Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species
Abstract Background Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs...
Main Authors: | , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2018-09-01
|
Series: | BMC Genomics |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12864-018-5037-7 |
id |
doaj-23e9e760eb6c474f9711e87e26f60d37 |
---|---|
record_format |
Article |
spelling |
doaj-23e9e760eb6c474f9711e87e26f60d372020-11-24T22:25:25ZengBMCBMC Genomics1471-21642018-09-0119111410.1186/s12864-018-5037-7Genome-wide identification of tissue-specific long non-coding RNA in three farm animal speciesColin Kern0Ying Wang1James Chitwood2Ian Korf3Mary Delany4Hans Cheng5Juan F. Medrano6Alison L. Van Eenennaam7Catherine Ernst8Pablo Ross9Huaijun Zhou10Department of Animal Science, University of California, DavisDepartment of Animal Science, University of California, DavisDepartment of Animal Science, University of California, DavisGenome Center, University of California, DavisDepartment of Animal Science, University of California, DavisUSDA-ARS, Avian Disease and Oncology LaboratoryDepartment of Animal Science, University of California, DavisDepartment of Animal Science, University of California, DavisDepartment of Animal Science, Michigan State UniversityDepartment of Animal Science, University of California, DavisDepartment of Animal Science, University of California, DavisAbstract Background Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs identified lncRNAs in specific developmental stages or differentially expressed under specific conditions in a limited number of tissues, more comprehensive identification of lncRNAs in these species is needed. The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs. As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs. Results Comprehensive lncRNA annotations for the chicken, cattle, and pig genomes were generated by utilizing RNA-seq from eight tissue types from two biological replicates per species at the adult developmental stage. A total of 9393 lncRNAs in chickens, 7235 lncRNAs in cattle, and 14,429 lncRNAs in pigs were identified. Including novel isoforms and lncRNAs from novel loci, 5288 novel lncRNAs were identified in chickens, 3732 in cattle, and 4870 in pigs. These transcripts match previously known patterns of lncRNAs, such as generally lower expression levels than mRNAs and higher tissue specificity. An analysis of lncRNA conservation across species identified a set of conserved lncRNAs with potential functions associated with chromatin structure and gene regulation. Tissue-specific lncRNAs were identified. Genes proximal to tissue-specific lncRNAs were enriched for GO terms associated with the tissue of origin, such as leukocyte activation in spleen. Conclusions LncRNAs were identified in three important farm animal species using eight tissues from adult individuals. About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species. While lncRNAs are less conserved than protein-coding genes, a set of positionally conserved lncRNAs were identified among chickens, cattle, and pigs with potential functions related to chromatin structure and gene regulation. Tissue-specific lncRNAs have potential regulatory functions on genes enriched for tissue-specific GO terms. Future work will include epigenetic data from ChIP-seq experiments to further refine these annotations.http://link.springer.com/article/10.1186/s12864-018-5037-7Long non-coding RNAsGene regulationEpigenetics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Colin Kern Ying Wang James Chitwood Ian Korf Mary Delany Hans Cheng Juan F. Medrano Alison L. Van Eenennaam Catherine Ernst Pablo Ross Huaijun Zhou |
spellingShingle |
Colin Kern Ying Wang James Chitwood Ian Korf Mary Delany Hans Cheng Juan F. Medrano Alison L. Van Eenennaam Catherine Ernst Pablo Ross Huaijun Zhou Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species BMC Genomics Long non-coding RNAs Gene regulation Epigenetics |
author_facet |
Colin Kern Ying Wang James Chitwood Ian Korf Mary Delany Hans Cheng Juan F. Medrano Alison L. Van Eenennaam Catherine Ernst Pablo Ross Huaijun Zhou |
author_sort |
Colin Kern |
title |
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species |
title_short |
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species |
title_full |
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species |
title_fullStr |
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species |
title_full_unstemmed |
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species |
title_sort |
genome-wide identification of tissue-specific long non-coding rna in three farm animal species |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2018-09-01 |
description |
Abstract Background Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs identified lncRNAs in specific developmental stages or differentially expressed under specific conditions in a limited number of tissues, more comprehensive identification of lncRNAs in these species is needed. The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs. As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs. Results Comprehensive lncRNA annotations for the chicken, cattle, and pig genomes were generated by utilizing RNA-seq from eight tissue types from two biological replicates per species at the adult developmental stage. A total of 9393 lncRNAs in chickens, 7235 lncRNAs in cattle, and 14,429 lncRNAs in pigs were identified. Including novel isoforms and lncRNAs from novel loci, 5288 novel lncRNAs were identified in chickens, 3732 in cattle, and 4870 in pigs. These transcripts match previously known patterns of lncRNAs, such as generally lower expression levels than mRNAs and higher tissue specificity. An analysis of lncRNA conservation across species identified a set of conserved lncRNAs with potential functions associated with chromatin structure and gene regulation. Tissue-specific lncRNAs were identified. Genes proximal to tissue-specific lncRNAs were enriched for GO terms associated with the tissue of origin, such as leukocyte activation in spleen. Conclusions LncRNAs were identified in three important farm animal species using eight tissues from adult individuals. About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species. While lncRNAs are less conserved than protein-coding genes, a set of positionally conserved lncRNAs were identified among chickens, cattle, and pigs with potential functions related to chromatin structure and gene regulation. Tissue-specific lncRNAs have potential regulatory functions on genes enriched for tissue-specific GO terms. Future work will include epigenetic data from ChIP-seq experiments to further refine these annotations. |
topic |
Long non-coding RNAs Gene regulation Epigenetics |
url |
http://link.springer.com/article/10.1186/s12864-018-5037-7 |
work_keys_str_mv |
AT colinkern genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT yingwang genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT jameschitwood genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT iankorf genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT marydelany genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT hanscheng genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT juanfmedrano genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT alisonlvaneenennaam genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT catherineernst genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT pabloross genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies AT huaijunzhou genomewideidentificationoftissuespecificlongnoncodingrnainthreefarmanimalspecies |
_version_ |
1725757735209795584 |