1
|
Chen M, Lian D, Li Y, Zhao Y, Xu X, Liu Z, Zhang J, Zhang X, Wu S, Qi S, Deng S, Yu K, Lian Z. Global Long Noncoding RNA Expression Profiling of MSTN and FGF5 Double-Knockout Sheep Reveals the Key Gatekeepers of Skeletal Muscle Development. DNA Cell Biol 2023; 42:163-175. [PMID: 36917699 DOI: 10.1089/dna.2022.0574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Improving livestock and poultry growth rates and increasing meat production are urgently needed worldwide. Previously, we produced a myostatin (MSTN) and fibroblast growth factor 5 (FGF5) double-knockout (MF-/-) sheep by CRISPR Cas9 system to improve meat production, and also wool production. Both MF-/- sheep and the F1 generation (MF+/-) sheep showed an obvious "double-muscle" phenotype. In this study, we identified the expression profiles of long noncoding RNAs (lncRNAs) in wild-type and MF+/- sheep, then screened out the key candidate lncRNAs that can regulate myogenic differentiation and skeletal muscle development. These key candidate lncRNAs can serve as critical gatekeepers for muscle contraction, calcium ion transport and skeletal muscle cell differentiation, apoptosis, autophagy, and skeletal muscle inflammation, further revealing that lncRNAs play crucial roles in regulating muscle phenotype in MF+/- sheep. In conclusion, our newly identified lncRNAs may emerge as novel molecules for muscle development or muscle disease and provide a new reference for MSTN-mediated regulation of skeletal muscle development.
Collapse
Affiliation(s)
- Mingming Chen
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yan Li
- Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing, China
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xueling Xu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhimei Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Sujun Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyu Qi
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Kun Yu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
2
|
Heidari M, Pakdel A, Bakhtiarizadeh MR, Dehghanian F. A framework for non-preserved consensus gene module detection in Johne's disease. Front Vet Sci 2022; 9:974444. [PMID: 35968017 PMCID: PMC9363878 DOI: 10.3389/fvets.2022.974444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022] Open
Abstract
Johne's disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) is a major concern in dairy industry. Since, the pathogenesis of the disease is not clearly known, it is necessary to develop an approach to discover molecular mechanisms behind this disease with high confidence. Biological studies often suffer from issues with reproducibility. Lack of a method to find stable modules in co-expression networks from different datasets related to Johne's disease motivated us to present a computational pipeline to identify non-preserved consensus modules. Two RNA-Seq datasets related to MAP infection were analyzed, and consensus modules were detected and were subjected to the preservation analysis. The non-preserved consensus modules in both datasets were determined as they are modules whose connectivity and density are affected by the disease. Long non-coding RNAs (lncRNAs) and TF genes in the non-preserved consensus modules were identified to construct integrated networks of lncRNA-mRNA-TF. These networks were confirmed by protein-protein interactions (PPIs) networks. Also, the overlapped hub genes between two datasets were considered hub genes of the consensus modules. Out of 66 consensus modules, 21 modules were non-preserved consensus modules, which were common in both datasets and 619 hub genes were members of these modules. Moreover, 34 lncRNA and 152 TF genes were identified in 12 and 19 non-preserved consensus modules, respectively. The predicted PPIs in 17 non-preserved consensus modules were significant, and 283 hub genes were commonly identified in both co-expression and PPIs networks. Functional enrichment analysis revealed that eight out of 21 modules were significantly enriched for biological processes associated with Johne's disease including “inflammatory response,” “interleukin-1-mediated signaling pathway”, “type I interferon signaling pathway,” “cytokine-mediated signaling pathway,” “regulation of interferon-beta production,” and “response to interferon-gamma.” Moreover, some genes (hub mRNA, TF, and lncRNA) were introduced as potential candidates for Johne's disease pathogenesis such as TLR2, NFKB1, IRF1, ATF3, TREM1, CDH26, HMGB1, STAT1, ISG15, CASP3. This study expanded our knowledge of molecular mechanisms involved in Johne's disease, and the presented pipeline enabled us to achieve more valid results.
