Editing Xenopus (section)

=== Investigation of fundamental biological processes ===

[[Signal transduction]]:  ''Xenopus'' embryos and cell-free extracts are widely used for basic research in signal transduction.  In just the last few years, ''Xenopus'' embryos have provided crucial insights into the mechanisms of TGF-beta and Wnt signal transduction.  For example, ''Xenopus'' embryos were used to identify the enzymes that control ubiquitination of Smad4,<ref>{{cite journal | vauthors = Dupont S, Mamidi A, Cordenonsi M, Montagner M, Zacchigna L, Adorno M, Martello G, Stinchfield MJ, Soligo S, Morsut L, Inui M, Moro S, Modena N, Argenton F, Newfeld SJ, Piccolo S | display-authors = 6 | title = FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination | journal = Cell | volume = 136 | issue = 1 | pages = 123–135 | date = January 2009 | pmid = 19135894 | doi = 10.1016/j.cell.2008.10.051 | s2cid = 16458957 | doi-access = free }}</ref> and to demonstrate direct links between TGF-beta superfamily signaling pathways and other important networks, such as the MAP kinase pathway<ref>{{cite journal | vauthors = Cordenonsi M, Montagner M, Adorno M, Zacchigna L, Martello G, Mamidi A, Soligo S, Dupont S, Piccolo S | display-authors = 6 | title = Integration of TGF-beta and Ras/MAPK signaling through p53 phosphorylation | journal = Science | volume = 315 | issue = 5813 | pages = 840–843 | date = February 2007 | pmid = 17234915 | doi = 10.1126/science.1135961 | s2cid = 83962686 | bibcode = 2007Sci...315..840C | doi-access = free }}</ref> and the Wnt pathway.<ref>{{cite journal | vauthors = Fuentealba LC, Eivers E, Ikeda A, Hurtado C, Kuroda H, Pera EM, De Robertis EM | title = Integrating patterning signals: Wnt/GSK3 regulates the duration of the BMP/Smad1 signal | journal = Cell | volume = 131 | issue = 5 | pages = 980–993 | date = November 2007 | pmid = 18045539 | pmc = 2200633 | doi = 10.1016/j.cell.2007.09.027 }}</ref>  Moreover, new methods using egg extracts revealed novel, important targets of the Wnt/GSK3 destruction complex.<ref>{{cite journal | vauthors = Kim NG, Xu C, Gumbiner BM | title = Identification of targets of the Wnt pathway destruction complex in addition to beta-catenin | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 13 | pages = 5165–5170 | date = March 2009 | pmid = 19289839 | pmc = 2663984 | doi = 10.1073/pnas.0810185106 | doi-access = free | bibcode = 2009PNAS..106.5165K }}</ref>

