Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1
Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine...
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| Veröffentlicht in: | Nature chemical biology 2024-07, Vol.21 (2), p.227-237 |
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| creator | Lee, Kwangwoon Barone, Marco Waterbury, Amanda L. Jiang, Hanjie Nam, Eunju DuBois-Coyne, Sarah E. Whedon, Samuel D. Wang, Zhipeng A. Caroli, Jonatan Neal, Katherine Ibeabuchi, Brian Dhoondia, Zuzer Kuroda, Mitzi I. Liau, Brian B. Beck, Samuel Mattevi, Andrea Cole, Philip A. |
| description | Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the
cis
-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
Lee, Barone et al. engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation of histone H3, providing a useful tool to illuminate the functional consequences of disconnecting histone modification crosstalk. |
| doi_str_mv | 10.1038/s41589-024-01671-9 |
| format | Article |
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cis
-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
Lee, Barone et al. engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation of histone H3, providing a useful tool to illuminate the functional consequences of disconnecting histone modification crosstalk.</description><identifier>ISSN: 1552-4450</identifier><identifier>ISSN: 1552-4469</identifier><identifier>EISSN: 1552-4469</identifier><identifier>DOI: 10.1038/s41589-024-01671-9</identifier><identifier>PMID: 38965385</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>631/45/612/100/2285 ; 631/92/607 ; Acetylation ; Biochemical Engineering ; Biochemistry ; Bioorganic Chemistry ; Cell activation ; Cell adhesion ; Cell Biology ; Chemistry ; Chemistry and Materials Science ; Chemistry/Food Science ; Chromatin ; CRISPR ; Demethylation ; Enzymes ; Epigenesis, Genetic ; Epigenetics ; Gene silencing ; Genes ; Histone Demethylases - genetics ; Histone Demethylases - metabolism ; Histone H3 ; Histones ; Histones - genetics ; Histones - metabolism ; Humans ; K562 Cells ; Lysine ; Lysine - metabolism ; Mutants ; Protein Engineering ; Regulatory sequences ; Transcription activation</subject><ispartof>Nature chemical biology, 2024-07, Vol.21 (2), p.227-237</ispartof><rights>The Author(s), under exclusive licence to Springer Nature America, Inc. 2024 Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2024. The Author(s), under exclusive licence to Springer Nature America, Inc.</rights><rights>Copyright Nature Publishing Group Feb 2025</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c326t-330e3e12ff6bc1ea79bdddc669b4706ac53584633b1cd846d86cf537b217c6283</cites><orcidid>0000-0002-9523-7128 ; 0000-0003-0801-9331 ; 0000-0003-0840-3608 ; 0000-0001-7184-2940 ; 0000-0002-0390-8140 ; 0000-0002-3745-5645 ; 0000-0001-6090-4552 ; 0000-0002-2021-5186 ; 0000-0003-4171-1944 ; 0000-0002-0184-8367 ; 0000-0002-5693-7359 ; 0000-0002-4473-2866 ; 0000-0001-6873-7824 ; 0000-0002-2985-462X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41589-024-01671-9$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41589-024-01671-9$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38965385$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Kwangwoon</creatorcontrib><creatorcontrib>Barone, Marco</creatorcontrib><creatorcontrib>Waterbury, Amanda L.</creatorcontrib><creatorcontrib>Jiang, Hanjie</creatorcontrib><creatorcontrib>Nam, Eunju</creatorcontrib><creatorcontrib>DuBois-Coyne, Sarah E.</creatorcontrib><creatorcontrib>Whedon, Samuel D.</creatorcontrib><creatorcontrib>Wang, Zhipeng A.</creatorcontrib><creatorcontrib>Caroli, Jonatan</creatorcontrib><creatorcontrib>Neal, Katherine</creatorcontrib><creatorcontrib>Ibeabuchi, Brian</creatorcontrib><creatorcontrib>Dhoondia, Zuzer</creatorcontrib><creatorcontrib>Kuroda, Mitzi I.</creatorcontrib><creatorcontrib>Liau, Brian B.</creatorcontrib><creatorcontrib>Beck, Samuel</creatorcontrib><creatorcontrib>Mattevi, Andrea</creatorcontrib><creatorcontrib>Cole, Philip A.</creatorcontrib><title>Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1</title><title>Nature chemical biology</title><addtitle>Nat Chem Biol</addtitle><addtitle>Nat Chem Biol</addtitle><description>Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the
cis
-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