Collapse
Affiliation(s)
- Maryam Heidari
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
- *Correspondence: Abbas Pakdel
| | - Mohammad Reza Bakhtiarizadeh
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
- Mohammad Reza Bakhtiarizadeh
| | | |
Collapse
|
3
|
Jara E, Peñagaricano F, Armstrong E, Menezes C, Tardiz L, Rodons G, Iriarte A. Identification of Long Noncoding RNAs Involved in Eyelid Pigmentation of Hereford Cattle. Front Genet 2022; 13:864567. [PMID: 35601493 PMCID: PMC9114348 DOI: 10.3389/fgene.2022.864567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/20/2022] [Indexed: 12/05/2022] Open
Abstract
Several ocular pathologies in cattle, such as ocular squamous cell carcinoma and infectious keratoconjunctivitis, have been associated with low pigmentation of the eyelids. The main objective of this study was to analyze the transcriptome of eyelid skin in Hereford cattle using strand-specific RNA sequencing technology to characterize and identify long noncoding RNAs (lncRNAs). We compared the expression of lncRNAs between pigmented and unpigmented eyelids and analyzed the interaction of lncRNAs and putative target genes to reveal the genetic basis underlying eyelid pigmentation in cattle. We predicted 4,937 putative lncRNAs mapped to the bovine reference genome, enriching the catalog of lncRNAs in Bos taurus. We found 27 differentially expressed lncRNAs between pigmented and unpigmented eyelids, suggesting their involvement in eyelid pigmentation. In addition, we revealed potential links between some significant differentially expressed lncRNAs and target mRNAs involved in the immune response and pigmentation. Overall, this study expands the catalog of lncRNAs in cattle and contributes to a better understanding of the biology of eyelid pigmentation.
Collapse
Affiliation(s)
- Eugenio Jara
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Eileen Armstrong
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Claudia Menezes
- Laboratorio de Endocrinología y Metabolismo Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Lucía Tardiz
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Gastón Rodons
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
- *Correspondence: Andrés Iriarte,
| |
Collapse
|
4
|
Karimi P, Bakhtiarizadeh MR, Salehi A, Izadnia HR. Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken. Sci Rep 2022; 12:2558. [PMID: 35169237 PMCID: PMC8847365 DOI: 10.1038/s41598-022-06528-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.
Collapse
Affiliation(s)
- Parastoo Karimi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
| |
Collapse
|
5
|
Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
Collapse
Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
| |
Collapse
|
6
|
Li J, Li N, Zhu L, Zhang Z, Li X, Wang J, Xun H, Zhao J, Wang X, Wang T, Wang H, Liu B, Li Y, Gong L. Mutation of a major CG methylase alters genome-wide lncRNA expression in rice. G3-GENES GENOMES GENETICS 2021; 11:6146525. [PMID: 33617633 PMCID: PMC8049413 DOI: 10.1093/g3journal/jkab049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/08/2021] [Indexed: 11/14/2022]
Abstract
Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (5mC) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2-/-) and its isogenic wild type (OsMET1-2+/+). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2+/+, was transcriptionally de-repressed in OsMET1-2-/- due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5'-upstream genomic regions of lncRNAs in OsMET1-2-/-. The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.
Collapse
Affiliation(s)
- Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ling Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongwei Xun
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yu Li
- Engineering Research Center of the Ministry of Education (MOE) for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| |
Collapse
|
7
|
Wu S, Zhang J, Liu B, Huang Y, Li S, Wen H, Zhang M, Li J, Li Y, He F. Identification and Characterization of lncRNAs Related to the Muscle Growth and Development of Japanese Flounder ( Paralichthys olivaceus). Front Genet 2020; 11:1034. [PMID: 33033494 PMCID: PMC7510837 DOI: 10.3389/fgene.2020.01034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 08/11/2020] [Indexed: 01/28/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play an important role in many life activities, but the expression pattern and function of lncRNAs in Japanese flounder skeletal muscle are unclear. In this study, 751 lncRNAs were selected from skeletal muscle in different development stages of the Japanese flounder [stage A: larval 7 days post hatching (dph); stage B: juvenile about 90 dph; stage C (female) and stage D (male): adult about 24 months] using coding potential analysis methods. In total, 232, 211, 194, 28, 29, and 14 differentially expressed lncRNAs and 9549, 8673, 9181, 1821, 1080, and 557 differentially expressed mRNAs were identified in comparisons of A versus B, A versus C, A versus D, B versus C, B versus D, and C versus D, respectively. We identified the cis- and trans-regulatory target genes of differentially expressed lncRNAs, and lncRNA-gene interaction networks were constructed using the Cytoscape program. In total, there were 200, 200, 200, 93, 47, and 11 cis-regulation relationships, and 29, 19, 24, 38, 8, and 47 trans-regulation relationships in the comparisons between A versus B, A versus C, A versus D, B versus C, B versus D, and C versus D, respectively. These results indicate that lncRNA may participate in the development of Japanese flounder skeletal muscle through cis- or trans-acting mechanisms, thus providing a scientific basis for further study of the biological function of lncRNA in Japanese flounder skeletal muscle. Based on these relationships, functional annotation of the related lncRNAs was performed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Differentially expressed genes associated with muscle development were enriched in multiple pairs of comparisons (e.g., differentially expressed genes LOC109640370, LOC109634180, LOC109643555, rusc1, and LOC109626999 were enriched in the actin-binding term, and differentially expressed genes LOC109640370, was, LOC109644970, LOC109643555, and itga9 were enriched in the regulation of the actin cytoskeleton pathway in the KEGG pathway analysis in the comparison of stages C and D). We predicted lncRNA-mRNA, miRNA-mRNA, and lncRNA-miRNA regulatory relationships and constructed interactive networks using Cytoscape software. Co-expression networks show that most lncRNAs interact with one or two predicted miRNAs involved in muscle growth and development. These results provide a basis for further study of the function of lncRNAs on skeletal muscle in different developmental stages of Japanese flounder.
