Holway DA, Suarez AV. Animal behavior: an essential component of invasion biology. Trends Ecol Evol. 1999;14:328–30.
Article
CAS
PubMed
Google Scholar
Sutherland WJ. The importance of behavioural studies in conservation biology. Anim Behav. 1998;56:801–9.
Article
CAS
PubMed
Google Scholar
Vermeij GJ. When biotas meet: understanding biotic interchange. Science. 1991;253:1099–104.
Article
CAS
PubMed
Google Scholar
Wong BBM, Candolin U. Behavioral responses to changing environments. Behav Ecol. 2015;26:665–73.
Article
Google Scholar
Sapolsky RM, Romero LM, Munck AU. How do glucocorticoids influence stress responses? Integrating permissive, suppressive, stimulatory, and preparative actions. Endocr Rev. 2000;21:55–89.
CAS
PubMed
Google Scholar
Zhao C, Wang P, Si T, Hsu C-C, Wang L, Zayed O, Yu Z, Zhu Y, Dong J, Tao WA, Zhu J-K. MAP kinase cascades regulate the cold response by modulating ICE1 protein stability. Dev Cell. 2017;43:618–629.e5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Calisi RM, Austin SH, Lang AS, MacManes MD. Sex-biased transcriptomic response of the reproductive axis to stress. Horm Behav. 2018;100:56–68.
Article
PubMed
Google Scholar
Ohama N, Sato H, Shinozaki K, Yamaguchi-Shinozaki K. Transcriptional regulatory network of plant heat stress response. Trends Plant Sci. 2017;22:53–65.
Article
CAS
PubMed
Google Scholar
Smith CW, Patton JG, Nadal-Ginard B. Alternative splicing in the control of gene expression. Annu Rev Genet. 1989;23:527–77.
Article
CAS
PubMed
Google Scholar
Tapial J, Ha KCH, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, Quesnel-Vallières M, Permanyer J, Sodaei R, Marquez Y, Cozzuto L, Wang X, Gómez-Velázquez M, Rayon T, Manzanares M, Ponomarenko J, Blencowe BJ, Irimia M. An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Res. 2017;27:1759–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Izquierdo J-M, Valcárcel J. A simple principle to explain the evolution of pre-mRNA splicing. Genes Dev. 2006;20:1679–84.
Article
CAS
PubMed
Google Scholar
Gudlaugsdottir S, Boswell DR, Wood GR, Ma J. Exon size distribution and the origin of introns. Genetica. 2007;131:299–306.
Article
CAS
PubMed
Google Scholar
Krawczak M, Thomas NST, Hundrieser B, Mort M, Wittig M, Hampe J, Cooper DN. Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Hum Mutat. 2007;28:150–8.
Article
CAS
PubMed
Google Scholar
Sakharkar MK, Chow VTK, Kangueane P. Distributions of exons and introns in the human genome. In Silico Biol. 2004;4:387–93.
CAS
PubMed
Google Scholar
Birzele F, Csaba G, Zimmer R. Alternative splicing and protein structure evolution. Nucleic Acids Res. 2008;36:550–8.
Article
CAS
PubMed
Google Scholar
Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci. 2017;372. https://doi.org/10.1098/rstb.2015.0474.
Kim E, Magen A, Ast G. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res. 2007;35:125–31.
Article
CAS
PubMed
Google Scholar
Gueroussov S, Gonatopoulos-Pournatzis T, Irimia M, Raj B, Lin Z-Y, Gingras A-C, Blencowe BJ. An alternative splicing event amplifies evolutionary differences between vertebrates. Science. 2015;349:868–73.
Article
CAS
PubMed
Google Scholar
Tian B, Manley JL. Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol. 2017;18:18–30.
Article
CAS
PubMed
Google Scholar
Wang Y, Liu J, Huang BO, Xu Y-M, Li J, Huang L-F, Lin J, Zhang J, Min Q-H, Yang W-M, Wang X-Z. Mechanism of alternative splicing and its regulation. Biomed Rep. 2015;3:152–8.
