Research Progress on the Biological Function of lncRNA and Its Role in Regulating Residual Feed Intake in Cattle (Bos taurus)
MING Wen-Xuan1, ZHAO Zhi-Yan1,2, KANG Xiao-Long1,*
1 School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; 2 Yinchuan City Animal Husbandry Technology Extension Service Center, Yinchuan 750000, China
Abstract:Long non-coding RNA (lncRNA) is an important epigenetic regulator affecting gene expression and cell function, and its expression pattern is tissue-specific. The biological roles of lncRNA have been widely verified in many diseases and biological phenotypes. Feed intake is one of the main factors affecting the economic benefits of livestock. A large number of studies have focused on the effects of nutrition and immune factors on feed intake of livestock, but its genetic analysis and functional research are still slow. In order to explore the biological role of lncRNA in the regulation of feeding behavior and residual feed intake (RFI) in cattle (Bos taurus), the molecular characteristics and main regulatory functions of lncRNA were summarized in this paper. In addition, the biological roles of lncRNA in regulating RFI variation were summarized from important tissues (hypothalamic-pituitary-adrenal cortex axis, liver, skeletal muscle, and brain-gut axis) that affected the phenotype changes of feed intake in cattle. This review provides a basis for subsequent studies to reveal the phenotypic regulation of RFI by lncRNA from a cellular function perspective, and provides reference for efficient production and breed improvement of cattle.
明文轩, 赵志艳, 康晓龙. lncRNA生物学作用及其调控牛剩余采食量的研究进展[J]. 农业生物技术学报, 2023, 31(10): 2200-2208.
MING Wen-Xuan, ZHAO Zhi-Yan, KANG Xiao-Long. Research Progress on the Biological Function of lncRNA and Its Role in Regulating Residual Feed Intake in Cattle (Bos taurus). 农业生物技术学报, 2023, 31(10): 2200-2208.
[1] 刘志宇, 曹安, 蒋林树, 等. 2018. 长链非编码RNA(lncRNA)生物学功能及其调控机制[J]. 农业生物技术学报, 26(08):1419-1430. (Liu Z Y, Cao A, Jiang L S, et al.2018. Biological function and regulatory mechanism of long non-coding RNA (lncRNA)[J]. Journal of Agricultural Biotechnology, 26(08): 1419-1430.) [2] 朱运昌, 闪欣悦, 王豪靖, 等. 2022. 皮南牛与南阳牛脂肪组织差异表达lncRNA筛选及其调控网络构建[J]. 农业生物技术学报, 30(10): 1913-1925. (Zhu Y C, Shan X Y, Wang H J, et al.2022. Screening of differentially expressed lncRNA in adipose tissues of Pinan and Nanyang cattle (Bos taurus) and construction of regulatory networks[J]. Journal of Agricultural Biotechnology, 30(10): 1913-1925.) [3] Abo-Ismail M K, Lansink N, Akanno E, et al.2018. Development and validation of a small SNP panel for feed efficiency in beef cattle[J]. Journal of Animal Science, 96(2): 375-397. [4] Alexandre P A, Reverter A, Berezin R B, et al.2020. Exploring the regulatory potential of long non-coding RNA in feed efficiency of indicine cattle[J]. Genes (Basel), 11(9): 997. [5] Alvarez R C, Ansell B R, Hall R S, et al.2015. Transcriptional analysis identifies key genes involved in metabolism, fibrosis/tissue repair and the immune response against Fasciola hepatica in sheep liver[J]. Parasites & Vectors, 8(1): 1-14. [6] Baldassini W A, Ramsey J J, Branco R H, et al.2018. Estimated heat production, blood parameters and mitochondrial DNA copy number of Nellore bulls (Bos indicus) with high and low residual feed intake[J]. Livestock Science, 217: 140-147. [7] Billerey C, Boussaha M, Esquerre D, et al.2014. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing[J]. BMC Genomics, 15(1): 1-10. [8] Cajigas I, Leib D E, Cochrane J, et al.2015. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling[J]. Development, 142(15): 2641-2652. [9] Cantalapiedra-Hijar G, Abo-Ismail M, Carstens G E, et al.2018. Biological determinants of between-animal variation in feed efficiency of growing beef cattle[J]. Animal, 12(s2): s321-s335. [10] Castro B F, Paulino P V, Sanches A C, et al.2007. Growth, carcass quality, and protein and energy metabolism in beef cattle with different growth potentials and residual feed intakes[J]. Journal of Animal Science, 85(4): 928-936. [11] Chen G, Guo H, Song Y, et al.2016. Long noncoding RNA AK055347 is upregulated in patients with atrial fibrillation and regulates mitochondrial energy production in myocardiocytes[J]. Molecular Medicine Reports, 14(6): 5311-5317. [12] Chen Y, Wang Q, Gao W, et al.2021. Changes and correlations of the intestinal flora and liver metabolite profiles in mice with gallstones[J]. Frontiers in Physiology, 12: 716654. [13] Consolo N, Silva J D, Buarque V, et al.2020. Selection for growth and precocity alters muscle metabolism in Nellore cattle[J]. Metabolites, 10(2): 58. [14] Denton C, Price A, Friend J, et al.2018. Role of the gut-liver axis in driving parenteral nutrition-associated injury[J]. Children, 5(10): 136. [15] DiGiacomo K, Norris E, Dunshea F R, et al.2018. Responses of dairy cows with divergent residual feed intake as calves to metabolic challenges during midlactation and the nonlactating period[J]. Journal of Dairy Science, 101(7): 6474-6485. [16] Dimitrova N, Zamudio J R, Jong R M, et al.2014. LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint.[J]. Molecular Cell, 54(5): 777-790. [17] Dorji J, MacLeod I M, Chamberlain A J, et al.2021. Mitochondrial protein gene expression and the oxidative phosphorylation pathway associated with feed efficiency and energy balance in dairy cattle[J]. Journal of Dairy Science, 104(1): 575-587. [18] Engreitz J M, Haines J E, Perez E M, et al.2016. Local regulation of gene expression by lncRNA promoters, transcription and splicing[J]. Nature, 539(7629): 452-455. [19] Esfandyari H, Jensen J.2021. Simultaneous Bayesian estimation of genetic parameters for curves of weight, feed intake, and residual feed intake in beef cattle[J]. Journal of Animal Science, 99(9): b231. [20] Freetly H C, Kuehn L A, Thallman R M, et al.2020. Heritability and genetic correlations of feed intake, body weight gain, residual gain, and residual feed intake of beef cattle as heifers and cows[J]. Journal of Animal Science, 98(1): skz394. [21] Gil N, Ulitsky I.2020. Regulation of gene expression by cis-acting long non-coding RNAs[J]. Nature Reviews Genetics, 21(2): 102-117. [22] Han Y, Zhao Q, Tang C, et al.2020. Butyrate mitigates weanling piglets from lipopolysaccharide-induced colitis by regulating microbiota and energy metabolism of the gut-liver axis[J]. Frontiers in Microbiology, 11: 588666. [23] Higgins M G, Fitzsimons C, McClure M C, et al.2018. GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle[J]. Scientific Reports, 8(1): 1-12. [24] Hou X, Pu L, Wang L, et al.2020. Transcriptome analysis of skeletal muscle in pigs with divergent residual feed intake phenotypes[J]. DNA and Cell Biology, 39(3): 404-416. [25] Huang W, Long N, Khatib H.2012. Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data[J]. Animal Genetics, 43(6): 674-682. [26] Ibeagha-Awemu E M, Do D N, Dudemaine P-L, et al.2018. Integration of lncRNA and mRNA transcriptome analyses reveals genes and pathways potentially involved in calf intestinal growth and development during the early weeks of life[J]. Genes, 9(3): 142. [27] Kelly A K, Waters S M, McGee M, et al.2011. mRNA expression of genes regulating oxidative phosphorylation in the muscle of beef cattle divergently ranked on residual feed intake[J]. Physiological Genomics, 43(1): 12-23. [28] Kong L, Liu G, Deng M, et al.2020. Growth retardation-responsive analysis of mRNAs and long noncoding RNAs in the liver tissue of Leiqiong cattle[J]. Scientific Reports, 10(1): 1-12. [29] Kopp F, Mendell J T.2018. Functional classification and experimental dissection of long noncoding RNAs[J]. Cell, 172(3): 393-407. [30] Kosinska-Selbi B, Mielczarek M, Szyda J.2020. Long non-coding RNA in livestock[J]. Animal, 14(10): 2003-2013. [31] Koufariotis L T, Chen Y P, Chamberlain A, et al.2015. A catalogue of novel bovine long noncoding RNA across 18 tissues[J]. PLOS ONE, 10(10): e0141225. [32] Lam S, Miglior F, Fonseca P, et al.2021. Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing[J]. Journal of Dairy Science, 104(2): 1928-1950. [33] Li T, Wang S, Wu R, et al.2012. Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing[J]. Genomics, 99(5): 292-298. [34] Liang Y, Yu B, Wang Y, et al.2018. Jejunal long noncoding RNAs are associated with glycemic control via gut-brain axis after bariatric surgery in diabetic mice.[J]. Surgery for Obesity and Related Diseases, 14(6): 821-832. [35] Liu Y, Liu C, Wu H, et al.2022. Small intestine microbiome and metabolome of high and low residual feed intake Angus heifers[J]. Frontiers in Microbiology, 13: 862151. [36] Long J, Badal S S, Ye Z, et al.2016. Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy[J]. Journal of Clinical Investigation, 126(11): 4205-4218. [37] Lopes D R G, de Souza Duarte M, La Reau A J, et al.2021. Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers[J]. Journal of Animal Science and Biotechnology, 12(1): 1-17. [38] Lu Y, Vandehaar M J, Spurlock D M, et al.2018. Genome-wide association analyses based on a multiple-trait approach for modeling feed efficiency[J]. Journal of Dairy Science, 101(4): 3140-3154. [39] Ma L, Bajic V B, Zhang Z.2013. On the classification of long non-coding RNAs[J]. RNA Biology, 10(6): 924-933. [40] Man H J, Marsden P A.2019. LncRNAs and epigenetic regulation of vascular endothelium: Genome positioning system and regulators of chromatin modifiers[J]. Current Opinion in Pharmacology, 45: 72-80. [41] Marchese F P, Raimondi I, Huarte M.2017. The multidimensional mechanisms of long noncoding RNA function[J]. Genome Biology, 18: 1-13. [42] Martín-Mateos R, Albillos A.2021. The role of the gut-liver axis in metabolic dysfunction-associated fatty liver disease[J]. Frontiers in Immunology, 12: 660179. [43] McHugh C A, Chen C, Chow A, et al.2015. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3[J]. Nature, 521(7551): 232-236. [44] McKenna C, Porter R K, Keogh K A, et al.2018. Residual feed intake phenotype and gender affect the expression of key genes of the lipogenesis pathway in subcutaneous adipose tissue of beef cattle[J]. Journal of Animal Science and Biotechnology, 9(1): 1-10. [45] Mohammad T M, Hossein F, Zohreh R.2019. Interaction of long noncoding RNA MEG3 with miRNAs: A reciprocal regulation[J]. Journal of Cellular Biochemistry, 120(3): 3339-3352. [46] Mormede P, Terenina E.2012. Molecular genetics of the adrenocortical axis and breeding for robustness[J]. Domestic Animal Endocrinology, 43(2): 116-131. [47] Mukiibi R, Vinsky M, Keogh K, et al.2019. Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes[J]. Journal of Animal Science, 97(11): 4386-4404. [48] Neary N M, Goldstone A P, Bloom S R.2004. Appetite regulation: From the gut to the hypothalamus[J]. Clinical Endocrinology, 60(2): 153-160. [49] Nolte W, Weikard R, Brunner R M, et al.2019. Biological network approach for the identification of regulatory long non-coding RNAs associated with metabolic efficiency in cattle[J]. Frontiers in Genetics, 10: 1130. [50] Nolte W, Weikard R, Brunner R M, et al.2020. Identification and annotation of potential function of regulatory antisense long non-coding RNAs related to feed efficiency in Bos taurus bulls[J]. International Journal of Molecular Sciences, 21(9): 3292. [51] Perkins S D, Key C N, Garrett C F, et al.2014a. Residual feed intake studies in Angus-sired cattle reveal a potential role for hypothalamic gene expression in regulating feed efficiency[J]. Journal of Animal Science, 92(2): 549-560. [52] Perkins S D, Key C N, Marvin M N, et al.2014b. Effect of residual feed intake on hypothalamic gene expression and meat quality in Angus-sired cattle grown during the hot season[J]. Journal of Animal Science, 92(4): 1451-1461. [53] Place R F, Noonan E J.2014. Non-coding RNAs turn up the heat: An emerging layer of novel regulators in the mammalian heat shock response[J]. Cell Stress Chaperones, 19(2): 