627
Views
0
CrossRef citations to date
0
Altmetric
Articles

KRAB family is involved in network shifts in response to osmotic stress in camels

, , , , , & show all
Pages 348-357 | Received 12 Apr 2022, Accepted 31 Oct 2022, Published online: 11 Nov 2022

Reference

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403–410.
  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. Nat Genet. 25:25–29.
  • Audic S, Claverie JM. 1997. The significance of digital gene expression profiles. Genome Res. 7:986–995.
  • Bellefroid EJ, Marine JC, Matera AG, Bourguignon C, Desai T, Healy KC, Bray-Ward P, Martial JA, Ihle JN, Ward DC. 1995. Emergence of the ZNF91 Krüppel-associated box-containing zinc finger gene family in the last common ancestor of anthropoidea. Proc Natl Acad Sci USA. 92:10757–10761.
  • Boggess SF, Aspinall D, Paleg LG. 1976. Stress metabolism. IX. The significance of end-product inhibition of proline biosynthesis and of compartmentation in relation to stress-induced proline accumulation. Aust J Plant Physiol. 3:513–525.
  • Bolen DW. 2001. Protein stabilization by naturally occurring osmolytes. Methods Mol Biol. 168:17–36.
  • Brocker C, Thompson DC, Vasiliou V. 2012. The role of hyperosmotic stress in inflammation and disease. Biomol Concepts. 3:345–364.
  • Brooke SM, McLaughlin JR, Cortopassi KM, Sapolsky RM. 2002. Effect of GP120 on glutathione peroxidase activity in cortical cultures and the interaction with steroid hormones. J Neurochem. 81:277–284.
  • Dandekar AM, Uratsu L. 1988. A single base pair change in proline biosynthesis genes causes osmotic stress tolerance. J Bacteriol. 170:5943–5945.
  • Dmitrieva NI, Burg MB. 2007. Osmotic stress and DNA damage. Methods Enzymol. 428:241–252.
  • Dufourc EJ. 2008. Sterols and membrane dynamics. J Chem Biol. 1:63–77.
  • Dupont S, Beney L, Ferreira T, Gervais P. 2011. Nature of sterols affects plasma membrane behavior and yeast survival during dehydration. Biochim Biophys Acta. 1808:1520–1528.
  • Erickson G, Guilak F. 2000. Osmotic stress initiates intracellular calcium waves in chondrocytes through extracellular influx, the inositol phosphate and a G-protein mediated pathway. Trans Orthop Res Soc. 25:0923.
  • Hamilton AT, Huntley S, Kim J, Branscomb E, Stubbs I. 2003. Lineage-specific expansion of KRAB zinc-finger transcription factor genes: implications for the evolution of vertebrate regulatory networks. Cold Spring Harb Symp Quant Biol. 68:131–140.
  • Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Shan Y, Kim J, Gordon L, Branscomb E, Stubbs L. 2006. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 16:669–677.
  • Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. 2014. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature. 516:242–245.
  • Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27–30.
  • Koga K, Kenessey A, Powell SR, Sison CP, Miller EJ, Ojamaa K. 2011. Macrophage migration inhibitory factor provides cardioprotection during ischemia/reperfusion by reducing oxidative stress. Antioxid Redox Signal. 14:1191–1202.
  • Kültz D. 2005. DNA damage signals facilitate osmotic stress adaptation. Am J Physiol Renal Physiol. 289(3):F504–F505.
  • Kültz D, Chakravarty D. 2001. Hyperosmolality in the form of elevated NaCl but not urea causes DNA damage in murine kidney cells. Proc Natl Acad Sci USA. 98:1999–2004.
  • Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 9:559.
  • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
  • Li RQ, Yu C, Li YR, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 25:1966–1967.
  • Looman C, Abrink M, Mark C, Hellman L. 2002. KRAB zinc finger proteins: an analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution. Mol Biol Evol. 19:2118–2130.
  • Lukic S, Nicolas JC, Levine AJ. 2014. The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses. Cell Death Differ. 21:381–387.
  • Matthews CC, Feldman EL. 1996. Insulin-like growth factor I rescues SH-SY5Y human neuroblastoma cells from hyperosmotic induced programmed cell death. J Cell Physiol. 166:323–331.
  • Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L, Wingett SW, Andrews S, Grey W, Ewels PA, et al. 2015. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet. 47:598–606.
  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 5:621–628.
  • Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Ally Y, Albu M, Weirauch MT, Radovani E, Kim PM, et al. 2015. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol. 33:555–562.
  • Neuhofer W. 2010. Role of NFAT5 in inflammatory disorders associated with osmotic stress. Curr Genomics. 11:584–590.
  • Pan Z, Wang Z, Yang H, Zhang F, Reinach PS. 2011. Trpv1 activation Is required for hypertonicity-stimulated inflammatory cytokine release in human corneal epithelial cells. Invest Ophthalmol Vis Sci. 52:485–493.
  • Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genet. 2:e190.
  • Resch A, Xing Y, Modrek B, Gorlick M, Riley R, Lee C. 2004. Assessing the impact of alternative splicing on domain interactions in the human proteome. J Proteome Res. 3:76–83.
  • Roberson MS, Zhang T, Li HL, Mulvaney JM. 1999. Activation of the p38 mitogen-activated protein kinase pathway by gonadotropin-releasing hormone. Endocrinology. 140:1310–1318.
  • Rosati M, Franze A, Matarazzo MR, Grimaldi G. 1999. Coding region intron/exon organization, alternative splicing, and X-chromosome inactivation of the KRAB/FPB-domain-containing human zinc finger gene ZNF41. Cytogenet Cell Genet. 85:291–296.
  • Schilli R, Breuer RI, Klein F, Dunn K, Gnaedinger A, Bernstein J, Paige M, Kaufman M. 1982. Comparison of the composition of faecal fluid in Crohn’s disease and ulcerative colitis. Gut. 23:326–332.
  • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 25:1105–1111.
  • van der Houven van Oordt W, Diaz-Meco MT, Lozano J, Krainer AR, Moscat J, Cáceres JF. 2000. The Mkk3/6-p38–signaling cascade alters the subcellular distribution of hnrnp A1 and modulates alternative splicing regulation. J Cell Biol. 149:307–316.
  • Vernia P, Gnaedinger A, Hauck W, Breuer RI. 1988. Organic anions and the diarrhea of inflammatory bowel disease. Digest Dis Sci. 33:1353–1358.
  • Wu HG, Guang XM, Al-Fageeh MB, Cao JW, Pan SK, Zhou HM, Zhang L, Abutarboush MH, Xing YP, Xie ZY, et al. 2015. Erratum: Camelid genomes reveal evolution and adaptation to desert environments. Nat Commun. 6:6107.
  • Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, Liu JY. 2013. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature. 500:593–597.
  • Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, et al. 2010. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 20:646–654.