Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks
Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome‐wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with repl...
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| Veröffentlicht in: | EMBO reports 2018-09, Vol.19 (9), p.n/a |
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| creator | Hiraga, Shin‐ichiro Monerawela, Chandre Katou, Yuki Shaw, Sophie Clark, Kate RM Shirahige, Katsuhiko Donaldson, Anne D |
| description | Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome‐wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with replication progressing normally or blocked by hydroxyurea. Rif1 associates strongly with telomeres through interaction with Rap1. By comparing genomic binding of wild‐type Rif1 and truncated Rif1 lacking the Rap1‐interaction domain, we identify hundreds of Rap1‐dependent and Rap1‐independent chromosome interaction sites. Rif1 binds to centromeres, highly transcribed genes and replication origins in a Rap1‐independent manner, associating with both early and late‐initiating origins. Interestingly, Rif1 also binds around activated origins when replication progression is blocked by hydroxyurea, suggesting association with blocked forks. Using nascent DNA labelling and DNA combing techniques, we find that in cells treated with hydroxyurea, yeast Rif1 stabilises recently synthesised DNA. Our results indicate that, in addition to controlling DNA replication initiation, budding yeast Rif1 plays an ongoing role after initiation and controls events at blocked replication forks.
Synopsis
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation.
ChIP‐Seq analysis revealed Rap1‐dependent and –independent budding yeast Rif1 chromosomal binding sites.
Rif1 binds early and late origins without apparent preference.
Rif1 binds stalled replication forks or post‐replicative chromatin under replication stress, and protects nascent DNA from degradation.
Rif1 associates with centromeres in S phase.
Graphical Abstract
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation. |
| doi_str_mv | 10.15252/embr.201846222 |
| format | Article |
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Synopsis
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation.
ChIP‐Seq analysis revealed Rap1‐dependent and –independent budding yeast Rif1 chromosomal binding sites.
Rif1 binds early and late origins without apparent preference.
Rif1 binds stalled replication forks or post‐replicative chromatin under replication stress, and protects nascent DNA from degradation.
Rif1 associates with centromeres in S phase.
Graphical Abstract
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation.</description><identifier>ISSN: 1469-221X</identifier><identifier>EISSN: 1469-3178</identifier><identifier>DOI: 10.15252/embr.201846222</identifier><identifier>PMID: 30104203</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>Binding sites ; Binding Sites - physiology ; Biodegradation ; Cell Cycle ; Cell Cycle Proteins - metabolism ; centromere ; Centromere - metabolism ; Centromeres ; ChIP‐Seq ; Chromatin ; Chromosomes, Plant - chemistry ; Degradation ; Deoxyribonucleic acid ; DNA ; DNA - metabolism ; DNA biosynthesis ; DNA Replication - physiology ; DNA replication origin ; DNA Replication Timing - physiology ; EMBO13 ; G1 phase ; Genomes ; Hydroxyurea ; Immunoprecipitation ; Labeling ; Minichromosome Maintenance Proteins - metabolism ; Mutation ; nascent DNA ; Origins ; Protein Phosphatase 1 - metabolism ; Protein Serine-Threonine Kinases - metabolism ; Proteins ; Rap1 protein ; Replication ; Replication forks ; Replication initiation ; Replication Origin - physiology ; Replication origins ; Repressor Proteins - chemistry ; Repressor Proteins - genetics ; Repressor Proteins - metabolism ; Rif1 ; S phase ; S Phase - physiology ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae - metabolism ; Saccharomyces cerevisiae Proteins - chemistry ; Saccharomyces cerevisiae Proteins - genetics ; Saccharomyces cerevisiae Proteins - metabolism ; Shelterin Complex ; Telomere - metabolism ; Telomere-Binding Proteins - chemistry ; Telomere-Binding Proteins - genetics ; Telomere-Binding Proteins - metabolism ; Telomeres ; Transcription Factors - metabolism ; Yeast ; Yeasts</subject><ispartof>EMBO reports, 2018-09, Vol.19 (9), p.n/a</ispartof><rights>The Author(s) 2018</rights><rights>2018 The Authors. Published under the terms of the CC BY 4.0 license</rights><rights>2018 The Authors. Published under the terms of the CC BY 4.0 license.