Long-read and short-read RNA-seq reveal the transcriptional regulation characteristics of PICK1 in Baoshan pig testis
Xia Zhang; Hailong Huo; Guowen Fu; Changyao Li; Wan Lin; Hongmei Dai; Xuemin Xi; Lan Zhai; Qingting Yuan; Guiying Zhao; Jinlong Huo
Abstract
Keywords
References
Cai L, Ye L, Hu X, He W, Zhuang D, Guo Q, Shu K, Jie Y. MicroRNA miR-330-3p suppresses the progression of ovarian cancer by targeting RIPK4. Bioengineered. 2021;12(1):440-9.
Cao M, Mao Z, Kam C, Xiao N, Cao X, Shen C, Cheng KK, Xu A, Lee KM, Jiang L, Xia J. PICK1 and ICA69 control insulin granule trafficking and their deficiencies lead to impaired glucose tolerance. PLoS Biol. 2013;11(4):e1001541.
Chang WL, Cui L, Gu Y, Li M, Ma Q, Zhang Z, Ye J, Zhang F, Yu J, Gui Y. TBC1D20 deficiency induces Sertoli cell apoptosis by triggering irreversible endoplasmic reticulum stress in mice. Mol Hum Reprod. 2019;25(12):773-86.
Chen J, Wang M, Guo M, Xie Y, Cong YS. miR-127 regulates cell proliferation and senescence by targeting BCL6. PLoS One. 2013;8(11):e80266.
Chu Y, Yao Y, Li X. MiR-370 enhances cell cycle and represses lipid accumulation in porcine adipocytes. Anim Biotechnol. 2021;32(3):334-42.
Cui L, Gu Y, Liu S, Li M, Ye J, Zhang F, Luo X, Chang WL, Gui Y. TBC1D20 is essential for mouse blood–testis barrier integrity through maintaining the epithelial phenotype and modulating the maturation of sertoli cells. Reprod Sci. 2020;27(7):1443-54.
Diao S, Huang S, Chen Z, Teng J, Ma Y, Yuan X, Chen Z, Zhang H, Li J, Zhang Z. Genome-wide signatures of selection detection in three South China indigenous pigs. Genes (Basel). 2019;10(5):346.
Dou Q, Tong H, Yang Y, Zhang H, Gan H. PICK1 deficiency exacerbates sepsis-associated acute kidney injury. BioMed Res Int. 2021;2021:9884297.
Erlendsson S, Madsen KL. Membrane binding and modulation of the PDZ domain of PICK1. Membranes (Basel). 2015;5(4):597-615.
Gao Y, Wang Y, Chen X, Peng Y, Chen F, He Y, Pang W, Yang G, Yu T. MiR‐127 attenuates adipogenesis by targeting MAPK4 and HOXC6 in porcine adipocytes. J Cell Physiol. 2019;234(12):21838-50.
Ge J, Zhu J, Xia B, Cao H, Peng Y, Li X, Yu T, Chu G, Yang G, Shi X. miR‐423‐5p inhibits myoblast proliferation and differentiation by targeting Sufu. J Cell Biochem. 2018;119(9):7610-20.
Gorospe M, Abdelmohsen K. MicroRegulators come of age in senescence. Trends Genet. 2011;27(6):233-41.
Guo B, Xiao C, Liu Y, Zhang N, Bai H, Yang T, Xiang Y, Nan Y, Li Q, Zhang W, Huang D. miR-744-5p inhibits multiple myeloma proliferation, epithelial mesenchymal transformation and glycolysis by targeting SOX12/Wnt/β-catenin signaling. OncoTargets Ther. 2021;14:1161-72.
Holst B, Madsen KL, Jansen AM, Jin C, Rickhag M, Lund VK, Jensen M, Bhatia V, Sørensen G, Madsen AN, Xue Z, Møller SK, Woldbye D, Qvortrup K, Huganir R, Stamou D, Kjærulff O, Gether U. PICK1 deficiency impairs secretory vesicle biogenesis and leads to growth retardation and decreased glucose tolerance. PLoS Biol. 2013;11(4):e1001542.
Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol. 2021;82(11):801-11.
Ikawa M, Inoue N, Benham AM, Okabe M. Fertilization: a sperm’s journey to and interaction with the oocyte. J Clin Invest. 2010;120(4):984-94.
Jin W, Ge WP, Xu J, Cao M, Peng L, Yung W, Liao D, Duan S, Zhang M, Xia J. Lipid binding regulates synaptic targeting of PICK1, AMPA receptor trafficking, and synaptic plasticity. J Neurosci. 2006;26(9):2380-90.
Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol. 2009;10(2):126-39.
Krishnan ML, Van Steenwinckel J, Schang AL, Yan J, Arnadottir J, Le Charpentier T, Csaba Z, Dournaud P, Cipriani S, Auvynet C, Titomanlio L, Pansiot J, Ball G, Boardman JP, Walley AJ, Saxena A, Mirza G, Fleiss B, Edwards AD, Petretto E, Gressens P. Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants. Nat Commun. 2017;8(1):428.
Li W, Wu X, Xiang D, Zhang W, Wu L, Meng X, Huo J, Yin Z, Fu G, Zhao G. Genome-wide detection for runs of homozygosity in Baoshan pigs using whole genome resequencing. Genes (Basel). 2024;15(2):233.
Liu G, Shi QW, Lu GX. A newly discovered mutation in PICK1 in a human with globozoospermia. Asian J Androl. 2010;12(4):556-60.
Lujambio A, Lowe SW. The microcosmos of cancer. Nature. 2012;482(7385):347-55.
Mo Y, Lou Y, Zhang A, Zhang J, Zhu C, Zheng B, Li D, Zhang M, Jin W, Zhang L, Wang J. PICK1 deficiency induces autophagy dysfunction via lysosomal impairment and amplifies sepsis-induced acute lung injury. Mediators Inflamm. 2018;2018:6757368.
Peter BJ, Kent HM, Mills IG, Vallis Y, Butler PJG, Evans PR, McMahon HT. BAR domains as sensors of membrane curvature: the amphiphysin BAR structure. Science. 2004;303(5657):495-9.
Rao X, Huang X, Zhou Z, Lin X. An improvement of the 2^ (–delta delta CT) method for quantitative real-time polymerase chain reaction data analysis. Biostat Bioinforma Biomath. 2013;3(3):71-85. PMid:25558171.
Rodríguez-Palmero A, Boerrigter MM, Gómez-Andrés D, Aldinger KA, Marcos-Alcalde Í, Popp B, Everman DB, Lovgren AK, Arpin S, Bahrambeigi V, Beunders G, Bisgaard AM, Bjerregaard VA, Bruel AL, Challman TD, Cogné B, Coubes C, de Man SA, Denommé-Pichon AS, Dye TJ, Elmslie F, Feuk L, García-Miñaúr S, Gertler T, Giorgio E, Gruchy N, Haack TB, Haldeman-Englert CR, Haukanes BI, Hoyer J, Hurst ACE, Isidor B, Soller MJ, Kushary S, Kvarnung M, Landau YE, Leppig KA, Lindstrand A, Kleinendorst L, MacKenzie A, Mandrile G, Mendelsohn BA, Moghadasi S, Morton JE, Moutton S, Müller AJ, O’Leary M, Pacio-Míguez M, Palomares-Bralo M, Parikh S, Pfundt R, Pode-Shakked B, Rauch A, Repnikova E, Revah-Politi A, Ross MJ, Ruivenkamp CAL, Sarrazin E, Savatt JM, Schlüter A, Schönewolf-Greulich B, Shad Z, Shaw-Smith C, Shieh JT, Shohat M, Spranger S, Thiese H, Mau-Them FT, van Bon B, van de Burgt I, van de Laar IMBH, van Drie E, van Haelst MM, van Ravenswaaij-Arts CM, Verdura E, Vitobello A, Waldmüller S, Whiting S, Zweier C, Prada CE, de Vries BBA, Dobyns WB, Reiter SF, Gómez-Puertas P, Pujol A, Tümer Z. DLG4-related synaptopathy: a new rare brain disorder. Genet Med. 2021;23(5):888-99.
