Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue
Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenot...
Gespeichert in:
Veröffentlicht in: | Animal genetics 2023-08, Vol.54 (4), p.536-543 |
---|---|
Hauptverfasser: | , , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 543 |
---|---|
container_issue | 4 |
container_start_page | 536 |
container_title | Animal genetics |
container_volume | 54 |
creator | Aldersey, J. E. Liu, N. Tearle, R. Low, W. Y. Breen, J. Williams, J. L. Bottema, C. D. K. |
description | Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300‐kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus‐ and Brahman‐specific Hi‐C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus‐ and Brahman‐specific Hi‐C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses. |
doi_str_mv | 10.1111/age.13322 |
format | Article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2792902046</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2792902046</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3882-6ca12710f8319e8b91c8bcc3ae3cade9fcaddc15d9d0957bbac944be77f54fbd3</originalsourceid><addsrcrecordid>eNp1kc9u1DAQxi0EokvhwAsgS1zgkNZ_sol93C7bFmmlcijnaGKPs66SeLETob3xCH3GPklNt3BAYg4z-ka_-TTSR8h7zs54rnPo8IxLKcQLsuCyWhaCLcVLsmCiUoXmZXVC3qR0xxhTvOavyYmstGa1qBfk_jbsQx86b6DvDxRSCsbD5MeO2jCAHxP1I512SL_dbLebLzRi58NIIeLTNsGA1IVIV2M3p4df9xRGSy8i7AYYs0x7NN55Q699Vut8DjZRF8NALzndHdroLXU4QU8nn9KMb8krB33Cd8_zlHy_3Nyur4vtzdXX9WpbGKmUKCoDXNScOSW5RtVqblRrjASUBixql7s1fGm1ZXpZty0YXZYt1rVblq618pR8OvruY_gxY5qawSeDfQ8jhjk1otZCM8HKKqMf_0HvwhzH_F0jlBRKM6V4pj4fKRNDShFds49-gHhoOGt-x9TkmJqnmDL74dlxbge0f8k_uWTg_Aj89D0e_u_UrK42R8tH-S2fuw</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2832890881</pqid></control><display><type>article</type><title>Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue</title><source>MEDLINE</source><source>Access via Wiley Online Library</source><creator>Aldersey, J. E. ; Liu, N. ; Tearle, R. ; Low, W. Y. ; Breen, J. ; Williams, J. L. ; Bottema, C. D. K.</creator><creatorcontrib>Aldersey, J. E. ; Liu, N. ; Tearle, R. ; Low, W. Y. ; Breen, J. ; Williams, J. L. ; Bottema, C. D. K.</creatorcontrib><description>Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300‐kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus‐ and Brahman‐specific Hi‐C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus‐ and Brahman‐specific Hi‐C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.</description><identifier>ISSN: 0268-9146</identifier><identifier>EISSN: 1365-2052</identifier><identifier>DOI: 10.1111/age.13322</identifier><identifier>PMID: 36990727</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Alleles ; Animals ; Bovidae ; Cattle ; Cattle - genetics ; Celtic ; Chromatin ; Chromosome 1 ; Enhancers ; Fetuses ; Friesian ; Genetic diversity ; Genetic variance ; Goats - genetics ; Guarani ; headgear ; Histones ; Horns ; Immunoprecipitation ; Mongolian ; Mutation ; Phenotype ; Phenotypes ; polled</subject><ispartof>Animal genetics, 2023-08, Vol.54 (4), p.536-543</ispartof><rights>2023 The Authors. published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.</rights><rights>2023 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.</rights><rights>2023. This article is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). 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><citedby>FETCH-LOGICAL-c3882-6ca12710f8319e8b91c8bcc3ae3cade9fcaddc15d9d0957bbac944be77f54fbd3</citedby><cites>FETCH-LOGICAL-c3882-6ca12710f8319e8b91c8bcc3ae3cade9fcaddc15d9d0957bbac944be77f54fbd3</cites><orcidid>0000-0001-6184-0925 ; 0000-0002-5480-857X ; 0000-0002-9487-9305 ; 0000-0003-2243-5091 ; 0000-0001-5188-7957 ; 0000-0001-6245-0099</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fage.13322$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fage.13322$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36990727$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Aldersey, J. E.