Article
CAS
PubMed
Google Scholar
Wang Z, Burge CB. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA. 2008;14:802–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Xiao X, Van Nostrand E, Burge CB. General and specific functions of exonic splicing silencers in splicing control. Mol Cell. 2006;23:61–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Preußner M, Goldammer G, Neumann A, Haltenhof T, Rautenstrauch P, Müller-McNicoll M, Heyd F. Body temperature cycles control rhythmic alternative splicing in mammals. Mol Cell. 2017;67:433–446.e4.
Article
PubMed
CAS
Google Scholar
Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013;25:3640–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sun H. Deciphering alternative splicing and nonsense-mediated decay modulate expression in primary lymphoid tissues of birds infected with avian pathogenic E. coli (APEC). BMC Genet. 2017;18:21.
Article
PubMed
PubMed Central
CAS
Google Scholar
Laloum T, Martín G, Duque P. Alternative splicing control of abiotic stress responses. Trends Plant Sci. 2018;23:140–50.
Article
CAS
PubMed
Google Scholar
Nijholt I, Farchi N, Kye M, Sklan EH, Shoham S, Verbeure B, Owen D, Hochner B, Spiess J, Soreq H, Blank T. Stress-induced alternative splicing of acetylcholinesterase results in enhanced fear memory and long-term potentiation. Mol Psychiatry. 2004;9:174–83.
Article
CAS
PubMed
Google Scholar
Climente-Gonzalez H, Porta-Pardo E, Godzik A, Eyras E. The functional impact of alternative splicing in cancer. bioRxiv. 2017:076653. https://doi.org/10.1101/076653.
Chen J, Weiss WA. Alternative splicing in cancer: implications for biology and therapy. Oncogene. 2015;34:1–14.
Article
PubMed
CAS
Google Scholar
Siegfried Z, Karni R. The role of alternative splicing in cancer drug resistance. Curr Opin Genet Dev. 2018;48:16–21.
Article
CAS
PubMed
Google Scholar
Gibilisco L, Zhou Q, Mahajan S, Bachtrog D. Alternative splicing within and between Drosophila species, sexes, tissues, and developmental stages. PLoS Genet. 2016;12:e1006464.
Article
PubMed
PubMed Central
CAS
Google Scholar
McIntyre LM, Bono LM, Genissel A, Westerman R, Junk D, Telonis-Scott M, Harshman L, Wayne ML, Kopp A, Nuzhdin SV. Sex-specific expression of alternative transcripts in Drosophila. Genome Biol. 2006;7:R79.
Article
PubMed
PubMed Central
Google Scholar
Telonis-Scott M, Kopp A, Wayne ML, Nuzhdin SV, McIntyre LM. Sex-specific splicing in Drosophila: widespread occurrence, tissue specificity and evolutionary conservation. Genetics. 2009;181:421–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trabzuni D, Ramasamy A, Imran S, Walker R, Smith C, Weale ME, Hardy J, Ryten M, North American Brain Expression Consortium. Widespread sex differences in gene expression and splicing in the adult human brain. Nat Commun. 2013;4:2771.
Article
PubMed
CAS
Google Scholar
MacManes MD, Austin SH, Lang AS, Booth A, Farrar V, Calisi RM. Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis. Sci Rep. 2017;7:45125.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nozaki M. Hypothalamic-pituitary-gonadal endocrine system in the hagfish. Front Endocrinol. 2013;4:200.
Article
Google Scholar
Sower SA, Freamat M, Kavanaugh SI. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol. 2009;161:20–9.
Article
CAS
PubMed
Google Scholar
Geraghty AC, Kaufer D. Glucocorticoid Regulation of Reproduction. Adv Exp Med Biol. 2015;872:253–78.
Article
CAS
PubMed
Google Scholar
Johnson JE, Kalmar GB, Sohal PS, Walkey CJ, Yamashita S, Cornell RB. Comparison of the lipid regulation of yeast and rat CTP: phosphocholine cytidylyltransferase expressed in COS cells. Biochem J. 1992;285(Pt 3):815–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Toufexis D, Rivarola MA, Lara H, Viau V. Stress and the reproductive axis. J Neuroendocrinol. 2014;26:573–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ball GF, Silver R. Timing of incubation bouts by ring doves (Streptopelia risoria). J Comp Psychol. 1983;97:213–25.
