NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region

Radha Raman Pandey, Michele Ceribelli, Prim B Singh, Johan Ericsson, Roberto Mantovani, Chandrasekhar Kanduri

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Antisense transcription has been shown to be one of the hierarchies that control gene expression in eukaryotes. Recently, we have documented that the mouse Kcnq1 imprinting control region (ICR) harbors bidirectional silencing property, and this feature is linked to an antisense RNA, Kcnq1ot1. In this investigation, using genomic footprinting, we have identified three NF-Y transcription factor binding sites appearing in a methylation-sensitive manner in the Kcnq1ot1 promoter. By employing a dominant negative mutant to the NF-Y transcription factor, we have shown that the NF-Y transcription factor positively regulates antisense transcription. Selective mutation of the conserved nucleotides in the NF-Y binding sites resulted in the loss of antisense transcription. The loss of antisense transcription from the Kcnq1ot1 promoter coincides with an enrichment in the levels of deacetylation and methylation at the lysine 9 residue of histone H3 and DNA methylation at the CpG residues, implying a crucial role for the NF-Y transcription factor in organizing the parent of origin-specific chromatin conformation in the Kcnq1 ICR. Parallel to the loss of antisense transcription, the loss of silencing of the flanking reporter genes was observed, suggesting that NF-Y-mediated Kcnq1ot1 transcription is critical in the bidirectional silencing process of the Kcnq1 ICR. These data highlight the NF-Y transcription factor as a crucial regulator of antisense promoter-mediated bidirectional silencing and the parent of origin-specific epigenetic marks at the Kcnq1 ICR. More importantly, for the first time, we document that NF-Y is involved in maintaining the antisense promoter activity against strong silencing conditions.

Original languageEnglish
Pages (from-to)52685-93
Number of pages9
JournalJournal of Biological Chemistry
Volume279
Issue number50
DOIs
Publication statusPublished - Dec 10 2004

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Transcription
Epigenomics
Transcription Factors
Methylation
Binding Sites
Antisense RNA
DNA Methylation
Eukaryota
Reporter Genes
Histones
Lysine
Chromatin
Ports and harbors
Gene expression
Nucleotides
Conformations
Gene Expression
Genes
Mutation

Keywords

  • Animals
  • Antisense Elements (Genetics)
  • Base Sequence
  • Binding Sites
  • CCAAT-Binding Factor
  • Cell Line
  • DNA
  • Epigenesis, Genetic
  • Gene Expression Regulation
  • Gene Silencing
  • Genomic Imprinting
  • Humans
  • KCNQ Potassium Channels
  • KCNQ1 Potassium Channel
  • Membrane Proteins
  • Mice
  • Potassium Channels, Voltage-Gated
  • Promoter Regions, Genetic
  • Recombinant Proteins
  • Sequence Deletion
  • Journal Article
  • Research Support, Non-U.S. Gov't

Cite this

NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region. / Pandey, Radha Raman; Ceribelli, Michele; Singh, Prim B; Ericsson, Johan; Mantovani, Roberto; Kanduri, Chandrasekhar.

In: Journal of Biological Chemistry, Vol. 279, No. 50, 10.12.2004, p. 52685-93.

Research output: Contribution to journalArticle

Pandey, Radha Raman ; Ceribelli, Michele ; Singh, Prim B ; Ericsson, Johan ; Mantovani, Roberto ; Kanduri, Chandrasekhar. / NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region. In: Journal of Biological Chemistry. 2004 ; Vol. 279, No. 50. pp. 52685-93.
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T1 - NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region

AU - Pandey, Radha Raman

AU - Ceribelli, Michele

AU - Singh, Prim B

AU - Ericsson, Johan

AU - Mantovani, Roberto

AU - Kanduri, Chandrasekhar

PY - 2004/12/10

Y1 - 2004/12/10

N2 - Antisense transcription has been shown to be one of the hierarchies that control gene expression in eukaryotes. Recently, we have documented that the mouse Kcnq1 imprinting control region (ICR) harbors bidirectional silencing property, and this feature is linked to an antisense RNA, Kcnq1ot1. In this investigation, using genomic footprinting, we have identified three NF-Y transcription factor binding sites appearing in a methylation-sensitive manner in the Kcnq1ot1 promoter. By employing a dominant negative mutant to the NF-Y transcription factor, we have shown that the NF-Y transcription factor positively regulates antisense transcription. Selective mutation of the conserved nucleotides in the NF-Y binding sites resulted in the loss of antisense transcription. The loss of antisense transcription from the Kcnq1ot1 promoter coincides with an enrichment in the levels of deacetylation and methylation at the lysine 9 residue of histone H3 and DNA methylation at the CpG residues, implying a crucial role for the NF-Y transcription factor in organizing the parent of origin-specific chromatin conformation in the Kcnq1 ICR. Parallel to the loss of antisense transcription, the loss of silencing of the flanking reporter genes was observed, suggesting that NF-Y-mediated Kcnq1ot1 transcription is critical in the bidirectional silencing process of the Kcnq1 ICR. These data highlight the NF-Y transcription factor as a crucial regulator of antisense promoter-mediated bidirectional silencing and the parent of origin-specific epigenetic marks at the Kcnq1 ICR. More importantly, for the first time, we document that NF-Y is involved in maintaining the antisense promoter activity against strong silencing conditions.

AB - Antisense transcription has been shown to be one of the hierarchies that control gene expression in eukaryotes. Recently, we have documented that the mouse Kcnq1 imprinting control region (ICR) harbors bidirectional silencing property, and this feature is linked to an antisense RNA, Kcnq1ot1. In this investigation, using genomic footprinting, we have identified three NF-Y transcription factor binding sites appearing in a methylation-sensitive manner in the Kcnq1ot1 promoter. By employing a dominant negative mutant to the NF-Y transcription factor, we have shown that the NF-Y transcription factor positively regulates antisense transcription. Selective mutation of the conserved nucleotides in the NF-Y binding sites resulted in the loss of antisense transcription. The loss of antisense transcription from the Kcnq1ot1 promoter coincides with an enrichment in the levels of deacetylation and methylation at the lysine 9 residue of histone H3 and DNA methylation at the CpG residues, implying a crucial role for the NF-Y transcription factor in organizing the parent of origin-specific chromatin conformation in the Kcnq1 ICR. Parallel to the loss of antisense transcription, the loss of silencing of the flanking reporter genes was observed, suggesting that NF-Y-mediated Kcnq1ot1 transcription is critical in the bidirectional silencing process of the Kcnq1 ICR. These data highlight the NF-Y transcription factor as a crucial regulator of antisense promoter-mediated bidirectional silencing and the parent of origin-specific epigenetic marks at the Kcnq1 ICR. More importantly, for the first time, we document that NF-Y is involved in maintaining the antisense promoter activity against strong silencing conditions.

KW - Animals

KW - Antisense Elements (Genetics)

KW - Base Sequence

KW - Binding Sites

KW - CCAAT-Binding Factor

KW - Cell Line

KW - DNA

KW - Epigenesis, Genetic

KW - Gene Expression Regulation

KW - Gene Silencing

KW - Genomic Imprinting

KW - Humans

KW - KCNQ Potassium Channels

KW - KCNQ1 Potassium Channel

KW - Membrane Proteins

KW - Mice

KW - Potassium Channels, Voltage-Gated

KW - Promoter Regions, Genetic

KW - Recombinant Proteins

KW - Sequence Deletion

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1074/jbc.M408084200

DO - 10.1074/jbc.M408084200

M3 - Article

C2 - 15459184

VL - 279

SP - 52685

EP - 52693

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 50

ER -