Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>gene
<p>Abstract</p> <p>Background</p> <p>Random monoallelic expression contributes to phenotypic variation of cells and organisms. However, the epigenetic mechanisms by which individual alleles are randomly selected for expression are not known. Taking cues from chromatin s...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-08-01
|
| Series: | Epigenetics & Chromatin |
| Online Access: | http://www.epigeneticsandchromatin.com/content/4/1/14 |
| _version_ | 1828217584756981760 |
|---|---|
| author | Thomas Brandon J Rubio Eric D Krumm Niklas Broin Pilib Ó Bomsztyk Karol Welcsh Piri Greally John M Golden Aaron A Krumm Anton |
| author_facet | Thomas Brandon J Rubio Eric D Krumm Niklas Broin Pilib Ó Bomsztyk Karol Welcsh Piri Greally John M Golden Aaron A Krumm Anton |
| author_sort | Thomas Brandon J |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Random monoallelic expression contributes to phenotypic variation of cells and organisms. However, the epigenetic mechanisms by which individual alleles are randomly selected for expression are not known. Taking cues from chromatin signatures at imprinted gene loci such as the insulin-like growth factor 2 gene 2 (<it>IGF2</it>), we evaluated the contribution of CTCF, a zinc finger protein required for parent-of-origin-specific expression of the <it>IGF2 </it>gene, as well as a role for allele-specific association with DNA methylation, histone modification and RNA polymerase II.</p> <p>Results</p> <p>Using array-based chromatin immunoprecipitation, we identified 293 genomic loci that are associated with both CTCF and histone H3 trimethylated at lysine 9 (H3K9me3). A comparison of their genomic positions with those of previously published monoallelically expressed genes revealed no significant overlap between allele-specifically expressed genes and colocalized CTCF/H3K9me3. To analyze the contributions of CTCF and H3K9me3 to gene regulation in more detail, we focused on the monoallelically expressed <it>IGF2BP1 </it>gene. <it>In vitro </it>binding assays using the CTCF target motif at the <it>IGF2BP1 </it>gene, as well as allele-specific analysis of cytosine methylation and CTCF binding, revealed that CTCF does not regulate mono- or biallelic <it>IGF2BP1 </it>expression. Surprisingly, we found that RNA polymerase II is detected on both the maternal and paternal alleles in B lymphoblasts that express <it>IGF2BP1 </it>primarily from one allele. Thus, allele-specific control of RNA polymerase II elongation regulates the allelic bias of <it>IGF2BP1 </it>gene expression.</p> <p>Conclusions</p> <p>Colocalization of CTCF and H3K9me3 does not represent a reliable chromatin signature indicative of monoallelic expression. Moreover, association of individual alleles with both active (H3K4me3) and silent (H3K27me3) chromatin modifications (allelic bivalent chromatin) or with RNA polymerase II also fails to identify monoallelically expressed gene loci. The selection of individual alleles for expression occurs in part during transcription elongation.</p> |
| first_indexed | 2024-04-12T15:50:00Z |
| format | Article |
| id | doaj.art-b73d9d4b4fae4b3588c19ff5280edc8c |
| institution | Directory Open Access Journal |
| issn | 1756-8935 |
| language | English |
| last_indexed | 2024-04-12T15:50:00Z |
| publishDate | 2011-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Epigenetics & Chromatin |
| spelling | doaj.art-b73d9d4b4fae4b3588c19ff5280edc8c2022-12-22T03:26:33ZengBMCEpigenetics & Chromatin1756-89352011-08-01411410.1186/1756-8935-4-14Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>geneThomas Brandon JRubio Eric DKrumm NiklasBroin Pilib ÓBomsztyk KarolWelcsh PiriGreally John MGolden Aaron AKrumm Anton<p>Abstract</p> <p>Background</p> <p>Random monoallelic expression contributes to phenotypic variation of cells and organisms. However, the epigenetic mechanisms by which individual alleles are randomly selected for expression are not known. Taking cues from chromatin signatures at imprinted gene loci such as the insulin-like growth factor 2 gene 2 (<it>IGF2</it>), we evaluated the contribution of CTCF, a zinc finger protein required for parent-of-origin-specific expression of the <it>IGF2 </it>gene, as well as a role for allele-specific association with DNA methylation, histone modification and RNA polymerase II.</p> <p>Results</p> <p>Using array-based chromatin immunoprecipitation, we identified 293 genomic loci that are associated with both CTCF and histone H3 trimethylated at lysine 9 (H3K9me3). A comparison of their genomic positions with those of previously published monoallelically expressed genes revealed no significant overlap between allele-specifically expressed genes and colocalized CTCF/H3K9me3. To analyze the contributions of CTCF and H3K9me3 to gene regulation in more detail, we focused on the monoallelically expressed <it>IGF2BP1 </it>gene. <it>In vitro </it>binding assays using the CTCF target motif at the <it>IGF2BP1 </it>gene, as well as allele-specific analysis of cytosine methylation and CTCF binding, revealed that CTCF does not regulate mono- or biallelic <it>IGF2BP1 </it>expression. Surprisingly, we found that RNA polymerase II is detected on both the maternal and paternal alleles in B lymphoblasts that express <it>IGF2BP1 </it>primarily from one allele. Thus, allele-specific control of RNA polymerase II elongation regulates the allelic bias of <it>IGF2BP1 </it>gene expression.</p> <p>Conclusions</p> <p>Colocalization of CTCF and H3K9me3 does not represent a reliable chromatin signature indicative of monoallelic expression. Moreover, association of individual alleles with both active (H3K4me3) and silent (H3K27me3) chromatin modifications (allelic bivalent chromatin) or with RNA polymerase II also fails to identify monoallelically expressed gene loci. The selection of individual alleles for expression occurs in part during transcription elongation.</p>http://www.epigeneticsandchromatin.com/content/4/1/14 |
| spellingShingle | Thomas Brandon J Rubio Eric D Krumm Niklas Broin Pilib Ó Bomsztyk Karol Welcsh Piri Greally John M Golden Aaron A Krumm Anton Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>gene Epigenetics & Chromatin |
| title | Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>gene |
| title_full | Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>gene |
| title_fullStr | Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>gene |
| title_full_unstemmed | Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>gene |
| title_short | Allele-specific transcriptional elongation regulates monoallelic expression of the <it>IGF2BP1 </it>gene |
| title_sort | allele specific transcriptional elongation regulates monoallelic expression of the it igf2bp1 it gene |
| url | http://www.epigeneticsandchromatin.com/content/4/1/14 |
| work_keys_str_mv | AT thomasbrandonj allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT rubioericd allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT krummniklas allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT broinpilibo allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT bomsztykkarol allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT welcshpiri allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT greallyjohnm allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT goldenaarona allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene AT krummanton allelespecifictranscriptionalelongationregulatesmonoallelicexpressionoftheitigf2bp1itgene |