Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

The ciliate maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:RNA (Cambridge) 2017-08, Vol.23 (8), p.1200-1208
Hauptverfasser: Lindblad, Kelsi A, Bracht, John R, Williams, April E, Landweber, Laura F
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 1208
container_issue 8
container_start_page 1200
container_title RNA (Cambridge)
container_volume 23
creator Lindblad, Kelsi A
Bracht, John R
Williams, April E
Landweber, Laura F
description The ciliate maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.
doi_str_mv 10.1261/rna.058511.116
format Article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5513065</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2138067314</sourcerecordid><originalsourceid>FETCH-LOGICAL-c418t-fa2616e87ec601912ddcfd5a71f036a6159148286977d217adb872ed7f3e416e3</originalsourceid><addsrcrecordid>eNpdUctu1TAQjRCIlsKWJbLEhk0unjh-ZINUVRSQKiqhsrZce9K4JHGwk0L_vgO3VMDK1pyHPedU1UvgO2gUvM2z23FpJMAOQD2qDqFVXd1xDo_pLqSsjTDNQfWslGsaCoKfVgeNaSWXAg6rbxdD2oqbQ2GpZ18-H9fe-QED82mJ-Hv4Y0gjMj_kNKWSJhq6jGzJWHBeWZzZOhAcx-hWZOc_b9cc_eBY2HKcr1jAGxzTMhH3efWkd2PBF_fnUfX19P3Fycf67PzDp5Pjs9q3YNa6d7SYQqPRKw4dNCH4PkinoedCOQWyg9Y0RnVahwa0C5dGNxh0L7AloTiq3u19l-1ywuDp6exGu-Q4uXxrk4v2X2SOg71KN1ZKEFxJMnhzb5DT9w3LaqdYPI6jm5HSsmA6ISlnoYn6-j_qddqolLHYBoThSlPkxNrtWT6nUjL2D58Bbn_1aEli9z1a6pEEr_5e4YH-pzhxB479mlQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2138067314</pqid></control><display><type>article</type><title>Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development</title><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><creator>Lindblad, Kelsi A ; Bracht, John R ; Williams, April E ; Landweber, Laura F</creator><creatorcontrib>Lindblad, Kelsi A ; Bracht, John R ; Williams, April E ; Landweber, Laura F</creatorcontrib><description>The ciliate maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.</description><identifier>ISSN: 1355-8382</identifier><identifier>EISSN: 1469-9001</identifier><identifier>DOI: 10.1261/rna.058511.116</identifier><identifier>PMID: 28450531</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Animals ; Chromosomes ; Chromosomes - genetics ; Deoxyribonucleic acid ; DNA ; DNA Copy Number Variations ; Genome, Protozoan - genetics ; Genomes ; High-Throughput Nucleotide Sequencing - methods ; Nucleotide sequence ; Oxytricha ; Oxytricha - genetics ; Oxytricha - growth &amp; development ; Ribonucleic acid ; RNA ; RNA, Long Noncoding - genetics ; RNA, Protozoan - genetics ; Telomere - genetics ; Temporal distribution ; Transcription</subject><ispartof>RNA (Cambridge), 2017-08, Vol.23 (8), p.1200-1208</ispartof><rights>2017 Lindblad et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.</rights><rights>Copyright Cold Spring Harbor Laboratory Press Aug 2017</rights><rights>2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c418t-fa2616e87ec601912ddcfd5a71f036a6159148286977d217adb872ed7f3e416e3</citedby><cites>FETCH-LOGICAL-c418t-fa2616e87ec601912ddcfd5a71f036a6159148286977d217adb872ed7f3e416e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513065/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513065/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28450531$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lindblad, Kelsi A</creatorcontrib><creatorcontrib>Bracht, John R</creatorcontrib><creatorcontrib>Williams, April E</creatorcontrib><creatorcontrib>Landweber, Laura F</creatorcontrib><title>Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development</title><title>RNA (Cambridge)</title><addtitle>RNA</addtitle><description>The ciliate maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.