Article
CAS
PubMed
Google Scholar
Buntin JD, Ruzycki E, Witebsky J. Prolactin receptors in dove brain: autoradiographic analysis of binding characteristics in discrete brain regions and accessibility to blood-borne prolactin. Neuroendocrinology. 1993;57:738–50.
Article
CAS
PubMed
Google Scholar
Lehrman DS. The physiological basis of parental feeding behavior in the ring dove (Streptopelia Risoria). Behaviour. 1955;7:241–85.
Article
Google Scholar
Darwin C. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. British Foreign Medico Chirurgical Rev. 1860;25:367–404.
Google Scholar
Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. eLife. 2016;5:e12115.
Article
PubMed
PubMed Central
Google Scholar
Gillespie MJ, Crowley TM, Haring VR, Wilson SL, Harper JA, Payne JS, Green D, Monaghan P, Stanley D, Donald JA, Nicholas KR, Moore RJ. Transcriptome analysis of pigeon milk production - role of cornification and triglyceride synthesis genes. BMC Genomics. 2013;14:169.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SCA, Stringham SA, Hu H, Willerslev E, Gilbert MTP, Yandell M, Zhang G, Wang J. Genomic diversity and evolution of the head crest in the rock pigeon. Science. 2013;339:1063–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chandran UR, DeFranco DB. Regulation of gonadotropin-releasing hormone gene transcription. Behav Brain Res. 1999;105:29–36.
Article
CAS
PubMed
Google Scholar
Cheng CK, Yeung CM, Hoo RLC, Chow BKC, Leung PCK. Oct-1 is involved in the transcriptional repression of the gonadotropin-releasing hormone receptor gene. Endocrinology. 2002;143:4693–701.
Article
CAS
PubMed
Google Scholar
Campbell BK, Dobson H, Scaramuzzi RJ. Ovarian function in ewes made hypogonadal with GnRH antagonist and stimulated with FSH in the presence or absence of low amplitude LH pulses. J Endocrinol. 1998;156:213–22.
Article
CAS
PubMed
Google Scholar
Pohl CR, Richardson DW, Hutchison JS, Germak JA, Knobil E. Hypophysiotropic signal frequency and the functioning of the pituitary-ovarian system in the rhesus monkey. Endocrinology. 1983;112:2076–80.
Article
CAS
PubMed
Google Scholar
Takahashi A, Kanda S, Abe T, Oka Y. Evolution of the hypothalamic-pituitary-gonadal Axis regulation in vertebrates revealed by knockout Medaka. Endocrinology. 2016;157:3994–4002.
Article
CAS
PubMed
Google Scholar
Jin J-M, Yang W-X. Molecular regulation of hypothalamus-pituitary-gonads axis in males. Gene. 2014;551:15–25.
Article
CAS
PubMed
Google Scholar
Rosen H, Jameel ML, Barkan AL. Dexamethasone suppresses gonadotropin-releasing hormone (GnRH) secretion and has direct pituitary effects in male rats: differential regulation of GnRH receptor and gonadotropin responses to GnRH. Endocrinology. 1988;122:2873–80.
Article
CAS
PubMed
Google Scholar
Schneider F, Tomek W, Gründker C. Gonadotropin-releasing hormone (GnRH) and its natural analogues: a review. Theriogenology. 2006;66:691–709.
Article
CAS
PubMed
Google Scholar
Nellore A, Paziana K, Ma C, Tsygankova OM, Wang Y, Puttaswamy K, Iqbal AU, Franks SR, Lv Y, Troxel AB, Feldman MD, Meinkoth JL, Brose MS. Loss of Rap1GAP in papillary thyroid cancer. J Clin Endocrinol Metab. 2009;94:1026–32.