Collapse
Affiliation(s)
- Shuxian Wu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Jingru Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Binghua Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Yajuan Huang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Siping Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Haishen Wen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Meizhao Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Jifang Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Yun Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Feng He
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| |
Collapse
|
8
|
Bakhtiarizadeh MR, Alamouti AA. RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep. Sci Rep 2020; 10:13525. [PMID: 32782325 PMCID: PMC7419499 DOI: 10.1038/s41598-020-70527-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.
Collapse
Affiliation(s)
| | - Ali A Alamouti
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| |
Collapse
|
9
|
Xia Q, Li Q, Gan S, Guo X, Zhang X, Zhang J, Chu M. Exploring the roles of fecundity-related long non-coding RNAs and mRNAs in the adrenal glands of small-tailed Han Sheep. BMC Genet 2020; 21:39. [PMID: 32252625 PMCID: PMC7137433 DOI: 10.1186/s12863-020-00850-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between follicular phases and luteal phases in FecBBB (MM) and FecB++ (WW) sheep, respectively, and differentially expressed lncRNAs and genes associated with reproduction were identified. RESULTS In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 513 differentially expressed lncRNAs and 2481 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Differentially expressed lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761, XLOC_357966, 105,614,839 and XLOC_212877 targeting CREB1, PER3, SMAD1 and TGFBR2, respectively, appear to play key regulatory roles. CONCLUSION These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.
Collapse
Affiliation(s)
- Qing Xia
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Qiuling Li
- College of Life Sciences, Langfang Normal University, Langfang, 065000, P.R. China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Xiaofei Guo
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Xiaosheng Zhang
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China.
| |
Collapse
|
10
|
Li X, Li C, Xu Y, Yao R, Li H, Ni W, Quan R, Zhang M, Liu L, Yu S, Ullah Y, Hu R, Li Y, Guo T, Wang X, Hu S. Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus. Funct Integr Genomics 2020; 20:563-573. [PMID: 32114660 DOI: 10.1007/s10142-020-00735-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022]
Abstract
Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes such as growth, development, and reproduction of animals. Here, we used RNA-seq technology to study the expression profile of lncRNAs in the anterior pituitary of sheep during estrus and anestrus. In this study, we identified a total of 995 lncRNAs, of which 335 lncRNAs were differentially expressed in two states (including 38 up-regulated and 297 down-regulated lncRNAs). RT-qPCR verified the expression levels of several lncRNAs. Target predictive analysis revealed that these lncRNAs can act in cis or trans and regulate the expression of genes involved in the regulation of sheep estrus. Target gene enrichment analysis of differentially expressed lncRNAs indicates that these lncRNAs can regulate sheep estrus by regulating hormone metabolism and energy metabolism. Through our research, we provide the expression profile of lncRNAs in the pituitary of sheep, which provides a valuable resource for further understanding of the genetic regulation of seasonal estrus in sheep from the perspective of lncRNAs.