</rights><rights>2018 EMBO</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5132-203b394ff101638feeab80c7ffb983e16f7958a6492b4b53102708c5b7f5353</citedby><cites>FETCH-LOGICAL-c5132-203b394ff101638feeab80c7ffb983e16f7958a6492b4b53102708c5b7f5353</cites><orcidid>0000-0002-8722-3869 ; 0000-0001-7842-8136 ; 0000-0003-2367-2670</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123642/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123642/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1416,1432,27923,27924,41119,42188,45573,45574,46408,46832,51575,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30104203$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hiraga, Shin‐ichiro</creatorcontrib><creatorcontrib>Monerawela, Chandre</creatorcontrib><creatorcontrib>Katou, Yuki</creatorcontrib><creatorcontrib>Shaw, Sophie</creatorcontrib><creatorcontrib>Clark, Kate RM</creatorcontrib><creatorcontrib>Shirahige, Katsuhiko</creatorcontrib><creatorcontrib>Donaldson, Anne D</creatorcontrib><title>Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks</title><title>EMBO reports</title><addtitle>EMBO Rep</addtitle><addtitle>EMBO Rep</addtitle><description>Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome‐wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with replication progressing normally or blocked by hydroxyurea. Rif1 associates strongly with telomeres through interaction with Rap1. By comparing genomic binding of wild‐type Rif1 and truncated Rif1 lacking the Rap1‐interaction domain, we identify hundreds of Rap1‐dependent and Rap1‐independent chromosome interaction sites. Rif1 binds to centromeres, highly transcribed genes and replication origins in a Rap1‐independent manner, associating with both early and late‐initiating origins. Interestingly, Rif1 also binds around activated origins when replication progression is blocked by hydroxyurea, suggesting association with blocked forks. Using nascent DNA labelling and DNA combing techniques, we find that in cells treated with hydroxyurea, yeast Rif1 stabilises recently synthesised DNA. Our results indicate that, in addition to controlling DNA replication initiation, budding yeast Rif1 plays an ongoing role after initiation and controls events at blocked replication forks.
Synopsis
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation.
ChIP‐Seq analysis revealed Rap1‐dependent and –independent budding yeast Rif1 chromosomal binding sites.
Rif1 binds early and late origins without apparent preference.
Rif1 binds stalled replication forks or post‐replicative chromatin under replication stress, and protects nascent DNA from degradation.
Rif1 associates with centromeres in S phase.
Graphical Abstract
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation.</description><subject>Binding sites</subject><subject>Binding Sites - physiology</subject><subject>Biodegradation</subject><subject>Cell Cycle</subject><subject>Cell Cycle Proteins - metabolism</subject><subject>centromere</subject><subject>Centromere - metabolism</subject><subject>Centromeres</subject><subject>ChIP‐Seq</subject><subject>Chromatin</subject><subject>Chromosomes, Plant - chemistry</subject><subject>Degradation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - metabolism</subject><subject>DNA biosynthesis</subject><subject>DNA Replication - physiology</subject><subject>DNA replication origin</subject><subject>DNA Replication Timing - physiology</subject><subject>EMBO13</subject><subject>G1 phase</subject><subject>Genomes</subject><subject>Hydroxyurea</subject><subject>Immunoprecipitation</subject><subject>Labeling</subject><subject>Minichromosome Maintenance Proteins - metabolism</subject><subject>Mutation</subject><subject>nascent DNA</subject><subject>Origins</subject><subject>Protein Phosphatase 1 - metabolism</subject><subject>Protein Serine-Threonine Kinases - metabolism</subject><subject>Proteins</subject><subject>Rap1 protein</subject><subject>Replication</subject><subject>Replication forks</subject><subject>Replication initiation</subject><subject>Replication Origin - physiology</subject><subject>Replication origins</subject><subject>Repressor Proteins - chemistry</subject><subject>Repressor Proteins - genetics</subject><subject>Repressor Proteins - metabolism</subject><subject>Rif1</subject><subject>S phase</subject><subject>S Phase - physiology</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae - metabolism</subject><subject>Saccharomyces cerevisiae Proteins - chemistry</subject><subject>Saccharomyces cerevisiae Proteins - genetics</subject><subject>Saccharomyces cerevisiae Proteins - metabolism</subject><subject>Shelterin Complex</subject><subject>Telomere - metabolism</subject><subject>Telomere-Binding Proteins - chemistry</subject><subject>Telomere-Binding Proteins - genetics</subject><subject>Telomere-Binding Proteins - metabolism</subject><subject>Telomeres</subject><subject>Transcription Factors - metabolism</subject><subject>Yeast</subject><subject>Yeasts</subject><issn>1469-221X</issn><issn>1469-3178</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNqFkc1rFTEUxYMo9sOu3UnAjZvX5iaTmcSF0E8tVIXaRTclJJnkmXZe8kxmWt5_36nv-doK4upeuL9zOJeD0Fsgu8App3tuZvIuJSCqmlL6Am1CVcsJg0a8XO2UwuUG2irlmhDCZSNeow1GgFSUsE10dTC0bYhTvHC69Pg8eMAmxLbgPuHs5l2wug8p4pTDNMSCdWzxPKfe2b7go2_7WPfYdMneuPYZ71O-KW_QK6-74nZWcxv9ODm-OPwyOfv--fRw_2xiOTA6GZMYJivvgUDNhHdOG0Fs472RgjmofSO50HUlqakMZ0BoQ4TlpvGccbaNPi1d54OZuda62GfdqXkOM50XKumgnl9i-Kmm6VbVQFld0dHgw8ogp1-DK72ahWJd1-no0lAUJUJQCRzEiL7_C71OQ47jcyMlJeNEyIdEe0vK5lRKdn4dBoj6XZx6KE6tixsV757-sOb_NDUCH5fAXejc4n9-6vjrwflTd7IUl1EXpy4_pv5XoHt9YrUG</recordid><startdate>201809</startdate><enddate>201809</enddate><creator>Hiraga, Shin‐ichiro</creator><creator>Monerawela, Chandre</creator><creator>Katou, Yuki</creator><creator>Shaw, Sophie</creator><creator>Clark, Kate RM</creator><creator>Shirahige, Katsuhiko</creator><creator>Donaldson, Anne D</creator><general>Nature Publishing Group UK</general><general>Blackwell Publishing Ltd</general><general>John Wiley and Sons Inc</general><scope>C6C</scope><scope>24P</scope><scope>WIN</scope><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>7T5</scope><scope>7TM</scope><scope>7TO</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><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8722-3869</orcidid><orcidid>https://orcid.org/0000-0001-7842-8136</orcidid><orcidid>https://orcid.org/0000-0003-2367-2670</orcidid></search><sort><creationdate>201809</creationdate><title>Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks</title><author>Hiraga, Shin‐ichiro ; Monerawela, Chandre ; Katou, Yuki ; Shaw, Sophie ; Clark, Kate RM ; Shirahige, Katsuhiko ; Donaldson, Anne D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5132-203b394ff101638feeab80c7ffb983e16f7958a6492b4b53102708c5b7f5353</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Binding sites</topic><topic>Binding Sites - physiology</topic><topic>Biodegradation</topic><topic>Cell Cycle</topic><topic>Cell Cycle Proteins - metabolism</topic><topic>centromere</topic><topic>Centromere - metabolism</topic><topic>Centromeres</topic><topic>ChIP‐Seq</topic><topic>Chromatin</topic><topic>Chromosomes, Plant - chemistry</topic><topic>Degradation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - metabolism</topic><topic>DNA biosynthesis</topic><topic>DNA Replication - physiology</topic><topic>DNA replication origin</topic><topic>DNA Replication Timing - physiology</topic><topic>EMBO13</topic><topic>G1 phase</topic><topic>Genomes</topic><topic>Hydroxyurea</topic><topic>Immunoprecipitation</topic><topic>Labeling</topic><topic>Minichromosome Maintenance Proteins - metabolism</topic><topic>Mutation</topic><topic>nascent DNA</topic><topic>Origins</topic><topic>Protein Phosphatase 1 - metabolism</topic><topic>Protein Serine-Threonine Kinases - metabolism</topic><topic>Proteins</topic><topic>Rap1 protein</topic><topic>Replication</topic><topic>Replication forks</topic><topic>Replication initiation</topic><topic>Replication Origin - physiology</topic><topic>Replication origins</topic><topic>Repressor Proteins - chemistry</topic><topic>Repressor Proteins - genetics</topic><topic>Repressor Proteins - metabolism</topic><topic>Rif1</topic><topic>S phase</topic><topic>S Phase - physiology</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae - metabolism</topic><topic>Saccharomyces cerevisiae Proteins - chemistry</topic><topic>Saccharomyces cerevisiae Proteins - genetics</topic><topic>Saccharomyces cerevisiae Proteins - metabolism</topic><topic>Shelterin Complex</topic><topic>Telomere - metabolism</topic><topic>Telomere-Binding Proteins - chemistry</topic><topic>Telomere-Binding Proteins - genetics</topic><topic>Telomere-Binding Proteins - metabolism</topic><topic>Telomeres</topic><topic>Transcription Factors - metabolism</topic><topic>Yeast</topic><topic>Yeasts</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hiraga, Shin‐ichiro</creatorcontrib><creatorcontrib>Monerawela, Chandre</creatorcontrib><creatorcontrib>Katou, Yuki</creatorcontrib><creatorcontrib>Shaw, Sophie</creatorcontrib><creatorcontrib>Clark, Kate