</creatorcontrib><creatorcontrib>Liu, N.</creatorcontrib><creatorcontrib>Tearle, R.</creatorcontrib><creatorcontrib>Low, W. Y.</creatorcontrib><creatorcontrib>Breen, J.</creatorcontrib><creatorcontrib>Williams, J. L.</creatorcontrib><creatorcontrib>Bottema, C. D. K.</creatorcontrib><title>Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue</title><title>Animal genetics</title><addtitle>Anim Genet</addtitle><description>Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300‐kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus‐ and Brahman‐specific Hi‐C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus‐ and Brahman‐specific Hi‐C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.</description><subject>Alleles</subject><subject>Animals</subject><subject>Bovidae</subject><subject>Cattle</subject><subject>Cattle - genetics</subject><subject>Celtic</subject><subject>Chromatin</subject><subject>Chromosome 1</subject><subject>Enhancers</subject><subject>Fetuses</subject><subject>Friesian</subject><subject>Genetic diversity</subject><subject>Genetic variance</subject><subject>Goats - genetics</subject><subject>Guarani</subject><subject>headgear</subject><subject>Histones</subject><subject>Horns</subject><subject>Immunoprecipitation</subject><subject>Mongolian</subject><subject>Mutation</subject><subject>Phenotype</subject><subject>Phenotypes</subject><subject>polled</subject><issn>0268-9146</issn><issn>1365-2052</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNp1kc9u1DAQxi0EokvhwAsgS1zgkNZ_sol93C7bFmmlcijnaGKPs66SeLETob3xCH3GPklNt3BAYg4z-ka_-TTSR8h7zs54rnPo8IxLKcQLsuCyWhaCLcVLsmCiUoXmZXVC3qR0xxhTvOavyYmstGa1qBfk_jbsQx86b6DvDxRSCsbD5MeO2jCAHxP1I512SL_dbLebLzRi58NIIeLTNsGA1IVIV2M3p4df9xRGSy8i7AYYs0x7NN55Q699Vut8DjZRF8NALzndHdroLXU4QU8nn9KMb8krB33Cd8_zlHy_3Nyur4vtzdXX9WpbGKmUKCoDXNScOSW5RtVqblRrjASUBixql7s1fGm1ZXpZty0YXZYt1rVblq618pR8OvruY_gxY5qawSeDfQ8jhjk1otZCM8HKKqMf_0HvwhzH_F0jlBRKM6V4pj4fKRNDShFds49-gHhoOGt-x9TkmJqnmDL74dlxbge0f8k_uWTg_Aj89D0e_u_UrK42R8tH-S2fuw</recordid><startdate>202308</startdate><enddate>202308</enddate><creator>Aldersey, J. E.</creator><creator>Liu, N.</creator><creator>Tearle, R.</creator><creator>Low, W. Y.</creator><creator>Breen, J.</creator><creator>Williams, J. L.</creator><creator>Bottema, C. D. K.</creator><general>Wiley Subscription Services, Inc</general><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>7TK</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-6184-0925</orcidid><orcidid>https://orcid.org/0000-0002-5480-857X</orcidid><orcidid>https://orcid.org/0000-0002-9487-9305</orcidid><orcidid>https://orcid.org/0000-0003-2243-5091</orcidid><orcidid>https://orcid.org/0000-0001-5188-7957</orcidid><orcidid>https://orcid.org/0000-0001-6245-0099</orcidid></search><sort><creationdate>202308</creationdate><title>Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue</title><author>Aldersey, J. E. ; Liu, N. ; Tearle, R. ; Low, W. Y. ; Breen, J. ; Williams, J. L. ; Bottema, C. D. K.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3882-6ca12710f8319e8b91c8bcc3ae3cade9fcaddc15d9d0957bbac944be77f54fbd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Alleles</topic><topic>Animals</topic><topic>Bovidae</topic><topic>Cattle</topic><topic>Cattle - genetics</topic><topic>Celtic</topic><topic>Chromatin</topic><topic>Chromosome 1</topic><topic>Enhancers</topic><topic>Fetuses</topic><topic>Friesian</topic><topic>Genetic diversity</topic><topic>Genetic variance</topic><topic>Goats - genetics</topic><topic>Guarani</topic><topic>headgear</topic><topic>Histones</topic><topic>Horns</topic><topic>Immunoprecipitation</topic><topic>Mongolian</topic><topic>Mutation</topic><topic>Phenotype</topic><topic>Phenotypes</topic><topic>polled</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Aldersey, J. E.</creatorcontrib><creatorcontrib>Liu, N.</creatorcontrib><creatorcontrib>Tearle, R.