Article
CAS
PubMed
Google Scholar
Katagiri K, Hattori M, Minato N, Kinashi T. Rap1 functions as a key regulator of T-cell and antigen-presenting cell interactions and modulates T-cell responses. Mol Cell Biol. 2002;22:1001–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
González-Tajuelo R, Silván J, Pérez-Frías A, de la Fuente-Fernández M, Tejedor R, Espartero-Santos M, Vicente-Rabaneda E, Juarranz Á, Muñoz-Calleja C, Castañeda S, Gamallo C, Urzainqui A. P-Selectin preserves immune tolerance in mice and is reduced in human cutaneous lupus. Sci Rep. 2017;7:41841.
Article
PubMed
PubMed Central
CAS
Google Scholar
Matsumoto M, Miyasaka M, Hirata T. P-selectin glycoprotein ligand-1 negatively regulates T-cell immune responses. J Immunol. 2009;183:7204–11.
Article
CAS
PubMed
Google Scholar
Ariazi EA, Cunliffe HE, Lewis-Wambi JS, Slifker MJ, Willis AL, Ramos P, Tapia C, Kim HR, Yerrum S, Sharma CGN, Nicolas E, Balagurunathan Y, Ross EA, Jordan VC. Estrogen induces apoptosis in estrogen deprivation-resistant breast cancer through stress responses as identified by global gene expression across time. Proc Natl Acad Sci U S A. 2011;108:18879–86.
Article
PubMed
PubMed Central
Google Scholar
Acevedo-Rodriguez A, Kauffman AS, Cherrington BD, Borges CS, Roepke TA, Laconi M. Emerging insights into hypothalamic-pituitary-gonadal axis regulation and interaction with stress signalling. J Neuroendocrinol. 2018;30:e12590.
Article
CAS
PubMed
PubMed Central
Google Scholar
Handa RJ, Burgess LH, Kerr JE, O’Keefe JA. Gonadal steroid hormone receptors and sex differences in the hypothalamo-pituitary-adrenal axis. Horm Behav. 1994;28:464–76.
Article
CAS
PubMed
Google Scholar
Chinery R, Brockman JA, Dransfield DT, Coffey RJ. Antioxidant-induced nuclear translocation of CCAAT/enhancer-binding protein β: a critical role for protein kinase a-mediated phosphorylation of Ser299. J Biol Chem. 1997;272:30356–61.
Article
CAS
PubMed
Google Scholar
Pless O, Kowenz-Leutz E, Knoblich M, Lausen J, Beyermann M, Walsh MJ, Leutz A. G9a-mediated lysine methylation alters the function of CCAAT/enhancer-binding protein-beta. J Biol Chem. 2008;283:26357–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller AL, Bement WM. Regulation of cytokinesis by rho GTPase flux. Nat Cell Biol. 2009;11:71–7.
Article
CAS
PubMed
Google Scholar
Moon SY, Zheng Y. Rho GTPase-activating proteins in cell regulation. Trends Cell Biol. 2003;13:13–22.
Article
CAS
PubMed
Google Scholar
Godoy J, Nishimura M, Webster NJG. Gonadotropin-releasing hormone induces miR-132 and miR-212 to regulate cellular morphology and migration in immortalized LbetaT2 pituitary gonadotrope cells. Mol Endocrinol. 2011;25:810–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Naor Z, Benard O, Seger R. Activation of MAPK cascades by G-protein-coupled receptors: the case of gonadotropin-releasing hormone receptor. Trends Endocrinol Metab. 2000;11:91–9.
Article
CAS
PubMed
Google Scholar
Gerhardt C, Lier JM, Burmühl S, Struchtrup A, Deutschmann K, Vetter M, Leu T, Reeg S, Grune T, Rüther U. The transition zone protein Rpgrip1l regulates proteasomal activity at the primary cilium. J Cell Biol. 2015;210:115–33.
Article
CAS
PubMed
Google Scholar
Tokue S-I, Sasaki M, Nakahata N. Thromboxane A2-induced signal transduction is negatively regulated by KIAA1005 that directly interacts with thromboxane A2 receptor. Prostaglandins Other Lipid Mediat. 2009;89:8–15.
