Cargando…
HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205
BACKGROUND: The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associate...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135769/ https://www.ncbi.nlm.nih.gov/pubmed/27980680 http://dx.doi.org/10.1186/s13072-016-0106-0 |
_version_ | 1782471604446429184 |
---|---|
author | Labade, Ajay S. Karmodiya, Krishanpal Sengupta, Kundan |
author_facet | Labade, Ajay S. Karmodiya, Krishanpal Sengupta, Kundan |
author_sort | Labade, Ajay S. |
collection | PubMed |
description | BACKGROUND: The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown. RESULTS: Here, we examined the association of Nup93 with the HOXA gene cluster and its consequences on HOXA gene expression in diploid colorectal cancer cells (DLD1). Nup93 showed a specific enrichment ~1 Kb upstream of the transcription start site of each of the HOXA1, HOXA3 and HOXA5 promoters, respectively. Furthermore, the association of Nup93 with HOXA was assisted by its interacting partners Nup188 and Nup205. The depletion of the Nup93 sub-complex significantly upregulated HOXA gene expression levels. However, expression levels of a control gene locus (GLCCI1) on human chromosome 7 were unaffected. Three-dimensional fluorescence in situ hybridization (3D-FISH) analyses revealed that the depletion of the Nup93 sub-complex (but not Nup98) disengages the HOXA gene locus from the nuclear periphery, suggesting a potential role for Nup93 in tethering and repressing the HOXA gene cluster. Consistently, Nup93 knockdown increased active histone marks (H3K9ac), decreased repressive histone marks (H3K27me3) on the HOXA1 promoter and increased transcription elongation marks (H3K36me3) within the HOXA1 gene. Moreover, the combined depletion of Nup93 and CTCF (a known organizer of HOXA gene cluster) but not Nup93 alone, significantly increased GLCCI1 gene expression levels. Taken together, this suggests a novel role for Nup93 and its interactors in repressing the HOXA gene cluster. CONCLUSIONS: This study reveals that the nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 mediates the repression of HOXA gene expression. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13072-016-0106-0) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5135769 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-51357692016-12-15 HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 Labade, Ajay S. Karmodiya, Krishanpal Sengupta, Kundan Epigenetics Chromatin Research BACKGROUND: The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown. RESULTS: Here, we examined the association of Nup93 with the HOXA gene cluster and its consequences on HOXA gene expression in diploid colorectal cancer cells (DLD1). Nup93 showed a specific enrichment ~1 Kb upstream of the transcription start site of each of the HOXA1, HOXA3 and HOXA5 promoters, respectively. Furthermore, the association of Nup93 with HOXA was assisted by its interacting partners Nup188 and Nup205. The depletion of the Nup93 sub-complex significantly upregulated HOXA gene expression levels. However, expression levels of a control gene locus (GLCCI1) on human chromosome 7 were unaffected. Three-dimensional fluorescence in situ hybridization (3D-FISH) analyses revealed that the depletion of the Nup93 sub-complex (but not Nup98) disengages the HOXA gene locus from the nuclear periphery, suggesting a potential role for Nup93 in tethering and repressing the HOXA gene cluster. Consistently, Nup93 knockdown increased active histone marks (H3K9ac), decreased repressive histone marks (H3K27me3) on the HOXA1 promoter and increased transcription elongation marks (H3K36me3) within the HOXA1 gene. Moreover, the combined depletion of Nup93 and CTCF (a known organizer of HOXA gene cluster) but not Nup93 alone, significantly increased GLCCI1 gene expression levels. Taken together, this suggests a novel role for Nup93 and its interactors in repressing the HOXA gene cluster. CONCLUSIONS: This study reveals that the nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 mediates the repression of HOXA gene expression. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13072-016-0106-0) contains supplementary material, which is available to authorized users. BioMed Central 2016-12-03 /pmc/articles/PMC5135769/ /pubmed/27980680 http://dx.doi.org/10.1186/s13072-016-0106-0 Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Labade, Ajay S. Karmodiya, Krishanpal Sengupta, Kundan HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 |
title | HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 |
title_full | HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 |
title_fullStr | HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 |
title_full_unstemmed | HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 |
title_short | HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 |
title_sort | hoxa repression is mediated by nucleoporin nup93 assisted by its interactors nup188 and nup205 |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135769/ https://www.ncbi.nlm.nih.gov/pubmed/27980680 http://dx.doi.org/10.1186/s13072-016-0106-0 |
work_keys_str_mv | AT labadeajays hoxarepressionismediatedbynucleoporinnup93assistedbyitsinteractorsnup188andnup205 AT karmodiyakrishanpal hoxarepressionismediatedbynucleoporinnup93assistedbyitsinteractorsnup188andnup205 AT senguptakundan hoxarepressionismediatedbynucleoporinnup93assistedbyitsinteractorsnup188andnup205 |