</creatorcontrib><creatorcontrib>Low, W. Y.</creatorcontrib><creatorcontrib>Breen, J.</creatorcontrib><creatorcontrib>Williams, J. L.</creatorcontrib><creatorcontrib>Bottema, C. D. K.</creatorcontrib><collection>Wiley Online Library (Open Access Collection)</collection><collection>Wiley Online Library (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Animal genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Aldersey, J. E.</au><au>Liu, N.</au><au>Tearle, R.</au><au>Low, W. Y.</au><au>Breen, J.</au><au>Williams, J. L.</au><au>Bottema, C. D. K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue</atitle><jtitle>Animal genetics</jtitle><addtitle>Anim Genet</addtitle><date>2023-08</date><risdate>2023</risdate><volume>54</volume><issue>4</issue><spage>536</spage><epage>543</epage><pages>536-543</pages><issn>0268-9146</issn><eissn>1365-2052</eissn><abstract>Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian and Guarani) are associated with the polled phenotype, which are clustered in a 300‐kb region on chromosome 1. As the variants are intergenic, the functional effect is unknown. The aim of this study was to determine if the POLLED variants affect chromatin structure or disrupt enhancers using publicly available data. Topologically associating domains (TADs) were analyzed using Angus‐ and Brahman‐specific Hi‐C reads from lung tissue of an Angus (Celtic allele) cross Brahman (horned) fetus. Predicted bovine enhancers and chromatin immunoprecipitation sequencing peaks for histone modifications associated with enhancers (H3K27ac and H3K4me1) were mapped to the POLLED region. TADs analyzed from Angus‐ and Brahman‐specific Hi‐C reads were the same, therefore, the Celtic variant does not appear to affect this level of chromatin structure. The Celtic variant is located in a different TAD from the Friesian, Mongolian, and Guarani variants. Predicted enhancers and histone modifications overlapped with the Guarani and Friesian variants but not the Celtic or Mongolian variants. This study provides insight into the mechanisms of the POLLED variants for disrupting horn development. These results should be validated using data produced from the horn bud region of horned and polled bovine fetuses.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>36990727</pmid><doi>10.1111/age.13322</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0001-6184-0925</orcidid><orcidid>https://orcid.org/0000-0002-5480-857X</orcidid><orcidid>https://orcid.org/0000-0002-9487-9305</orcidid><orcidid>https://orcid.org/0000-0003-2243-5091</orcidid><orcidid>https://orcid.org/0000-0001-5188-7957</orcidid><orcidid>https://orcid.org/0000-0001-6245-0099</orcidid><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0268-9146 |
ispartof | Animal genetics, 2023-08, Vol.54 (4), p.536-543 |
issn | 0268-9146 1365-2052 |
language | eng |
recordid | cdi_proquest_miscellaneous_2792902046 |
source | MEDLINE; Access via Wiley Online Library |
subjects | Alleles Animals Bovidae Cattle Cattle - genetics Celtic Chromatin Chromosome 1 Enhancers Fetuses Friesian Genetic diversity Genetic variance Goats - genetics Guarani headgear Histones Horns Immunoprecipitation Mongolian Mutation Phenotype Phenotypes polled |
title | Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T17%3A35%3A11IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Topologically%20associating%20domains%20in%20the%20POLLED%20region%20are%20the%20same%20for%20Angus%E2%80%90%20and%20Brahman%E2%80%90specific%20Hi%E2%80%90C%20reads%20from%20F1%20hybrid%20fetal%20tissue&rft.jtitle=Animal%20genetics&rft.au=Aldersey,%20J.%20E.&rft.date=2023-08&rft.volume=54&rft.issue=4&rft.spage=536&rft.epage=543&rft.pages=536-543&rft.issn=0268-9146&rft.eissn=1365-2052&rft_id=info:doi/10.1111/age.13322&rft_dat=%3Cproquest_cross%3E2792902046%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2832890881&rft_id=info:pmid/36990727&rfr_iscdi=true |