Collapse
Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.,College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaseen Ullah
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaxin Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Tao Guo
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaokui Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
| |
Collapse
|
11
|
Yang H, Wang F, Li F, Ren C, Pang J, Wan Y, Wang Z, Feng X, Zhang Y. Comprehensive analysis of long noncoding RNA and mRNA expression patterns in sheep testicular maturation. Biol Reprod 2019; 99:650-661. [PMID: 29668837 DOI: 10.1093/biolre/ioy088] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/12/2018] [Indexed: 02/03/2023] Open
Abstract
Long noncoding RNAs (LncRNAs) have been identified as important regulators of testis development; however, their expression patterns and roles in sheep are not yet clear. Thus, we used stranded specific RNA-seq to profile the testis transcriptome (lncRNAs and mRNAs) in premature and mature sheep. Hormone levels and the testis index were examined, and histological analyses were performed at five stages of testis development, 5-day-old (D5), 3-month-old (3M), 6-month-old (6M), 9-month-old (9M), and 2-year-old (2Y), the results of which indicate a significant difference in hormone levels and testis morphometries between the 3M and 9M stages (P < 0.05). Based on the comparison between 3M and 9M samples, we found 1,118 differentially expressed (DE) lncRNAs and 7,253 DE mRNAs in the testes, and qRT-PCR analysis showed that the results correlated well with the transcriptome data. Furthermore, we constructed lncRNA-protein-coding gene interaction networks. Forty-seven DE lncRNA-targeted genes enriched for male reproduction were obtained by cis- and trans-acting; 51 DE lncRNAs and 45 cis-targets, 2 DE lncRNAs and 2 trans-targets were involved in this network. Of these, 5 lncRNAs and their targets, PRKCD, NANOS3, SERPINA5, and CYP19A1, were enriched for spermatogenesis and male gonad development signaling pathways. We further examined the expression levels of 5 candidate lncRNAs and their target genes during testis development. Lastly, the interaction of lncRNA TCONS__00863147 and its target gene PRKCD was validated in vitro in sheep Leydig cells. This study provides a valuable resource for further study of lncRNA function in sheep testis development and spermatogenesis.
Collapse
Affiliation(s)
- Hua Yang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Fengzhe Li
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Caifang Ren
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Jing Pang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Ziyu Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Xu Feng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, NO. 1 Weigang, Nanjing, 210095, P.R. China
| |
Collapse
|
12
|
Sun QM, Hu B, Fu PY, Tang WG, Zhang X, Zhan H, Sun C, He YF, Song K, Xiao YS, Sun J, Xu Y, Zhou J, Fan J. Long non-coding RNA 00607 as a tumor suppressor by modulating NF-κB p65/p53 signaling axis in hepatocellular carcinoma. Carcinogenesis 2019; 39:1438-1446. [PMID: 30169594 DOI: 10.1093/carcin/bgy113] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence suggests that long non-coding RNA (lncRNA) plays important roles in some malignant tumors. However, the mechanism underlying how lncRNA regulates hepatocellular carcinoma (HCC) process remains largely unknown. In this study, we explored the potential role of lncRNA 00607 as a novel tumor suppressor in HCC. In this study, we examined the regulation of lncRNA 00607 by the important inflammatory cytokine tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). We also determined the expression of LINC000607 in 159 HCC tumors and paired adjacent tissues. Effects of LINC000607 in HCC proliferation and apoptosis were examined in vitro in HCC cell lines and in vivo tumor xenografts. Furthermore, we also examine underlying mechanism by which lncRNA 00607 regulates NF-κB p65 and how LIN00607 exerts its tumor suppressor role in HCC. We found that lncRNA 00607 expression level is lower in HCC tumors compared with matched normal liver tissue, and its low expression predicts worse prognosis in HCC. Functionally, lncRNA 00607 overexpression leads to decreased HCC cell proliferation in vitro and in vivo, enhanced apoptosis and chemotherapeutic drug sensitivity. Mechanistically, lncRNA 00607 inhibits the p65 transcription by binding to the p65 promoter region, therefore contributing to increased p53 levels in HCC. Taken together, the findings of this study show that the TNF-α/IL-6-lncRNA 00607-NF-κB p65/p53 signaling axis represents a novel therapeutic avenue in cancer chemotherapy.
