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Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide
Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 wi...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Impact Journals LLC
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047668/ https://www.ncbi.nlm.nih.gov/pubmed/30034620 http://dx.doi.org/10.18632/oncotarget.25451 |
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author | Alagarswamy, Kokiladevi Shinohara, Ken-Ichi Takayanagi, Shihori Fukuyo, Masaki Okabe, Atsushi Rahmutulla, Bahityar Yoda, Natsumi Qin, Rui Shiga, Naoki Sugiura, Masahiro Sato, Hiroaki Kita, Kazuko Suzuki, Takayoshi Nemoto, Tetsuhiro Kaneda, Atsushi |
author_facet | Alagarswamy, Kokiladevi Shinohara, Ken-Ichi Takayanagi, Shihori Fukuyo, Masaki Okabe, Atsushi Rahmutulla, Bahityar Yoda, Natsumi Qin, Rui Shiga, Naoki Sugiura, Masahiro Sato, Hiroaki Kita, Kazuko Suzuki, Takayoshi Nemoto, Tetsuhiro Kaneda, Atsushi |
author_sort | Alagarswamy, Kokiladevi |
collection | PubMed |
description | Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 with a potent small molecule called pyrrole (Py) imidazole (Im) polyamide, to analyze whether targets of the inhibitor could be regulated in a sequence-specific manner. We synthesized two conjugates using β-Ala (β) as a linker, i.e., NCD38-β-β-Py-Py-Py-Py (NCD38-β(2)P(4)) recognizing WWWWWW sequence, and NCD38-β-β-Py-Im-Py-Py (NCD38-β(2)PIPP) recognizing WWCGWW sequence. When RKO cells were treated with NCD38, H3K4me2 levels increased in 103 regions with significant activation of nearby genes (P = 0.03), whereas H3K4me3 levels were not obviously increased. H3K27ac levels were also increased in 458 regions with significant activation of nearby genes (P = 3 × 10(−10)), and these activated regions frequently included GC-rich sequences, but less frequently included AT-rich sequences (P < 1 × 10(−15)) or WWCGWW sequences (P = 2 × 10(−13)). When treated with NCD38-β(2)P(4), 234 regions showed increased H3K27ac levels with significant activation of nearby genes (P = 2 × 10(−11)), including significantly fewer GC-rich sequences (P < 1 × 10(−15)) and significantly more AT-rich sequences (P < 1 × 10(−15)) compared with NCD38 treatment. When treated with NCD38-β(2)PIPP, 82 regions showed increased H3K27ac levels, including significantly fewer GC-rich sequences (P = 1 × 10(−11)) and fewer AT-rich sequences (P = 0.005), but significantly more WWCGWW sequences (P = 0.0001) compared with NCD38 treatment. These indicated that target regions of epigenomic inhibitors could be modified in a sequence-specific manner and that conjugation of Py-Im polyamides may be useful for this purpose. |
format | Online Article Text |
id | pubmed-6047668 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Impact Journals LLC |
record_format | MEDLINE/PubMed |
spelling | pubmed-60476682018-07-20 Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide Alagarswamy, Kokiladevi Shinohara, Ken-Ichi Takayanagi, Shihori Fukuyo, Masaki Okabe, Atsushi Rahmutulla, Bahityar Yoda, Natsumi Qin, Rui Shiga, Naoki Sugiura, Masahiro Sato, Hiroaki Kita, Kazuko Suzuki, Takayoshi Nemoto, Tetsuhiro Kaneda, Atsushi Oncotarget Research Paper Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 with a potent small molecule called pyrrole (Py) imidazole (Im) polyamide, to analyze whether targets of the inhibitor could be regulated in a sequence-specific manner. We synthesized two conjugates using β-Ala (β) as a linker, i.e., NCD38-β-β-Py-Py-Py-Py (NCD38-β(2)P(4)) recognizing WWWWWW sequence, and NCD38-β-β-Py-Im-Py-Py (NCD38-β(2)PIPP) recognizing WWCGWW sequence. When RKO cells were treated with NCD38, H3K4me2 levels increased in 103 regions with significant activation of nearby genes (P = 0.03), whereas H3K4me3 levels were not obviously increased. H3K27ac levels were also increased in 458 regions with significant activation of nearby genes (P = 3 × 10(−10)), and these activated regions frequently included GC-rich sequences, but less frequently included AT-rich sequences (P < 1 × 10(−15)) or WWCGWW sequences (P = 2 × 10(−13)). When treated with NCD38-β(2)P(4), 234 regions showed increased H3K27ac levels with significant activation of nearby genes (P = 2 × 10(−11)), including significantly fewer GC-rich sequences (P < 1 × 10(−15)) and significantly more AT-rich sequences (P < 1 × 10(−15)) compared with NCD38 treatment. When treated with NCD38-β(2)PIPP, 82 regions showed increased H3K27ac levels, including significantly fewer GC-rich sequences (P = 1 × 10(−11)) and fewer AT-rich sequences (P = 0.005), but significantly more WWCGWW sequences (P = 0.0001) compared with NCD38 treatment. These indicated that target regions of epigenomic inhibitors could be modified in a sequence-specific manner and that conjugation of Py-Im polyamides may be useful for this purpose. Impact Journals LLC 2018-06-29 /pmc/articles/PMC6047668/ /pubmed/30034620 http://dx.doi.org/10.18632/oncotarget.25451 Text en Copyright: © 2018 Alagarswamy et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (http://creativecommons.org/licenses/by/3.0/) (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Paper Alagarswamy, Kokiladevi Shinohara, Ken-Ichi Takayanagi, Shihori Fukuyo, Masaki Okabe, Atsushi Rahmutulla, Bahityar Yoda, Natsumi Qin, Rui Shiga, Naoki Sugiura, Masahiro Sato, Hiroaki Kita, Kazuko Suzuki, Takayoshi Nemoto, Tetsuhiro Kaneda, Atsushi Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide |
title | Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide |
title_full | Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide |
title_fullStr | Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide |
title_full_unstemmed | Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide |
title_short | Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide |
title_sort | region-specific alteration of histone modification by lsd1 inhibitor conjugated with pyrrole-imidazole polyamide |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047668/ https://www.ncbi.nlm.nih.gov/pubmed/30034620 http://dx.doi.org/10.18632/oncotarget.25451 |
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