159-172. [54] Quinn J J, Chang H Y.2016. Unique features of long non-coding RNA biogenesis and function[J]. Nature Reviews Genetics, 17(1): 47-62. [55] Romijn J A, Corssmit E P, Havekes L M, et al.2008. Gut-brain axis[J]. Current Opinion in Clinical Nutrition & Metabolic Care, 11(4): 518-521. [56] Santana M H, Utsunomiya Y T, Neves H H, et al.2014. Genome-wide association analysis of feed intake and residual feed intake in Nellore cattle[J]. BMC Genetics, 15(1): 1-8. [57] Schweer K R, Kachman S D, Kuehn L A, et al.2018. Genome-wide association study for feed efficiency traits using SNP and haplotype models[J]. Journal of Animal Science, 96(6): 2086-2098. [58] Sharifabadi H R, Zamiri M J, Rowghani E, et al.2012. Relationship between the activity of mitochondrial respiratory chain complexes and feed efficiency in fat-tailed Ghezel lambs[J]. Journal of Animal Science, 90(6): 1807-1815. [59] Silvestris D A, Scopa C, Hanchi S, et al.2020. De novo A-to-I RNA editing discovery in lncRNA[J]. Cancers, 12(10): 2959. [60] Sun T T, He J, Liang Q, et al.2016. LncRNA GClnc1 promotes gastric carcinogenesis and may act as a modular scaffold of WDR5 and KAT2A complexes to specify the histone modification patternRNA GClnc1 modifies histone complex[J]. Cancer discovery, 6(7): 784-801. [61] Tizioto P C, Coutinho L L, Decker J E, et al.2015. Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes[J]. BMC Genomics, 16(1): 1-14. [62] Tizioto P C, Coutinho L L, Oliveira P S, et al.2016. Gene expression differences in longissimus muscle of Nelore steers genetically divergent for residual feed intake[J]. Scientific Reports, 6(1): 39493. [63] Tripathi V, Ellis J D, Shen Z, et al.2010. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation[J]. Molecular Cell, 39(6): 925-938. [64] Trujillo A I, Casal A, Penagaricano F, et al.2013. Association of SNP of neuropeptide Y, leptin, and IGF-1 genes with residual feed intake in confinement and under grazing condition in Angus cattle[J]. Journal of Animal Science, 91(9): 4235-4244. [65] Vikram R P, Cristian C T, Peng H, et al.2016. Unlinking an lncRNA from its associated cis element[J]. Molecular Cell, 62(1): 104-110. [66] Weikard R, Hadlich F, Hammon H M, et al.2018. Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets[J]. Oncotarget, 9(30): 21052. [67] Weikard R, Hadlich F, Kuehn C.2013. Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing[J]. BMC Genomics, 14(1): 1-15. [68] Widmann P, Reverter A, Fortes M R, et al.2013. A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle[J]. BMC Genomics, 14(1): 1-17. [69] Xu X, Wang K, Zha X.2019. An antisense lncRNA functions in alternative splicing of Bmdsx in the silkworm, Bombyx mori[J]. Biochemical and Biophysical Research Communications, 516(3): 639-644. [70] Xue M, Chen W, Xiang A, et al.2017. Hypoxic exosomes facilitate bladder tumor growth and development through transferring long non-coding RNA-UCA1[J]. Molecular Cancer, 16: 1-13. [71] Yang C, Han L, Li P, et al.2021. Characterization and duodenal transcriptome analysis of chinese beef cattle with divergent feed efficiency using RNA-seq[J]. Frontiers in Genetics, 12: 741878. [72] Zhan S, Dong Y, Zhao W, et al.2016. Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat[J]. BMC Genomics, 17(1): 1-10. [73] Zhang D Y, Zhang X X, Li G Z, et al.2021. Transcriptome analysis of long noncoding RNAs ribonucleic acids from the livers of Hu sheep with different residual feed intake[J]. Animal, 15(2): 100098. [74] Zhou J, Yang L, Zhong T, et al.2015. H19 lncRNA alters DNA methylation genome wide by regulating S-adenosylhomocysteine hydrolase[J]. Nature Communications, 6(1): 10221. [75] Zhou Y, Connor E E, Wiggans G R, et al.2018. Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle[J]. BMC Genomics, 19(1): 1-9. [76] Zou C, Li J, Luo W, et al.2017. Transcriptome analysis reveals long intergenic non-coding RNAs involved in skeletal muscle growth and development in pig[J]. Scientific Reports, 7(1): 8704.