Collapse
Affiliation(s)
- Qi-Man Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Bo Hu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Pei-Yao Fu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Wei-Guo Tang
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, P. R. China
| | - Xin Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Hao Zhan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Chao Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Yi-Feng He
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Kang Song
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Yong-Sheng Xiao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Jian Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Yang Xu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai, P.R. China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Zhongshan Hospital of Fudan University, Shanghai, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai, P.R. China
| |
Collapse
|
13
|
Li X, Li C, Wureli H, Ni W, Zhang M, Li H, Xu Y, Rizabek K, Bolatkhan M, Askar D, Gulzhan K, Hou X, Hu S. Screening and evaluating of long non-coding RNAs in prenatal and postnatal pituitary gland of sheep. Genomics 2019; 112:934-942. [PMID: 31200027 DOI: 10.1016/j.ygeno.2019.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs are transcribed into RNA molecules that are >200 nucleotides in length. However, the expression and function analysis of lncRNAs in the sheep pituitary gland are still lacking. In this study, we identified 1755 lncRNAs (545 annotated lncRNAs and 1210 novel lncRNAs) from RNA-seq data in the pituitary gland of embryonic and adult sheep. A total of 235 lncRNAs were differentially expressed between embryonic and adult group. We verified the presence of some lncRNAs using RT-PCR and DNA sequencing, and identified some differentially expressed lncRNAs using qPCR. We also investigated the role of cis-acting lncRNAs on target genes. GO and KEGG enrichment analysis revealed that the target genes of lncRNAs were involved in the regulation of hormones secretion and some signaling pathways in the sheep pituitary gland. Our study provides comprehensive expression profiles of lncRNAs and valuable resource for understanding their function in the pituitary gland.
Collapse
Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China; College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Hazi Wureli
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Kadyken Rizabek
- Department of Food Engineering, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Makhatov Bolatkhan
- Department of Technology and Biological Resources, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Dzhunysov Askar
- Department of Technology and Biological Resources, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Kulmanova Gulzhan
- Department of Technology and Biological Resources, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
| |
Collapse
|
14
|
Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds. G3-GENES GENOMES GENETICS 2019; 9:1263-1276. [PMID: 30787031 PMCID: PMC6469412 DOI: 10.1534/g3.118.201014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.
Collapse
|
15
|
Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics 2018; 19:684. [PMID: 30227846 PMCID: PMC6145346 DOI: 10.1186/s12864-018-5037-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/27/2018] [Indexed: 03/08/2023] Open
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. Electronic supplementary material The online version of this article (10.1186/s12864-018-5037-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Colin Kern
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - James Chitwood
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ian Korf
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Mary Delany
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Hans Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, USA
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Catherine Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
| |
Collapse
|
16
|
Izadnia HR, Tahmoorespur M, Bakhtiarizadeh MR, Nassiri M, Esmaeilkhanien S. Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data. ITALIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1080/1828051x.2018.1507625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
| | - Mojtaba Tahmoorespur
- Faculty of Agriculture, Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammadreza Nassiri
- Faculty of Agriculture, Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | |
Collapse
|
17
|
Li Y, Fang C, Fu Y, Hu A, Li C, Zou C, Li X, Zhao S, Zhang C, Li C. A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing. DNA Res 2018; 25:421-437. [PMID: 29850846 PMCID: PMC6105124 DOI: 10.1093/dnares/dsy014] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/08/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the extend of epigenetic mechanisms have not been adequately addressed due to its limitation of uncertainties about the complete structure of mRNA. Here we combined single-molecule real-time sequencing, Illumina RNA-seq and DNA methylation data to characterize the landscapes of DNA methylation on AS, fusion isoforms formation and lncRNA feature and further to unveil the transcriptome complexity of pig. Our analysis identified an unprecedented scale of high-quality full-length isoforms with over 28,127 novel isoforms from 26,881 novel genes. More than 92,000 novel AS events were detected and intron retention predominated in AS model, followed by exon skipping. Interestingly, we found that DNA methylation played an important role in generating various AS isoforms by regulating splicing sites, promoter regions and first exons. Furthermore, we identified a large of fusion transcripts and novel lncRNAs, and found that DNA methylation of the promoter and gene body could regulate lncRNA expression. Our results significantly improved existed gene models of pig and unveiled that pig AS and epigenetic modify were more complex than previously thought.