</description><subject>Animals</subject><subject>Chromosomes</subject><subject>Chromosomes - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Copy Number Variations</subject><subject>Genome, Protozoan - genetics</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Nucleotide sequence</subject><subject>Oxytricha</subject><subject>Oxytricha - genetics</subject><subject>Oxytricha - growth &amp; development</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Protozoan - genetics</subject><subject>Telomere - genetics</subject><subject>Temporal distribution</subject><subject>Transcription</subject><issn>1355-8382</issn><issn>1469-9001</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdUctu1TAQjRCIlsKWJbLEhk0unjh-ZINUVRSQKiqhsrZce9K4JHGwk0L_vgO3VMDK1pyHPedU1UvgO2gUvM2z23FpJMAOQD2qDqFVXd1xDo_pLqSsjTDNQfWslGsaCoKfVgeNaSWXAg6rbxdD2oqbQ2GpZ18-H9fe-QED82mJ-Hv4Y0gjMj_kNKWSJhq6jGzJWHBeWZzZOhAcx-hWZOc_b9cc_eBY2HKcr1jAGxzTMhH3efWkd2PBF_fnUfX19P3Fycf67PzDp5Pjs9q3YNa6d7SYQqPRKw4dNCH4PkinoedCOQWyg9Y0RnVahwa0C5dGNxh0L7AloTiq3u19l-1ywuDp6exGu-Q4uXxrk4v2X2SOg71KN1ZKEFxJMnhzb5DT9w3LaqdYPI6jm5HSsmA6ISlnoYn6-j_qddqolLHYBoThSlPkxNrtWT6nUjL2D58Bbn_1aEli9z1a6pEEr_5e4YH-pzhxB479mlQ</recordid><startdate>201708</startdate><enddate>201708</enddate><creator>Lindblad, Kelsi A</creator><creator>Bracht, John R</creator><creator>Williams, April E</creator><creator>Landweber, Laura F</creator><general>Cold Spring Harbor Laboratory Press</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>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201708</creationdate><title>Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development</title><author>Lindblad, Kelsi A ; Bracht, John R ; Williams, April E ; Landweber, Laura F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c418t-fa2616e87ec601912ddcfd5a71f036a6159148286977d217adb872ed7f3e416e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Animals</topic><topic>Chromosomes</topic><topic>Chromosomes - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Copy Number Variations</topic><topic>Genome, Protozoan - genetics</topic><topic>Genomes</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Nucleotide sequence</topic><topic>Oxytricha</topic><topic>Oxytricha - genetics</topic><topic>Oxytricha - growth &amp; development</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Protozoan - genetics</topic><topic>Telomere - genetics</topic><topic>Temporal distribution</topic><topic>Transcription</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lindblad, Kelsi A</creatorcontrib><creatorcontrib>Bracht, John R</creatorcontrib><creatorcontrib>Williams, April E</creatorcontrib><creatorcontrib>Landweber, Laura F</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>RNA (Cambridge)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lindblad, Kelsi A</au><au>Bracht, John R</au><au>Williams, April E</au><au>Landweber, Laura F</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development</atitle><jtitle>RNA (Cambridge)</jtitle><addtitle>RNA</addtitle><date>2017-08</date><risdate>2017</risdate><volume>23</volume><issue>8</issue><spage>1200</spage><epage>1208</epage><pages>1200-1208</pages><issn>1355-8382</issn><eissn>1469-9001</eissn><abstract>The ciliate maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.</abstract><cop>United States</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>28450531</pmid><doi>10.1261/rna.058511.116</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1355-8382
ispartof RNA (Cambridge), 2017-08, Vol.23 (8), p.1200-1208
issn 1355-8382
1469-9001
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5513065
source MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection
subjects Animals
Chromosomes
Chromosomes - genetics
Deoxyribonucleic acid
DNA
DNA Copy Number Variations
Genome, Protozoan - genetics
Genomes
High-Throughput Nucleotide Sequencing - methods
Nucleotide sequence
Oxytricha
Oxytricha - genetics
Oxytricha - growth & development
Ribonucleic acid
RNA
RNA, Long Noncoding - genetics
RNA, Protozoan - genetics
Telomere - genetics
Temporal distribution
Transcription
title Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-26T23%3A35%3A17IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Thousands%20of%20RNA-cached%20copies%20of%20whole%20chromosomes%20are%20present%20in%20the%20ciliate%20Oxytricha%20during%20development&rft.jtitle=RNA%20(Cambridge)&rft.au=Lindblad,%20Kelsi%20A&rft.date=2017-08&rft.volume=23&rft.issue=8&rft.spage=1200&rft.epage=1208&rft.pages=1200-1208&rft.issn=1355-8382&rft.eissn=1469-9001&rft_id=info:doi/10.1261/rna.058511.116&rft_dat=%3Cproquest_pubme%3E2138067314%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2138067314&rft_id=info:pmid/28450531&rfr_iscdi=true