Non-random distribution of methyl-CpG sites and non-CpG methylation in the human rDNA promoter identified by next generation bisulfite sequencing

Maciej Pietrzak; Grzegorz A. Rempala; Peter T. Nelson; Michal Hetman

doi:10.1016/j.gene.2016.03.028

Non-random distribution of methyl-CpG sites and non-CpG methylation in the human rDNA promoter identified by next generation bisulfite sequencing

Maciej Pietrzak, Grzegorz A. Rempala, Peter T. Nelson, Michal Hetman

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

Abstract

A next generation bisulfite sequencing (NGBS) was used to study rDNA promoter methylation in human brain using postmortem samples of the parietal cortex. Qualitative analysis of patterns of CpG methylation was performed at the individual rDNA unit level. CpG site-specific differences in methylation frequency were observed with the core promoter harboring three out of four most methylated CpGs. Moreover, there was an overall trend towards co-methylation for all possible pairs of 26 CpG sites. The hypermethylated CpGs from the core promoter were also most likely to be co-methylated. Finally, although rare, non-CpG (CpH) methylation was detected at several sites with one of them confirmed using the PspGI-qPCR assay. Similar trends were observed in samples from control individuals as well as patients suffering of Alzheimer's disease (AD), mild cognitive impairment (MCI) or ataxia telangiectasia (AT). Taken together, while some methyl-CpG sites including those in the core promoter may have relatively greater inhibitory effect on rRNA transcription, co-methylation at multiple sites may be required for full and/or long lasting silencing of human rDNA.

Original language	English
Pages (from-to)	35-43
Number of pages	9
Journal	Gene
Volume	585
Issue number	1
DOIs	https://doi.org/10.1016/j.gene.2016.03.028
State	Published - Jul 1 2016

Bibliographical note

Funding Information:
We are grateful for the research volunteers that contributed to this work. This work was supported by NIH (NS073584-01 and 8P30GM103507 to MH; CA152158 to GR; AG028383 to PN), NSF (IOS1021860 to MH; DMS1318886 to GR), The Commonwealth of Kentucky Challenge for Excellence, and the Kentucky Spinal Cord and Head Injury Research Trust. Some samples (young controls and AT) were provided by the NICHD Brain and Tissue Bank for Developmental Disorders and NICH Contract #HHSN275200900011C, Ref. No. NO1-HD-9-0011. The authors wish to thank Dr. Scott A. Myers for the critical reading of the manuscript and Ms. Jing-Juan Zheng for the excellent technical assistance.

Funding Information:
We are grateful for the research volunteers that contributed to this work. This work was supported by NIH ( NS073584-01 and 8P30GM103507 to MH; CA152158 to GR; AG028383 to PN), NSF ( IOS1021860 to MH; DMS1318886 to GR), The Commonwealth of Kentucky Challenge for Excellence , and the Kentucky Spinal Cord and Head Injury Research Trust . Some samples (young controls and AT) were provided by the NICHD Brain and Tissue Bank for Developmental Disorders and NICH Contract #HHSN275200900011C, Ref. No. NO1-HD-9-0011. The authors wish to thank Dr. Scott A. Myers for the critical reading of the manuscript and Ms. Jing-Juan Zheng for the excellent technical assistance.

Publisher Copyright:
© 2016 Elsevier B.V.

Keywords

Aging
Brain
DNA methylation
Neurodegeneration
Nucleolus
RDNA

ASJC Scopus subject areas

Genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.gene.2016.03.028

Cite this

@article{f1c02e6d046c4edaafe2220ed8417557,

title = "Non-random distribution of methyl-CpG sites and non-CpG methylation in the human rDNA promoter identified by next generation bisulfite sequencing",

abstract = "A next generation bisulfite sequencing (NGBS) was used to study rDNA promoter methylation in human brain using postmortem samples of the parietal cortex. Qualitative analysis of patterns of CpG methylation was performed at the individual rDNA unit level. CpG site-specific differences in methylation frequency were observed with the core promoter harboring three out of four most methylated CpGs. Moreover, there was an overall trend towards co-methylation for all possible pairs of 26 CpG sites. The hypermethylated CpGs from the core promoter were also most likely to be co-methylated. Finally, although rare, non-CpG (CpH) methylation was detected at several sites with one of them confirmed using the PspGI-qPCR assay. Similar trends were observed in samples from control individuals as well as patients suffering of Alzheimer's disease (AD), mild cognitive impairment (MCI) or ataxia telangiectasia (AT). Taken together, while some methyl-CpG sites including those in the core promoter may have relatively greater inhibitory effect on rRNA transcription, co-methylation at multiple sites may be required for full and/or long lasting silencing of human rDNA.",

keywords = "Aging, Brain, DNA methylation, Neurodegeneration, Nucleolus, RDNA",

author = "Maciej Pietrzak and Rempala, {Grzegorz A.} and Nelson, {Peter T.} and Michal Hetman",