Collapse
Affiliation(s)
- Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - An Hu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cencen Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
18
|
Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep. Biosci Rep 2018; 38:BSR20171350. [PMID: 29439142 PMCID: PMC5920141 DOI: 10.1042/bsr20171350] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
Reproductive ability, especially prolificacy, impacts sheep profitability. Hu sheep, a unique Chinese breed, is recognized for its high prolificacy (HP), early sexual maturity, and year-round estrus. However, little is known about the molecular mechanisms underlying HP in Hu sheep. To explore the potential mRNAs and long non-coding RNAs (lncRNAs) involved in Hu sheep prolificacy, we performed an ovarian genome-wide analysis of mRNAs and lncRNAs during the follicular stage using Hu sheep of HP (litter size = 3; three consecutive lambings) and low prolificacy (LP, litter size = 1; three consecutive lambings). Plasma luteinizing hormone (LH) concentration was higher in the HP group than in the LP group (P<0.05) during the follicular stage. Subsequently, 76 differentially expressed mRNAs (DE-mRNAs) and five differentially expressed lncRNAs (DE-lncRNAs) were identified by pairwise comparison; quantitative real-time PCR (qRT-PCR) analysis of ten randomly selected DE genes (mRNA and lncRNA) were consistent with the sequencing results. Gene Ontology (GO) analysis of DE-mRNAs revealed significant enrichment in immune response components, actin filament severing and phagocytosis. Pathway enrichment analysis of DE-mRNAs indicated a predominance of immune function pathways, including phagosomes, lysosomes, and antigen processing. We constructed a co-expression network of DE-mRNAs and mRNA-lncRNAs, with C1qA, CD53, cathepsin B (CTSB), CTSS, TYROBP, and AIF1 as the hub genes. Finally, the expression of lysosomal protease cathepsin genes, CTSB and cathepsin D (CTSD), were significantly up-regulated in sheep ovaries in the HP group compared with the LP group (P<0.05). These differential mRNAs and lncRNAs may provide information on the molecular mechanisms underlying sheep prolificacy.
Collapse
|
19
|
Bush SJ, Muriuki C, McCulloch MEB, Farquhar IL, Clark EL, Hume DA. Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. Genet Sel Evol 2018; 50:20. [PMID: 29690875 PMCID: PMC5926538 DOI: 10.1186/s12711-018-0391-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/13/2018] [Indexed: 02/06/2023] Open
Abstract
Background mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human. We then combined the novel lncRNAs with the sheep transcriptional atlas to identify co-regulated sets of protein-coding and non-coding loci. Results Few lncRNAs could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNAs that were assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNAs to identify a consensus set of ruminant lncRNAs and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. In sheep, 20 to 30% of lncRNAs were located close to protein-coding genes with which they are strongly co-expressed, which is consistent with the evolutionary origin of some ncRNAs in enhancer sequences. Nevertheless, most of the lncRNAs are not co-expressed with neighbouring protein-coding genes. Conclusions Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNAs in other species. Electronic supplementary material The online version of this article (10.1186/s12711-018-0391-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Stephen J Bush
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK. .,Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, OX3 9DU, UK.
| | - Charity Muriuki
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK
| | - Mary E B McCulloch
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK
| | - Iseabail L Farquhar
- Centre for Synthetic and Systems Biology, CH Waddington Building, Max Borne Crescent, King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK
| | - David A Hume
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK. .,Translational Research Institute, Mater Research-University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
| |
Collapse
|
20
|
Chao T, Ji Z, Hou L, Wang J, Zhang C, Wang G, Wang J. Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs. PeerJ 2018; 6:e4619. [PMID: 29666768 PMCID: PMC5899421 DOI: 10.7717/peerj.4619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/25/2018] [Indexed: 01/06/2023] Open
Abstract
As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA–mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep.
Collapse
Affiliation(s)
- Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Jin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Chunlan Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong, China
| |
Collapse
|
21
|
Abstract
Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar. A total of 15,040 lncRNA transcripts were identified among these samples. We found that the temporal expression pattern of lncRNAs was more restricted than observed for protein-coding genes. Time-series analysis showed two large modules for protein-coding genes and lncRNAs. The up-regulated module was enriched for genes related to immune and inflammatory function, while the down-regulated module was enriched for cell proliferation processes such as cell division and DNA replication. Co-expression networks indicated the functional relatedness between protein-coding genes and lncRNAs, which were enriched for similar functions over the series of time points examined. We identified numerous differentially expressed protein-coding genes and lncRNAs in all five developmental stages. Notably, ceruloplasmin precursor (CP), a protein-coding gene participating in antioxidant and iron transport processes, was differentially expressed in all stages. This study provides the first catalog of the developing pig spleen, and contributes to a fuller understanding of the molecular mechanisms underpinning mammalian spleen development.