Sheng M, Kim E. The postsynaptic organization of synapses. Cold Spring Harb Perspect Biol. 2011;3(12):a005678.
Shi T, Yan X, Qiao L, Li B, Cheng L, Pan Y, Jing J, Cao N, Liu W. MiR‐330‐5p negatively regulates ovine preadipocyte differentiation by targeting branched‐chain aminotransferase 2. Anim Sci J. 2018;89(6):858-67.
Shi XE, Li YF, Jia L, Ji HL, Song ZY, Cheng J, Wu GF, Song CC, Zhang QL, Zhu JY, Yang GS. MicroRNA-199a-5p affects porcine preadipocyte proliferation and differentiation. Int J Mol Sci. 2014;15(5):8526-38.
Sidjanin D, Park AK, Ronchetti A, Martins J, Jackson WT. TBC1D20 mediates autophagy as a key regulator of autophagosome maturation. Autophagy. 2016;12(10):1759-75.
Staudinger J, Zhou J, Burgess R, Elledge SJ, Olson EN. PICK1: a perinuclear binding protein and substrate for protein kinase C isolated by the yeast two-hybrid system. J Cell Biol. 1995;128(3):263-71.
Steinberg JP, Takamiya K, Shen Y, Xia J, Rubio ME, Yu S, Jin W, Thomas GM, Linden DJ, Huganir RL. Targeted in vivo mutations of the AMPA receptor subunit GluR2 and its interacting protein PICK1 eliminate cerebellar long-term depression. Neuron. 2006;49(6):845-60.
Wang K, Li W, Bai Y, Yang W, Ling Y, Fang M. ssc-miR-7134-3p regulates fat accumulation in castrated male pigs by targeting MARK4 gene. Int J Biol Sci. 2017;13(2):189-97.
Wang L, Lin F, Ren M, Liu X, Xie W, Zhang A, Qian M, Mo Y, Wang J, Lv Y. The PICK1/TLR4 complex on microglia is involved in the regulation of LPS-induced sepsis-associated encephalopathy. Int Immunopharmacol. 2021;100:108116.
Wang Y, Melton C, Li YP, Shenoy A, Zhang XX, Subramanyam D, Blelloch R. miR-294/miR-302 promotes proliferation, suppresses G1-S restriction point, and inhibits ESC differentiation through separable mechanisms. Cell Rep. 2013;4(1):99-109.
Xiao N, Kam C, Shen C, Jin W, Wang J, Lee KM, Jiang L, Xia J. PICK1 deficiency causes male infertility in mice by disrupting acrosome formation. J Clin Invest. 2009;119(4):802-12.
Xu J, Xia J. Structure and function of PICK1. Neurosignals. 2006;15(4):190-201.
Zhai L, Wu R, Han W, Zhang Y, Zhu D. miR-127 enhances myogenic cell differentiation by targeting S1PR3. Cell Death Dis. 2017;8(3):e2707.
Zhang R, Zuo Y, Cao S. Upregulated microRNA‐423‐5p promotes oxidative stress through targeting glutathione S‐transferase mu1 in asthenozoospermia. Mol Reprod Dev. 2021;88(2):158-66.
Zhang X, Han X, Tang Y, Wu Y, Qu B, Shen N. miR-744 enhances type I interferon signaling pathway by targeting PTP1B in primary human renal mesangial cells. Sci Rep. 2015;5(1):12987.
Submitted date:
04/16/2024
Accepted date:
07/04/2024
Facebook
Google+
Twitter
LinkedIn
Mendeley
StumbleUpon
CiteULike
Reddit
Email