note = "Funding Information: We are grateful for the research volunteers that contributed to this work. This work was supported by NIH (NS073584-01 and 8P30GM103507 to MH; CA152158 to GR; AG028383 to PN), NSF (IOS1021860 to MH; DMS1318886 to GR), The Commonwealth of Kentucky Challenge for Excellence, and the Kentucky Spinal Cord and Head Injury Research Trust. Some samples (young controls and AT) were provided by the NICHD Brain and Tissue Bank for Developmental Disorders and NICH Contract #HHSN275200900011C, Ref. No. NO1-HD-9-0011. The authors wish to thank Dr. Scott A. Myers for the critical reading of the manuscript and Ms. Jing-Juan Zheng for the excellent technical assistance. Funding Information: We are grateful for the research volunteers that contributed to this work. This work was supported by NIH ( NS073584-01 and 8P30GM103507 to MH; CA152158 to GR; AG028383 to PN), NSF ( IOS1021860 to MH; DMS1318886 to GR), The Commonwealth of Kentucky Challenge for Excellence , and the Kentucky Spinal Cord and Head Injury Research Trust . Some samples (young controls and AT) were provided by the NICHD Brain and Tissue Bank for Developmental Disorders and NICH Contract #HHSN275200900011C, Ref. No. NO1-HD-9-0011. The authors wish to thank Dr. Scott A. Myers for the critical reading of the manuscript and Ms. Jing-Juan Zheng for the excellent technical assistance. Publisher Copyright: {\textcopyright} 2016 Elsevier B.V.",

year = "2016",

month = jul,

day = "1",

doi = "10.1016/j.gene.2016.03.028",

language = "English",

volume = "585",

pages = "35--43",

number = "1",

}

TY - JOUR

T1 - Non-random distribution of methyl-CpG sites and non-CpG methylation in the human rDNA promoter identified by next generation bisulfite sequencing

AU - Pietrzak, Maciej

AU - Rempala, Grzegorz A.

AU - Nelson, Peter T.

AU - Hetman, Michal

N1 - Funding Information: We are grateful for the research volunteers that contributed to this work. This work was supported by NIH (NS073584-01 and 8P30GM103507 to MH; CA152158 to GR; AG028383 to PN), NSF (IOS1021860 to MH; DMS1318886 to GR), The Commonwealth of Kentucky Challenge for Excellence, and the Kentucky Spinal Cord and Head Injury Research Trust. Some samples (young controls and AT) were provided by the NICHD Brain and Tissue Bank for Developmental Disorders and NICH Contract #HHSN275200900011C, Ref. No. NO1-HD-9-0011. The authors wish to thank Dr. Scott A. Myers for the critical reading of the manuscript and Ms. Jing-Juan Zheng for the excellent technical assistance. Funding Information: We are grateful for the research volunteers that contributed to this work. This work was supported by NIH ( NS073584-01 and 8P30GM103507 to MH; CA152158 to GR; AG028383 to PN), NSF ( IOS1021860 to MH; DMS1318886 to GR), The Commonwealth of Kentucky Challenge for Excellence , and the Kentucky Spinal Cord and Head Injury Research Trust . Some samples (young controls and AT) were provided by the NICHD Brain and Tissue Bank for Developmental Disorders and NICH Contract #HHSN275200900011C, Ref. No. NO1-HD-9-0011. The authors wish to thank Dr. Scott A. Myers for the critical reading of the manuscript and Ms. Jing-Juan Zheng for the excellent technical assistance. Publisher Copyright: © 2016 Elsevier B.V.

PY - 2016/7/1

Y1 - 2016/7/1

N2 - A next generation bisulfite sequencing (NGBS) was used to study rDNA promoter methylation in human brain using postmortem samples of the parietal cortex. Qualitative analysis of patterns of CpG methylation was performed at the individual rDNA unit level. CpG site-specific differences in methylation frequency were observed with the core promoter harboring three out of four most methylated CpGs. Moreover, there was an overall trend towards co-methylation for all possible pairs of 26 CpG sites. The hypermethylated CpGs from the core promoter were also most likely to be co-methylated. Finally, although rare, non-CpG (CpH) methylation was detected at several sites with one of them confirmed using the PspGI-qPCR assay. Similar trends were observed in samples from control individuals as well as patients suffering of Alzheimer's disease (AD), mild cognitive impairment (MCI) or ataxia telangiectasia (AT). Taken together, while some methyl-CpG sites including those in the core promoter may have relatively greater inhibitory effect on rRNA transcription, co-methylation at multiple sites may be required for full and/or long lasting silencing of human rDNA.

AB - A next generation bisulfite sequencing (NGBS) was used to study rDNA promoter methylation in human brain using postmortem samples of the parietal cortex. Qualitative analysis of patterns of CpG methylation was performed at the individual rDNA unit level. CpG site-specific differences in methylation frequency were observed with the core promoter harboring three out of four most methylated CpGs. Moreover, there was an overall trend towards co-methylation for all possible pairs of 26 CpG sites. The hypermethylated CpGs from the core promoter were also most likely to be co-methylated. Finally, although rare, non-CpG (CpH) methylation was detected at several sites with one of them confirmed using the PspGI-qPCR assay. Similar trends were observed in samples from control individuals as well as patients suffering of Alzheimer's disease (AD), mild cognitive impairment (MCI) or ataxia telangiectasia (AT). Taken together, while some methyl-CpG sites including those in the core promoter may have relatively greater inhibitory effect on rRNA transcription, co-methylation at multiple sites may be required for full and/or long lasting silencing of human rDNA.

KW - Aging

KW - Brain

KW - DNA methylation

KW - Neurodegeneration

KW - Nucleolus

KW - RDNA

UR - http://www.scopus.com/inward/record.url?scp=84963690413&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84963690413&partnerID=8YFLogxK

U2 - 10.1016/j.gene.2016.03.028

DO - 10.1016/j.gene.2016.03.028

M3 - Article

C2 - 27008990

AN - SCOPUS:84963690413

VL - 585

SP - 35

EP - 43

IS - 1

ER -

Non-random distribution of methyl-CpG sites and non-CpG methylation in the human rDNA promoter identified by next generation bisulfite sequencing

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this