Lee, Barone et al. engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation of histone H3, providing a useful tool to illuminate the functional consequences of disconnecting histone modification crosstalk.</description><subject>631/45/612/100/2285</subject><subject>631/92/607</subject><subject>Acetylation</subject><subject>Biochemical Engineering</subject><subject>Biochemistry</subject><subject>Bioorganic Chemistry</subject><subject>Cell activation</subject><subject>Cell adhesion</subject><subject>Cell Biology</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Chemistry/Food Science</subject><subject>Chromatin</subject><subject>CRISPR</subject><subject>Demethylation</subject><subject>Enzymes</subject><subject>Epigenesis, Genetic</subject><subject>Epigenetics</subject><subject>Gene silencing</subject><subject>Genes</subject><subject>Histone Demethylases - genetics</subject><subject>Histone Demethylases - metabolism</subject><subject>Histone H3</subject><subject>Histones</subject><subject>Histones - genetics</subject><subject>Histones - metabolism</subject><subject>Humans</subject><subject>K562 Cells</subject><subject>Lysine</subject><subject>Lysine - metabolism</subject><subject>Mutants</subject><subject>Protein Engineering</subject><subject>Regulatory sequences</subject><subject>Transcription activation</subject><issn>1552-4450</issn><issn>1552-4469</issn><issn>1552-4469</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kL1OwzAURi0EoqXwAgwoEgtLwM6NHWdE_EuVQILOVuLctCmJE-JkyNvjNqVIDMiDv-Hcz76HkHNGrxkFeWNDxmXs0yD0KRMR8-MDMmWcB34YivhwnzmdkBNr15SCEEwekwnIWHCQfEreFkbXfVMWZumtCtvVBr2qzoq80ElX1MbTbW1tl5SfXjp4aJaFQWw3dDlYl70MK-xWQ5lY9Obv9-yUHOVJafFsd8_I4vHh4-7Zn78-vdzdzn0Ngeh8AIqALMhzkWqGSRSnWZZpIeI0jKhINAcuQwGQMp25kEmhcw5RGrBIi0DCjFyNvU1bf_VoO1UVVmNZJgbr3iqgkaBMukUdevkHXdd9a9zvFDDhTggQOSoYqe3GLeaqaYsqaQfFqNr4VqNv5XyrrW8Vu6GLXXWfVpjtR34EOwBGwDYba9j-vv1P7TdHIosO</recordid><startdate>20240704</startdate><enddate>20240704</enddate><creator>Lee, Kwangwoon</creator><creator>Barone, Marco</creator><creator>Waterbury, Amanda L.</creator><creator>Jiang, Hanjie</creator><creator>Nam, Eunju</creator><creator>DuBois-Coyne, Sarah E.</creator><creator>Whedon, Samuel D.</creator><creator>Wang, Zhipeng A.</creator><creator>Caroli, Jonatan</creator><creator>Neal, Katherine</creator><creator>Ibeabuchi, Brian</creator><creator>Dhoondia, Zuzer</creator><creator>Kuroda, Mitzi I.</creator><creator>Liau, Brian B.</creator><creator>Beck, Samuel</creator><creator>Mattevi, Andrea</creator><creator>Cole, Philip A.</creator><general>Nature Publishing Group US</general><general>Nature Publishing Group</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-9523-7128</orcidid><orcidid>https://orcid.org/0000-0003-0801-9331</orcidid><orcidid>https://orcid.org/0000-0003-0840-3608</orcidid><orcidid>https://orcid.org/0000-0001-7184-2940</orcidid><orcidid>https://orcid.org/0000-0002-0390-8140</orcidid><orcidid>https://orcid.org/0000-0002-3745-5645</orcidid><orcidid>https://orcid.org/0000-0001-6090-4552</orcidid><orcidid>https://orcid.org/0000-0002-2021-5186</orcidid><orcidid>https://orcid.org/0000-0003-4171-1944</orcidid><orcidid>https://orcid.org/0000-0002-0184-8367</orcidid><orcidid>https://orcid.org/0000-0002-5693-7359</orcidid><orcidid>https://orcid.org/0000-0002-4473-2866</orcidid><orcidid>https://orcid.org/0000-0001-6873-7824</orcidid><orcidid>https://orcid.org/0000-0002-2985-462X</orcidid></search><sort><creationdate>20240704</creationdate><title>Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1</title><author>Lee, Kwangwoon ; 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Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the
cis
-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
Lee, Barone et al. engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation of histone H3, providing a useful tool to illuminate the functional consequences of disconnecting histone modification crosstalk.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>38965385</pmid><doi>10.1038/s41589-024-01671-9</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-9523-7128</orcidid><orcidid>https://orcid.org/0000-0003-0801-9331</orcidid><orcidid>https://orcid.org/0000-0003-0840-3608</orcidid><orcidid>https://orcid.org/0000-0001-7184-2940</orcidid><orcidid>https://orcid.org/0000-0002-0390-8140</orcidid><orcidid>https://orcid.org/0000-0002-3745-5645</orcidid><orcidid>https://orcid.org/0000-0001-6090-4552</orcidid><orcidid>https://orcid.org/0000-0002-2021-5186</orcidid><orcidid>https://orcid.org/0000-0003-4171-1944</orcidid><orcidid>https://orcid.org/0000-0002-0184-8367</orcidid><orcidid>https://orcid.org/0000-0002-5693-7359</orcidid><orcidid>https://orcid.org/0000-0002-4473-2866</orcidid><orcidid>https://orcid.org/0000-0001-6873-7824</orcidid><orcidid>https://orcid.org/0000-0002-2985-462X</orcidid></addata></record> |
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| subjects | 631/45/612/100/2285 631/92/607 Acetylation Biochemical Engineering Biochemistry Bioorganic Chemistry Cell activation Cell adhesion Cell Biology Chemistry Chemistry and Materials Science Chemistry/Food Science Chromatin CRISPR Demethylation Enzymes Epigenesis, Genetic Epigenetics Gene silencing Genes Histone Demethylases - genetics Histone Demethylases - metabolism Histone H3 Histones Histones - genetics Histones - metabolism Humans K562 Cells Lysine Lysine - metabolism Mutants Protein Engineering Regulatory sequences Transcription activation |
| title | Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1 |
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