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In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F)
For several histone lysine methyltransferases (HKMTs), RNA binding has been already shown to be a functionally relevant feature, but detailed information on the RNA interactome of these proteins is not always known. Of the six human KMT2 proteins responsible for the methylation of the H3K4 residue,...
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Published in: | International journal of molecular sciences 2023-11, Vol.24 (22), p.16032 |
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description | For several histone lysine methyltransferases (HKMTs), RNA binding has been already shown to be a functionally relevant feature, but detailed information on the RNA interactome of these proteins is not always known. Of the six human KMT2 proteins responsible for the methylation of the H3K4 residue, two—SETD1A and SETD1B—contain RNA recognition domains (RRMs). Here we investigated the RNA binding capacity of SETD1A and identified a broad range of interacting RNAs within HEK293T cells. Our analysis revealed that similar to yeast Set1, SETD1A is also capable of binding several coding and non-coding RNAs, including RNA species related to RNA processing. We also show direct RNA binding activity of the individual RRM domain in vitro, which is in contrast with the RRM domain found in yeast Set1. Structural modeling revealed important details on the possible RNA recognition mode of SETD1A and highlighted some fundamental differences between SETD1A and Set1, explaining the differences in the RNA binding capacity of their respective RRMs. |
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Of the six human KMT2 proteins responsible for the methylation of the H3K4 residue, two—SETD1A and SETD1B—contain RNA recognition domains (RRMs). Here we investigated the RNA binding capacity of SETD1A and identified a broad range of interacting RNAs within HEK293T cells. Our analysis revealed that similar to yeast Set1, SETD1A is also capable of binding several coding and non-coding RNAs, including RNA species related to RNA processing. We also show direct RNA binding activity of the individual RRM domain in vitro, which is in contrast with the RRM domain found in yeast Set1. Structural modeling revealed important details on the possible RNA recognition mode of SETD1A and highlighted some fundamental differences between SETD1A and Set1, explaining the differences in the RNA binding capacity of their respective RRMs.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms242216032</identifier><language>eng</language><publisher>Basel: MDPI AG</publisher><subject>Analysis ; Datasets ; DNA damage ; DNA methylation ; Enzymes ; Experiments ; Genes ; histone lysine methyltransferase ; Insects ; KMT2F ; Lysine ; Methylation ; Methyltransferases ; Mutation ; non-coding RNA ; Pharmaceutical industry ; Proteins ; RNA ; RNA binding ; RRM domain ; Schizophrenia ; Scientific equipment and supplies industry ; SETD1A ; Stem cells</subject><ispartof>International journal of molecular sciences, 2023-11, Vol.24 (22), p.16032</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c426t-f4611f1ebb74f159990ca9c6afba3e9ff0dedab9815564e777a4cacf78c84a623</cites><orcidid>0000-0002-3006-2910 ; 0000-0003-1273-9841 ; 0000-0002-2135-2932</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2893075697/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2893075697?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,25753,27924,27925,37012,37013,44590,75126</link.rule.ids></links><search><creatorcontrib>Amin, Harem Muhamad</creatorcontrib><creatorcontrib>Szabo, Beata</creatorcontrib><creatorcontrib>Abukhairan, Rawan</creatorcontrib><creatorcontrib>Zeke, Andras</creatorcontrib><creatorcontrib>Kardos, József</creatorcontrib><creatorcontrib>Schad, Eva</creatorcontrib><creatorcontrib>Tantos, Agnes</creatorcontrib><title>In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F)</title><title>International journal of molecular sciences</title><description>For several histone lysine methyltransferases (HKMTs), RNA binding has been already shown to be a functionally relevant feature, but detailed information on the RNA interactome of these proteins is not always known. Of the six human KMT2 proteins responsible for the methylation of the H3K4 residue, two—SETD1A and SETD1B—contain RNA recognition domains (RRMs). Here we investigated the RNA binding capacity of SETD1A and identified a broad range of interacting RNAs within HEK293T cells. Our analysis revealed that similar to yeast Set1, SETD1A is also capable of binding several coding and non-coding RNAs, including RNA species related to RNA processing. We also show direct RNA binding activity of the individual RRM domain in vitro, which is in contrast with the RRM domain found in yeast Set1. Structural modeling revealed important details on the possible RNA recognition mode of SETD1A and highlighted some fundamental differences between SETD1A and Set1, explaining the differences in the RNA binding capacity of their respective RRMs.</description><subject>Analysis</subject><subject>Datasets</subject><subject>DNA damage</subject><subject>DNA methylation</subject><subject>Enzymes</subject><subject>Experiments</subject><subject>Genes</subject><subject>histone lysine methyltransferase</subject><subject>Insects</subject><subject>KMT2F</subject><subject>Lysine</subject><subject>Methylation</subject><subject>Methyltransferases</subject><subject>Mutation</subject><subject>non-coding RNA</subject><subject>Pharmaceutical industry</subject><subject>Proteins</subject><subject>RNA</subject><subject>RNA binding</subject><subject>RRM domain</subject><subject>Schizophrenia</subject><subject>Scientific equipment and supplies industry</subject><subject>SETD1A</subject><subject>Stem cells</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptkk1vEzEQhleISpTCkbslLuWwrb8_jiG0NGoLEg1crVmvnTpK1sF2kMqvZ5OgQhHywa9mnnlHM5qmeUPwGWMGn8flulBOKZGY0WfNMRl1i7FUz__SL5qXpSwxpowKc9zczQb0Lf5ICIYe7XXNCU3vIYOrPsefUGMaUAqo3nv05dMEvY9DH4cFmsIGXKwPu9zdxfwDmaDT69s5vXz3qjkKsCr-9e__pPl6eTGfXrU3nz_OppOb1nEqaxu4JCQQ33WKByKMMdiBcRJCB8ybEHDve-iMJkJI7pVSwB24oLTTHCRlJ83s4NsnWNpNjmvIDzZBtPtAygsLuUa38ha0Uthz3HFOuQlGa6a1FFpQLnomyOh1evDa5PR960u161icX61g8GlbLNWGac4JFyP69h90mbZ5GCfdU1gJadQfagFj_ziEVMeV7kztRCnOKCF4R539hxpf79fRpcGHOMafFLSHApdTKdmHx7kJtrsrsE-ugP0C8N-e6Q</recordid><startdate>20231101</startdate><enddate>20231101</enddate><creator>Amin, Harem Muhamad</creator><creator>Szabo, Beata</creator><creator>Abukhairan, Rawan</creator><creator>Zeke, Andras</creator><creator>Kardos, József</creator><creator>Schad, Eva</creator><creator>Tantos, Agnes</creator><general>MDPI AG</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-3006-2910</orcidid><orcidid>https://orcid.org/0000-0003-1273-9841</orcidid><orcidid>https://orcid.org/0000-0002-2135-2932</orcidid></search><sort><creationdate>20231101</creationdate><title>In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F)</title><author>Amin, Harem Muhamad ; 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subjects | Analysis Datasets DNA damage DNA methylation Enzymes Experiments Genes histone lysine methyltransferase Insects KMT2F Lysine Methylation Methyltransferases Mutation non-coding RNA Pharmaceutical industry Proteins RNA RNA binding RRM domain Schizophrenia Scientific equipment and supplies industry SETD1A Stem cells |
title | In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F) |
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