Collapse
|
22
|
Li CY, Li X, Liu Z, Ni W, Zhang X, Hazi W, Ma Q, Zhang Y, Cao Y, Qi J, Yao Y, Feng L, Wang D, Hou X, Yu S, Liu L, Zhang M, Hu S. Identification and characterization of long non-coding RNA in prenatal and postnatal skeletal muscle of sheep. Genomics 2018; 111:133-141. [PMID: 29366530 DOI: 10.1016/j.ygeno.2018.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/14/2017] [Accepted: 01/15/2018] [Indexed: 11/28/2022]
Abstract
lncRNAs are a class of transcriptional RNA molecules of >200 nucleotides in length. However, the overall expression pattern and function of lncRNAs in sheep muscle is not clear. Here, we identified 1566 lncRNAs and 404 differentially expressed lncRNAs in sheep muscle from prenatal (110 days of fetus) and postnatal (2 to 3 years old of adult sheep) developmental stages by using RNA-seq technology. Several lncRNAs were identified by using RT-PCR and DNA sequencing. The expression levels of several lncRNAs were confirmed by qRT-PCR. We analyzed the effect of lncRNAs that act cis to the target genes. lncRNA targeting genes were involved in signaling pathways associated with growth and development of muscle by GO and KEGG enrichment analysis. Through our study, we provide a comprehensive expression profile of muscle lncRNAs in sheep, which provides valuable resources for further understanding genetic regulation of muscle growth and development from the perspective of lncRNA.
Collapse
Affiliation(s)
- Cun-Yuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Qiman Ma
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yunfeng Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jiangjiao Qi
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Lin Feng
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
| |
Collapse
|
23
|
Stark BC, Lanier MH, Cooper JA. CARMIL family proteins as multidomain regulators of actin-based motility. Mol Biol Cell 2017; 28:1713-1723. [PMID: 28663287 PMCID: PMC5491179 DOI: 10.1091/mbc.e17-01-0019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/20/2017] [Accepted: 04/27/2017] [Indexed: 12/23/2022] Open
Abstract
CARMILs are large multidomain proteins that regulate the actin-binding activity of capping protein (CP), a major capper of actin filament barbed ends in cells. CARMILs bind directly to CP and induce a conformational change that allosterically decreases but does not abolish its actin-capping activity. The CP-binding domain of CARMIL consists of the CP-interaction (CPI) and CARMIL-specific interaction (CSI) motifs, which are arranged in tandem. Many cellular functions of CARMILs require the interaction with CP; however, a more surprising result is that the cellular function of CP in cells appears to require binding to a CARMIL or another protein with a CPI motif, suggesting that CPI-motif proteins target CP and modulate its actin-capping activity. Vertebrates have three highly conserved genes and expressed isoforms of CARMIL with distinct and overlapping localizations and functions in cells. Various domains of these CARMIL isoforms interact with plasma membranes, vimentin intermediate filaments, SH3-containing class I myosins, the dual-GEF Trio, and other adaptors and signaling molecules. These biochemical properties suggest that CARMILs play a variety of membrane-associated functions related to actin assembly and signaling. CARMIL mutations and variants have been implicated in several human diseases. We focus on roles for CARMILs in signaling in addition to their function as regulators of CP and actin.
Collapse
Affiliation(s)
- Benjamin C Stark
- Department of Biochemistry and Molecular Biophysics and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110
| | - M Hunter Lanier
- Department of Biochemistry and Molecular Biophysics and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110
| | - John A Cooper
- Department of Biochemistry and Molecular Biophysics and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110
| |
Collapse
|
24
|
Ousati Ashtiani Z, Pourmand G, Salami SA, Ayati M, Tavakkoly-Bazzaz J. Dysregulated Expression of Long Intergenic Non-coding RNAs (LincRNAs) in Urothelial Bladder Carcinoma. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2017; 6:212-221. [PMID: 29988223 PMCID: PMC6004296 DOI: 10.22088/bums.6.4.212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/06/2017] [Indexed: 12/29/2022]
Abstract
Long intergenic non-coding RNA (lincRNA) has been introduced as key regulators of diverse biological processes, including transcription, chromatin organization, cell growth and tumorigenesis. With regard to the potential role of lincRNAs in cancer development, one may postulate that differential expression of lincRNAs could be employed as a tool in cancer diagnosis, prognosis, and targeted therapy. In this study, we aimed to explore the putative correlation between the expression levels of two lincRNAs: LINC00152 and LINC01082 in the bladder cancer (BC), in comparison with its adjacent non-cancerous tissue. Fifty Iranian subjects diagnosed with BC, representing in different stages and grades participated in this study The mRNA expression levels of the abovementioned lincRNAs were comparatively analyzed in cancerous and their adjacent non-cancerous counterpart tissues, of each subject by Real-Time PCR. The expression levels of LINC00152, and LINC01082 were significantly lower in tumor tissues in comparison with their adjacent normal tissues (P<0.001). More notably, in the case of LINC01082 the reduced expression was differentiated by the muscle invasiveness pattern of the tumor (P= 0.05). Our study presents a new finding about the tumor suppressor potentiality of these lincRNAs in BC development that in turn may suggest them as candidate biomarkers. Replicating this study in higher number of BC subjects, coupled with functional analysis, is necessary to investigate interconnections between these RNAs and cancer development, leading to better understanding of cancer biology.