[[Cell division]]:  ''Xenopus'' egg extracts have allowed the study of many complicated cellular events ''in vitro''.  Because egg cytosol can support successive cycling between mitosis and interphase ''in vitro'', it has been critical to diverse studies of cell division.  For example, the small GTPase Ran was first found to regulate interphase nuclear transport, but ''Xenopus'' egg extracts revealed the critical role of Ran GTPase in mitosis independent of its role in interphase nuclear transport.<ref>{{cite journal | vauthors = Kaláb P, Pralle A, Isacoff EY, Heald R, Weis K | title = Analysis of a RanGTP-regulated gradient in mitotic somatic cells | journal = Nature | volume = 440 | issue = 7084 | pages = 697–701 | date = March 2006 | pmid = 16572176 | doi = 10.1038/nature04589 | s2cid = 4398374 | bibcode = 2006Natur.440..697K }}</ref> Similarly, the cell-free extracts were used to model nuclear envelope assembly from chromatin, revealing the function of RanGTPase in regulating nuclear envelope reassembly after mitosis.<ref>{{cite journal | vauthors = Tsai MY, Wang S, Heidinger JM, Shumaker DK, Adam SA, Goldman RD, Zheng Y | title = A mitotic lamin B matrix induced by RanGTP required for spindle assembly | journal = Science | volume = 311 | issue = 5769 | pages = 1887–1893 | date = March 2006 | pmid = 16543417 | doi = 10.1126/science.1122771 | s2cid = 12219529 | bibcode = 2006Sci...311.1887T }}</ref>  More recently, using ''Xenopus'' egg extracts, it was possible to demonstrate the mitosis-specific function of the nuclear lamin B in regulating spindle morphogenesis<ref>{{cite journal | vauthors = Ma L, Tsai MY, Wang S, Lu B, Chen R, Yates JR, Zhu X, Zheng Y | display-authors = 6 | title = Requirement for Nudel and dynein for assembly of the lamin B spindle matrix | journal = Nature Cell Biology | volume = 11 | issue = 3 | pages = 247–256 | date = March 2009 | pmid = 19198602 | pmc = 2699591 | doi = 10.1038/ncb1832 }}</ref> and to identify new proteins that mediate kinetochore attachment to microtubules.<ref>{{cite journal | vauthors = Emanuele MJ, Stukenberg PT | title = Xenopus Cep57 is a novel kinetochore component involved in microtubule attachment | journal = Cell | volume = 130 | issue = 5 | pages = 893–905 | date = September 2007 | pmid = 17803911 | doi = 10.1016/j.cell.2007.07.023 | s2cid = 17520550 | doi-access = free }}</ref> [[Cell-free system]]s have recently become practical investigatory tools, and ''Xenopus'' oocytes are often the source of the extracts used. This has produced significant results in understanding [[mitotic]] oscillation and [[microtubule]]s.<ref name="Noireaux-Liu-2020">{{cite journal | vauthors = Noireaux V, Liu AP | title = The New Age of Cell-Free Biology | journal = Annual Review of Biomedical Engineering | volume = 22 | issue = 1 | pages = 51–77 | date = June 2020 | pmid = 32151150 | doi = 10.1146/annurev-bioeng-092019-111110 | publisher = [[Annual Reviews (publisher)|Annual Reviews]] | s2cid = 212652742 | doi-access = free }}</ref>

[[Embryonic development]]:  ''Xenopus'' embryos are widely used in developmental biology. A summary of recent advances made by ''Xenopus'' research in recent years would include:

