression
Antigens
Mutation
Enzymes
Neoplasms

Cite this

O'Neill, K., Irwin, R. E., Mackin, S-J., Thakur, A., Thursby, S-J., Bertens, C., ... Walsh, CP. (2018). DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES. 54-64. Abstract from 20th Meeting of the Irish Society of Human Genetics, Dublin, Ireland.
O'Neill, Karla ; Irwin, Rachelle E ; Mackin, Sarah-Jayne ; Thakur, Avinash ; Thursby, Sara-Jayne ; Bertens, Ciske ; Masala, Laura ; Loughery, Jayne E.P. ; McArt, Darragh G ; Walsh, CP. / DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES. Abstract from 20th Meeting of the Irish Society of Human Genetics, Dublin, Ireland.
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title = "DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES",
abstract = "DNA methylation is a critical mechanism for regulating gene expression and ensuring genomic stability. However, loss of function mutations of methyltransferase enzymes such as DNMT1 in normal differentiated cells result in a lethal phenotype. Consequently, existing investigations have only assessed DNMT1 knockdowns in embryonic stem cells or cancer cell lines. Here, isogenic lines of hypomorphic, normal, immortalised fibroblasts have instead been generated via stable integration with short hairpin RNA. Enrichment analysis of epigenome-wide methylation arrays indicated widespread demethylation within promoter and gene body regions. In addition, four specific gene categories were highlighted as most affected; protocadherins, genes regulating body mass, olfactory receptors and cancer/testis antigens. Comparison of short-term siRNA and long-term shRNA-mediated depletion of DNMT1 indicated that many regions recover methylation as shRNA-containing cell lines adapt to lowered levels of DNMT1. Interestingly, polycomb-regulated genes are refractory to de novo DNA methylation in these cells following recovery, reinforcing the concept of mutually-exclusive domains that are regulated by these two major epigenetic mechanisms.",
author = "Karla O'Neill and Irwin, {Rachelle E} and Sarah-Jayne Mackin and Avinash Thakur and Sara-Jayne Thursby and Ciske Bertens and Laura Masala and Loughery, {Jayne E.P.} and McArt, {Darragh G} and CP Walsh",
year = "2018",
language = "English",
pages = "54--64",
note = "20th Meeting of the Irish Society of Human Genetics ; Conference date: 15-09-2017 Through 15-09-2018",
url = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849961/",

}

O'Neill, K, Irwin, RE, Mackin, S-J, Thakur, A, Thursby, S-J, Bertens, C, Masala, L, Loughery, JEP, McArt, DG & Walsh, CP 2018, 'DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES' 20th Meeting of the Irish Society of Human Genetics, Dublin, Ireland, 15/09/17 - 15/09/18, pp. 54-64.

DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES. / O'Neill, Karla; Irwin, Rachelle E; Mackin, Sarah-Jayne; Thakur, Avinash; Thursby, Sara-Jayne; Bertens, Ciske; Masala, Laura; Loughery, Jayne E.P.; McArt, Darragh G; Walsh, CP.

2018. 54-64 Abstract from 20th Meeting of the Irish Society of Human Genetics, Dublin, Ireland.

Research output: Contribution to conferenceAbstract

TY - CONF

T1 - DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES

AU - O'Neill, Karla

AU - Irwin, Rachelle E

AU - Mackin, Sarah-Jayne

AU - Thakur, Avinash

AU - Thursby, Sara-Jayne

AU - Bertens, Ciske

AU - Masala, Laura

AU - Loughery, Jayne E.P.

AU - McArt, Darragh G

AU - Walsh, CP

PY - 2018

Y1 - 2018

N2 - DNA methylation is a critical mechanism for regulating gene expression and ensuring genomic stability. However, loss of function mutations of methyltransferase enzymes such as DNMT1 in normal differentiated cells result in a lethal phenotype. Consequently, existing investigations have only assessed DNMT1 knockdowns in embryonic stem cells or cancer cell lines. Here, isogenic lines of hypomorphic, normal, immortalised fibroblasts have instead been generated via stable integration with short hairpin RNA. Enrichment analysis of epigenome-wide methylation arrays indicated widespread demethylation within promoter and gene body regions. In addition, four specific gene categories were highlighted as most affected; protocadherins, genes regulating body mass, olfactory receptors and cancer/testis antigens. Comparison of short-term siRNA and long-term shRNA-mediated depletion of DNMT1 indicated that many regions recover methylation as shRNA-containing cell lines adapt to lowered levels of DNMT1. Interestingly, polycomb-regulated genes are refractory to de novo DNA methylation in these cells following recovery, reinforcing the concept of mutually-exclusive domains that are regulated by these two major epigenetic mechanisms.

AB - DNA methylation is a critical mechanism for regulating gene expression and ensuring genomic stability. However, loss of function mutations of methyltransferase enzymes such as DNMT1 in normal differentiated cells result in a lethal phenotype. Consequently, existing investigations have only assessed DNMT1 knockdowns in embryonic stem cells or cancer cell lines. Here, isogenic lines of hypomorphic, normal, immortalised fibroblasts have instead been generated via stable integration with short hairpin RNA. Enrichment analysis of epigenome-wide methylation arrays indicated widespread demethylation within promoter and gene body regions. In addition, four specific gene categories were highlighted as most affected; protocadherins, genes regulating body mass, olfactory receptors and cancer/testis antigens. Comparison of short-term siRNA and long-term shRNA-mediated depletion of DNMT1 indicated that many regions recover methylation as shRNA-containing cell lines adapt to lowered levels of DNMT1. Interestingly, polycomb-regulated genes are refractory to de novo DNA methylation in these cells following recovery, reinforcing the concept of mutually-exclusive domains that are regulated by these two major epigenetic mechanisms.

M3 - Abstract

SP - 54

EP - 64

ER -

O'Neill K, Irwin RE, Mackin S-J, Thakur A, Thursby S-J, Bertens C et al. DEPLETION OF DNMT1 IN DIFFERENTIATED HUMAN CELLS HIGHLIGHTS KEY CLASSES OF DEPENDENT GENES. 2018. Abstract from 20th Meeting of the Irish Society of Human Genetics, Dublin, Ireland.