Collapse
Affiliation(s)
- Zahra Ousati Ashtiani
- Urology Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Pourmand
- Urology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohsen Ayati
- Uro-Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Tavakkoly-Bazzaz
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
25
|
Wang YM, Xu HB, Wang MS, Otecko NO, Ye LQ, Wu DD, Zhang YP. Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication. BMC Evol Biol 2017; 17:192. [PMID: 28810830 PMCID: PMC5558714 DOI: 10.1186/s12862-017-1036-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Background Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. Results We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome. Our population genomic analysis indicates that 419 lincRNAs potentially evolved during artificial selection related to the domestication of chicken, while a comparative transcriptomic analysis identified 68 lincRNAs that were differentially expressed under different conditions. We also found 47 lincRNAs linked to special phenotypes. Conclusions Our study provides a comprehensive view of the genome-wide landscape of lincRNAs in chicken. This will promote a better understanding of the roles of lincRNAs in domestication, and the genetic mechanisms associated with the artificial selection of domestic animals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1036-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Bo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Newton Otieno Otecko
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling-Qun Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
26
|
Weikard R, Demasius W, Kuehn C. Mining long noncoding RNA in livestock. Anim Genet 2016; 48:3-18. [DOI: 10.1111/age.12493] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 02/01/2023]
Affiliation(s)
- R. Weikard
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - W. Demasius
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - C. Kuehn
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
- Faculty of Agricultural and Environmental Sciences; University Rostock; 18059 Rostock Germany
| |
Collapse
|
27
|
Zhan S, Dong Y, Zhao W, Guo J, Zhong T, Wang L, Li L, Zhang H. Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genomics 2016; 17:666. [PMID: 27550073 PMCID: PMC4994410 DOI: 10.1186/s12864-016-3009-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/10/2016] [Indexed: 01/23/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been studied extensively over the past few years. Large numbers of lncRNAs have been identified in mouse, rat, and human, and some of them have been shown to play important roles in muscle development and myogenesis. However, there are few reports on the characterization of lncRNAs covering all the development stages of skeletal muscle in livestock. Results RNA libraries constructed from developing longissimus dorsi muscle of fetal (45, 60, and 105 days of gestation) and postnatal (3 days after birth) goat (Capra hircus) were sequenced. A total of 1,034,049,894 clean reads were generated. Among them, 3981 lncRNA transcripts corresponding to 2739 lncRNA genes were identified, including 3515 intergenic lncRNAs and 466 anti-sense lncRNAs. Notably, in pairwise comparisons between the libraries of skeletal muscle at the different development stages, a total of 577 transcripts were differentially expressed (P < 0.05) which were validated by qPCR using randomly selected six lncRNA genes. The identified goat lncRNAs shared some characteristics, such as fewer exons and shorter length, with the lncRNAs in other mammals. We also found 1153 lncRNAs genes were neighbored 1455 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in transcriptional regulation and development-related processes, indicating they may be in cis-regulatory relationships. Additionally, Pearson’s correlation coefficients of co-expression levels suggested 1737 lncRNAs and 19,422 mRNAs were possibly in trans-regulatory relationships (r > 0.95 or r < −0.95). These co-expressed mRNAs were enriched in development-related biological processes such as muscle system processes, regulation of cell growth, muscle cell development, regulation of transcription, and embryonic morphogenesis. Conclusions This study provides a catalog of goat muscle-related lncRNAs, and will contribute to a fuller understanding of the molecular mechanism underpinning muscle development in mammals. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3009-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yao Dong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|