The Rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone H1 and DNA methylation

James A. MacLean, Anilkumar Bettegowda, Byung Ju Kim, Chih Hong Lou, Seung Min Yang, Anjana Bhardwaj, Sreenath Shanker, Zhiying Hu, Yuhong Fan, Sigrid Eckardt, K. John McLaughlin, Arthur I. Skoultchi, Miles F. Wilkinson

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Histone H1 is an abundant and essential component of chromatin whose precise role in regulating gene expression is poorly understood. Here, we report that a major target of H1-mediated regulation in embryonic stem (ES) cells is the X-linked Rhox homeobox gene cluster. To address the underlying mechanism, we examined the founding member of the Rhox gene cluster - Rhox5 - and found that its distal promoter (Pd) loses H1, undergoes demethylation, and is transcriptionally activated in response to loss of H1 genes in ES cells. Demethylation of the Pd is required for its transcriptional induction and we identified a single cytosine in the Pd that, when methylated, is sufficient to inhibit Pd transcription. Methylation of this single cytosine prevents the Pd from binding GA-binding protein (GABP), a transcription factor essential for Pd transcription. Thus, H1 silences Rhox5 transcription by promoting methylation of one of its promoters, a mechanism likely to extend to other H1-regulated Rhox genes, based on analysis of ES cells lacking DNA methyltransferases. The Rhox cluster genes targeted for H1-mediated transcriptional repression are also subject to another DNA methylation-regulated process: Xp imprinting. Remarkably, we found that only H1-regulated Rhox genes are imprinted, not those immune to H1-mediated repression. Together, our results indicate that the Rhox gene cluster is a major target of H1-mediated transcriptional repression in ES cells and that H1 is a candidate to have a role in Xp imprinting.

Original languageEnglish (US)
Pages (from-to)1275-1287
Number of pages13
JournalMolecular and Cellular Biology
Volume31
Issue number6
DOIs
StatePublished - Mar 2011

Fingerprint

Homeobox Genes
DNA Methylation
Embryonic Stem Cells
Multigene Family
Histones
Cytosine
Methylation
GA-Binding Protein Transcription Factor
Genes
Methyltransferases
Chromatin
Carrier Proteins
Gene Expression
DNA

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

MacLean, J. A., Bettegowda, A., Kim, B. J., Lou, C. H., Yang, S. M., Bhardwaj, A., ... Wilkinson, M. F. (2011). The Rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone H1 and DNA methylation. Molecular and Cellular Biology, 31(6), 1275-1287. https://doi.org/10.1128/MCB.00734-10

The Rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone H1 and DNA methylation. / MacLean, James A.; Bettegowda, Anilkumar; Kim, Byung Ju; Lou, Chih Hong; Yang, Seung Min; Bhardwaj, Anjana; Shanker, Sreenath; Hu, Zhiying; Fan, Yuhong; Eckardt, Sigrid; McLaughlin, K. John; Skoultchi, Arthur I.; Wilkinson, Miles F.

In: Molecular and Cellular Biology, Vol. 31, No. 6, 03.2011, p. 1275-1287.

Research output: Contribution to journalArticle

MacLean, JA, Bettegowda, A, Kim, BJ, Lou, CH, Yang, SM, Bhardwaj, A, Shanker, S, Hu, Z, Fan, Y, Eckardt, S, McLaughlin, KJ, Skoultchi, AI & Wilkinson, MF 2011, 'The Rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone H1 and DNA methylation', Molecular and Cellular Biology, vol. 31, no. 6, pp. 1275-1287. https://doi.org/10.1128/MCB.00734-10
MacLean, James A. ; Bettegowda, Anilkumar ; Kim, Byung Ju ; Lou, Chih Hong ; Yang, Seung Min ; Bhardwaj, Anjana ; Shanker, Sreenath ; Hu, Zhiying ; Fan, Yuhong ; Eckardt, Sigrid ; McLaughlin, K. John ; Skoultchi, Arthur I. ; Wilkinson, Miles F. / The Rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone H1 and DNA methylation. In: Molecular and Cellular Biology. 2011 ; Vol. 31, No. 6. pp. 1275-1287.
@article{ab04021a891848c3aeca6edff9d1aea8,
title = "The Rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone H1 and DNA methylation",
abstract = "Histone H1 is an abundant and essential component of chromatin whose precise role in regulating gene expression is poorly understood. Here, we report that a major target of H1-mediated regulation in embryonic stem (ES) cells is the X-linked Rhox homeobox gene cluster. To address the underlying mechanism, we examined the founding member of the Rhox gene cluster - Rhox5 - and found that its distal promoter (Pd) loses H1, undergoes demethylation, and is transcriptionally activated in response to loss of H1 genes in ES cells. Demethylation of the Pd is required for its transcriptional induction and we identified a single cytosine in the Pd that, when methylated, is sufficient to inhibit Pd transcription. Methylation of this single cytosine prevents the Pd from binding GA-binding protein (GABP), a transcription factor essential for Pd transcription. Thus, H1 silences Rhox5 transcription by promoting methylation of one of its promoters, a mechanism likely to extend to other H1-regulated Rhox genes, based on analysis of ES cells lacking DNA methyltransferases. The Rhox cluster genes targeted for H1-mediated transcriptional repression are also subject to another DNA methylation-regulated process: Xp imprinting. Remarkably, we found that only H1-regulated Rhox genes are imprinted, not those immune to H1-mediated repression. Together, our results indicate that the Rhox gene cluster is a major target of H1-mediated transcriptional repression in ES cells and that H1 is a candidate to have a role in Xp imprinting.",
author = "MacLean, {James A.} and Anilkumar Bettegowda and Kim, {Byung Ju} and Lou, {Chih Hong} and Yang, {Seung Min} and Anjana Bhardwaj and Sreenath Shanker and Zhiying Hu and Yuhong Fan and Sigrid Eckardt and McLaughlin, {K. John} and Skoultchi, {Arthur I.} and Wilkinson, {Miles F.}",
year = "2011",
month = "3",
doi = "10.1128/MCB.00734-10",
language = "English (US)",
volume = "31",
pages = "1275--1287",
journal = "Molecular and Cellular Biology",
issn = "0270-7306",
publisher = "American Society for Microbiology",
number = "6",