Article
CAS
PubMed
Google Scholar
Struchtrup A, Wiegering A, Stork B, Rüther U, Gerhardt C. The ciliary protein RPGRIP1L governs autophagy independently of its proteasome-regulating function at the ciliary base in mouse embryonic fibroblasts. Autophagy. 2018;14:567–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Michael Romero L, Wingfield JC. Tempests, poxes, predators, and people: stress in wild animals and how they cope. United Kingdom: Oxford University Press; 2015.
Clarke AS, Wittwer DJ, Abbott DH, Schneider ML. Long-term effects of prenatal stress on HPA axis activity in juvenile rhesus monkeys. Dev Psychobiol. 1994;27:257–69.
Article
CAS
PubMed
Google Scholar
Gutierrez-Triana JA, Herget U, Lichtner P, Castillo-Ramírez LA, Ryu S. A vertebrate-conserved cis-regulatory module for targeted expression in the main hypothalamic regulatory region for the stress response. BMC Dev Biol. 2014;14:41.
PubMed
PubMed Central
Google Scholar
Leonard BE. The HPA and immune axes in stress: the involvement of the serotonergic system. Eur Psychiatry. 2005;20:S302–6.
Article
PubMed
Google Scholar
Taniuchi S, Miyake M, Tsugawa K, Oyadomari M, Oyadomari S. Integrated stress response of vertebrates is regulated by four eIF2α kinases. Sci Rep. 2016;6:32886.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsigos C, Chrousos GP. Hypothalamic–pituitary–adrenal axis, neuroendocrine factors and stress. J Psychosom Res. 2002;53:865–71.
Article
PubMed
Google Scholar
Helmreich DL, Parfitt DB, Lu X-Y, Akil H, Watson SJ. Relation between the hypothalamic-pituitary-thyroid (HPT) axis and the hypothalamic-pituitary-adrenal (HPA) axis during repeated stress. Neuroendocrinology. 2005;81:183–92.
Article
CAS
PubMed
Google Scholar
Herman JP, Ostrander MM, Mueller NK, Figueiredo H. Limbic system mechanisms of stress regulation: hypothalamo-pituitary-adrenocortical axis. Prog Neuro Psychopharmacol Biol Psychiatry. 2005;29:1201–13.
Article
CAS
Google Scholar
Romero-Ramírez L, Nieto-Sampedro M, Barreda-Manso MA. Integrated stress response as a therapeutic target for CNS injuries. Biomed Res Int. 2017;2017:6953156.
Article
PubMed
PubMed Central
CAS
Google Scholar
Arnold AP, Itoh Y. Factors causing sex differences in birds. Avian Biol Res. 2011;4. https://doi.org/10.3184/175815511X13070045977959.
Bundy JL, Vied C, Nowakowski RS. Sex differences in the molecular signature of the developing mouse hippocampus. BMC Genomics. 2017;18:237.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lee SK. Sex as an important biological variable in biomedical research. BMB Rep. 2018;51:167–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ngun TC, Ghahramani N, Sánchez FJ, Bocklandt S, Vilain E. The genetics of sex differences in brain and behavior. Front Neuroendocrinol. 2011;32:227–46.
Article
PubMed
Google Scholar
Goldstein DS. Adrenal responses to stress. Cell Mol Neurobiol. 2010;30:1433–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nicolaides NC, Kyratzi E, Lamprokostopoulou A, Chrousos GP, Charmandari E. Stress, the stress system and the role of glucocorticoids. Neuroimmunomodulation. 2015;22:6–19.
Article
CAS
PubMed
Google Scholar
Smulders TV. The avian hippocampal formation and the stress response. Brain Behav Evol. 2017;90:81–91.
Article
PubMed
Google Scholar
Wendelaar Bonga SE. The stress response in fish. Physiol Rev. 1997;77:591–625.