RM</creatorcontrib><creatorcontrib>Shirahige, Katsuhiko</creatorcontrib><creatorcontrib>Donaldson, Anne D</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Wiley-Blackwell Open Access Titles</collection><collection>Wiley Free Content</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Immunology Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>EMBO reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hiraga, Shin‐ichiro</au><au>Monerawela, Chandre</au><au>Katou, Yuki</au><au>Shaw, Sophie</au><au>Clark, Kate RM</au><au>Shirahige, Katsuhiko</au><au>Donaldson, Anne D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks</atitle><jtitle>EMBO reports</jtitle><stitle>EMBO Rep</stitle><addtitle>EMBO Rep</addtitle><date>2018-09</date><risdate>2018</risdate><volume>19</volume><issue>9</issue><epage>n/a</epage><issn>1469-221X</issn><eissn>1469-3178</eissn><abstract>Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome‐wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with replication progressing normally or blocked by hydroxyurea. Rif1 associates strongly with telomeres through interaction with Rap1. By comparing genomic binding of wild‐type Rif1 and truncated Rif1 lacking the Rap1‐interaction domain, we identify hundreds of Rap1‐dependent and Rap1‐independent chromosome interaction sites. Rif1 binds to centromeres, highly transcribed genes and replication origins in a Rap1‐independent manner, associating with both early and late‐initiating origins. Interestingly, Rif1 also binds around activated origins when replication progression is blocked by hydroxyurea, suggesting association with blocked forks. Using nascent DNA labelling and DNA combing techniques, we find that in cells treated with hydroxyurea, yeast Rif1 stabilises recently synthesised DNA. Our results indicate that, in addition to controlling DNA replication initiation, budding yeast Rif1 plays an ongoing role after initiation and controls events at blocked replication forks.
Synopsis
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation.
ChIP‐Seq analysis revealed Rap1‐dependent and –independent budding yeast Rif1 chromosomal binding sites.
Rif1 binds early and late origins without apparent preference.
Rif1 binds stalled replication forks or post‐replicative chromatin under replication stress, and protects nascent DNA from degradation.
Rif1 associates with centromeres in S phase.
Graphical Abstract
This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>30104203</pmid><doi>10.15252/embr.201846222</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-8722-3869</orcidid><orcidid>https://orcid.org/0000-0001-7842-8136</orcidid><orcidid>https://orcid.org/0000-0003-2367-2670</orcidid><oa>free_for_read</oa></addata></record> |
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| issn | 1469-221X 1469-3178 |
| language | eng |
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| source | MEDLINE; Springer Nature OA Free Journals; Wiley Free Content; EZB-FREE-00999 freely available EZB journals; Wiley Online Library All Journals; PubMed Central |
| subjects | Binding sites Binding Sites - physiology Biodegradation Cell Cycle Cell Cycle Proteins - metabolism centromere Centromere - metabolism Centromeres ChIP‐Seq Chromatin Chromosomes, Plant - chemistry Degradation Deoxyribonucleic acid DNA DNA - metabolism DNA biosynthesis DNA Replication - physiology DNA replication origin DNA Replication Timing - physiology EMBO13 G1 phase Genomes Hydroxyurea Immunoprecipitation Labeling Minichromosome Maintenance Proteins - metabolism Mutation nascent DNA Origins Protein Phosphatase 1 - metabolism Protein Serine-Threonine Kinases - metabolism Proteins Rap1 protein Replication Replication forks Replication initiation Replication Origin - physiology Replication origins Repressor Proteins - chemistry Repressor Proteins - genetics Repressor Proteins - metabolism Rif1 S phase S Phase - physiology Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins - chemistry Saccharomyces cerevisiae Proteins - genetics Saccharomyces cerevisiae Proteins - metabolism Shelterin Complex Telomere - metabolism Telomere-Binding Proteins - chemistry Telomere-Binding Proteins - genetics Telomere-Binding Proteins - metabolism Telomeres Transcription Factors - metabolism Yeast Yeasts |
| title | Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks |
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