}

TY - JOUR

T1 - The Rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone H1 and DNA methylation

AU - MacLean, James A.

AU - Bettegowda, Anilkumar

AU - Kim, Byung Ju

AU - Lou, Chih Hong

AU - Yang, Seung Min

AU - Bhardwaj, Anjana

AU - Shanker, Sreenath

AU - Hu, Zhiying

AU - Fan, Yuhong

AU - Eckardt, Sigrid

AU - McLaughlin, K. John

AU - Skoultchi, Arthur I.

AU - Wilkinson, Miles F.

PY - 2011/3

Y1 - 2011/3

N2 - Histone H1 is an abundant and essential component of chromatin whose precise role in regulating gene expression is poorly understood. Here, we report that a major target of H1-mediated regulation in embryonic stem (ES) cells is the X-linked Rhox homeobox gene cluster. To address the underlying mechanism, we examined the founding member of the Rhox gene cluster - Rhox5 - and found that its distal promoter (Pd) loses H1, undergoes demethylation, and is transcriptionally activated in response to loss of H1 genes in ES cells. Demethylation of the Pd is required for its transcriptional induction and we identified a single cytosine in the Pd that, when methylated, is sufficient to inhibit Pd transcription. Methylation of this single cytosine prevents the Pd from binding GA-binding protein (GABP), a transcription factor essential for Pd transcription. Thus, H1 silences Rhox5 transcription by promoting methylation of one of its promoters, a mechanism likely to extend to other H1-regulated Rhox genes, based on analysis of ES cells lacking DNA methyltransferases. The Rhox cluster genes targeted for H1-mediated transcriptional repression are also subject to another DNA methylation-regulated process: Xp imprinting. Remarkably, we found that only H1-regulated Rhox genes are imprinted, not those immune to H1-mediated repression. Together, our results indicate that the Rhox gene cluster is a major target of H1-mediated transcriptional repression in ES cells and that H1 is a candidate to have a role in Xp imprinting.

AB - Histone H1 is an abundant and essential component of chromatin whose precise role in regulating gene expression is poorly understood. Here, we report that a major target of H1-mediated regulation in embryonic stem (ES) cells is the X-linked Rhox homeobox gene cluster. To address the underlying mechanism, we examined the founding member of the Rhox gene cluster - Rhox5 - and found that its distal promoter (Pd) loses H1, undergoes demethylation, and is transcriptionally activated in response to loss of H1 genes in ES cells. Demethylation of the Pd is required for its transcriptional induction and we identified a single cytosine in the Pd that, when methylated, is sufficient to inhibit Pd transcription. Methylation of this single cytosine prevents the Pd from binding GA-binding protein (GABP), a transcription factor essential for Pd transcription. Thus, H1 silences Rhox5 transcription by promoting methylation of one of its promoters, a mechanism likely to extend to other H1-regulated Rhox genes, based on analysis of ES cells lacking DNA methyltransferases. The Rhox cluster genes targeted for H1-mediated transcriptional repression are also subject to another DNA methylation-regulated process: Xp imprinting. Remarkably, we found that only H1-regulated Rhox genes are imprinted, not those immune to H1-mediated repression. Together, our results indicate that the Rhox gene cluster is a major target of H1-mediated transcriptional repression in ES cells and that H1 is a candidate to have a role in Xp imprinting.

UR - http://www.scopus.com/inward/record.url?scp=79952258416&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79952258416&partnerID=8YFLogxK

U2 - 10.1128/MCB.00734-10

DO - 10.1128/MCB.00734-10

M3 - Article

C2 - 21245380

AN - SCOPUS:79952258416

VL - 31

SP - 1275

EP - 1287

JO - Molecular and Cellular Biology

JF - Molecular and Cellular Biology

SN - 0270-7306

IS - 6

ER -