Article
CAS
PubMed
Google Scholar
Dhabhar FS. Effects of stress on immune function: the good, the bad, and the beautiful. Immunol Res. 2014;58:193–210.
Article
CAS
PubMed
Google Scholar
Hara MR, Kovacs JJ, Whalen EJ, Rajagopal S, Strachan RT, Grant W, Towers AJ, Williams B, Lam CM, Xiao K, Shenoy SK, Gregory SG, Ahn S, Duckett DR, Lefkowitz RJ. A stress response pathway regulates DNA damage through β2-adrenoreceptors and β-arrestin-1. Nature. 2011;477:349–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koralewski TE, Krutovsky KV. Evolution of exon-intron structure and alternative splicing. PLoS One. 2011;6:e18055.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol. 2009;10:741–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rodrigues R, Grosso AR, Moita L. Genome-wide analysis of alternative splicing during dendritic cell response to a bacterial challenge. PLoS One. 2013;8:e61975.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yabas M, Elliott H, Hoyne GF. The role of alternative splicing in the control of immune homeostasis and cellular differentiation. Int J Mol Sci. 2015;17. https://doi.org/10.3390/ijms17010003.
Ge Y, Porse BT. The functional consequences of intron retention: alternative splicing coupled to NMD as a regulator of gene expression. Bioessays. 2014;36:236–43.
Article
CAS
PubMed
Google Scholar
Jacob AG, Smith CWJ. Intron retention as a component of regulated gene expression programs. Hum Genet. 2017;136:1043–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song S, Huang Q, Guo J, Li-Ling J, Chen X, Ma F. Comparative component analysis of exons with different splicing frequencies. PLoS One. 2009;4:e5387.
Article
PubMed
PubMed Central
CAS
Google Scholar
Black DL. Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell. 2000;103:367–70.
Article
CAS
PubMed
Google Scholar
Mittendorf KF, Deatherage CL, Ohi MD, Sanders CR. Tailoring of membrane proteins by alternative splicing of pre-mRNA. Biochemistry. 2012;51:5541–56.
Article
CAS
PubMed
Google Scholar
Álvarez D, Voß B, Maass D, Wüst F, Schaub P, Beyer P, Welsch R. Carotenogenesis is regulated by 5’UTR-mediated translation of Phytoene synthase splice variants. Plant Physiol. 2016;172:2314–26.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kramer M, Sponholz C, Slaba M, Wissuwa B, Claus RA, Menzel U, Huse K, Platzer M, Bauer M. Alternative 5′ untranslated regions are involved in expression regulation of human heme oxygenase-1. PLoS One. 2013;8:e77224.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ohta S, Nakagawara S, Hirai S, Miyagishima K, Horiguchi G, Kodama H. The 5′ UTR intron-mediated enhancement of constitutive splicing of the tobacco microsome ω-3 fatty acid desaturase gene. Plant Biotechnol Rep. 2018;12:105–14.
Article
Google Scholar
Canadell D, García-Martínez J, Alepuz P, Pérez-Ortín JE, Ariño J. Impact of high pH stress on yeast gene expression: a comprehensive analysis of mRNA turnover during stress responses. Biochim Biophys Acta. 2015;1849:653–64.
Article
CAS
PubMed
Google Scholar
Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008;18:188–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song L, Florea L. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. GigaScience. 2015;4:48.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sterne-Weiler T, Weatheritt RJ, Best A, Ha KCH, Blencowe BJ. Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity. bioRxiv. 2017:158519. https://doi.org/10.1101/158519.
Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, von Lindern M, Carmo-Fonseca M. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res. 2008;36:4823–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pineda JMB, Bradley RK. Most human introns are recognized via multiple and tissue-specific branchpoints. Genes Dev. 2018;32:577–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium, Engelhardt BE, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res. 2017;27:1843–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD. PANTHER version 11: expanded annotation data from gene ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res. 2017;45:D183–9.
Article
CAS
PubMed
Google Scholar
The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 2019;47:D330–8.
Article
CAS
Google Scholar
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44:D279–85.
Article
CAS
PubMed
Google Scholar