#[[Epigenetics]] of cell fate specification<ref>{{cite journal | vauthors = Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Veenstra GJ | title = A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos | journal = Developmental Cell | volume = 17 | issue = 3 | pages = 425–434 | date = September 2009 | pmid = 19758566 | pmc = 2746918 | doi = 10.1016/j.devcel.2009.08.005 }}</ref> and epigenome reference maps<ref>{{cite journal | vauthors = Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ | title = Embryonic transcription is controlled by maternally defined chromatin state | journal = Nature Communications | volume = 6 | pages = 10148 | date = December 2015 | pmid = 26679111 | pmc = 4703837 | doi = 10.1038/ncomms10148 | bibcode = 2015NatCo...610148H }}</ref>
#[[microRNA]] in germ layer patterning and eye development<ref>{{cite journal | vauthors = Walker JC, Harland RM | title = microRNA-24a is required to repress apoptosis in the developing neural retina | journal = Genes & Development | volume = 23 | issue = 9 | pages = 1046–1051 | date = May 2009 | pmid = 19372388 | pmc = 2682950 | doi = 10.1101/gad.1777709 }}</ref><ref>{{cite journal | vauthors = Rosa A, Spagnoli FM, Brivanlou AH | title = The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection | journal = Developmental Cell | volume = 16 | issue = 4 | pages = 517–527 | date = April 2009 | pmid = 19386261 | doi = 10.1016/j.devcel.2009.02.007 | doi-access = free }}</ref>
#Link between [[Wnt signaling]] and [[telomerase]]<ref>{{cite journal | vauthors = Park JI, Venteicher AS, Hong JY, Choi J, Jun S, Shkreli M, Chang W, Meng Z, Cheung P, Ji H, McLaughlin M, Veenstra TD, Nusse R, McCrea PD, Artandi SE | display-authors = 6 | title = Telomerase modulates Wnt signalling by association with target gene chromatin | journal = Nature | volume = 460 | issue = 7251 | pages = 66–72 | date = July 2009 | pmid = 19571879 | pmc = 4349391 | doi = 10.1038/nature08137 | bibcode = 2009Natur.460...66P }}</ref>
#Development of the [[vasculature]]<ref>{{cite journal | vauthors = De Val S, Chi NC, Meadows SM, Minovitsky S, Anderson JP, Harris IS, Ehlers ML, Agarwal P, Visel A, Xu SM, Pennacchio LA, Dubchak I, Krieg PA, Stainier DY, Black BL | display-authors = 6 | title = Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors | journal = Cell | volume = 135 | issue = 6 | pages = 1053–1064 | date = December 2008 | pmid = 19070576 | pmc = 2782666 | doi = 10.1016/j.cell.2008.10.049 }}</ref>
#Gut morphogenesis<ref>{{cite journal | vauthors = Li Y, Rankin SA, Sinner D, Kenny AP, Krieg PA, Zorn AM | title = Sfrp5 coordinates foregut specification and morphogenesis by antagonizing both canonical and noncanonical Wnt11 signaling | journal = Genes & Development | volume = 22 | issue = 21 | pages = 3050–3063 | date = November 2008 | pmid = 18981481 | pmc = 2577796 | doi = 10.1101/gad.1687308 }}</ref>
#Contact inhibition and [[neural crest]] cell migration<ref>{{cite journal | vauthors = Carmona-Fontaine C, Matthews HK, Kuriyama S, Moreno M, Dunn GA, Parsons M, Stern CD, Mayor R | display-authors = 6 | title = Contact inhibition of locomotion in vivo controls neural crest directional migration | journal = Nature | volume = 456 | issue = 7224 | pages = 957–961 | date = December 2008 | pmid = 19078960 | pmc = 2635562 | doi = 10.1038/nature07441 | bibcode = 2008Natur.456..957C }}</ref> and the generation of neural crest from pluripotent blastula cells<ref>{{cite journal | vauthors = Buitrago-Delgado E, Nordin K, Rao A, Geary L, LaBonne C | title = NEURODEVELOPMENT. Shared regulatory programs suggest retention of blastula-stage potential in neural crest cells | journal = Science | volume = 348 | issue = 6241 | pages = 1332–1335 | date = June 2015 | pmid = 25931449 | pmc = 4652794 | doi = 10.1126/science.aaa3655 }}</ref>
#{{visible anchor|Developmental fate}} - Role of ''[[Notch signaling pathway|Notch]]'': Dorsky et al 1995 elucidated a pattern of expression followed by downregulation<ref name="Gaiano-Fishell-2002">{{cite journal | vauthors = Gaiano N, Fishell G | title = The role of notch in promoting glial and neural stem cell fates | journal = Annual Review of Neuroscience | volume = 25 | issue = 1 | pages = 471–490 | year = 2002 | pmid = 12052917 | doi = 10.1146/annurev.neuro.25.030702.130823 | publisher = [[Annual Reviews (publisher)|Annual Reviews]] | s2cid = 15691580 }}</ref>

[[DNA replication]]:  ''Xenopus'' cell-free extracts also support the synchronous assembly and the activation of origins of DNA replication. They have been instrumental in characterizing the biochemical function of the prereplicative complex, including MCM proteins.<ref>{{cite journal | vauthors = Tsuji T, Lau E, Chiang GG, Jiang W | title = The role of Dbf4/Drf1-dependent kinase Cdc7 in DNA-damage checkpoint control | journal = Molecular Cell | volume = 32 | issue = 6 | pages = 862–869 | date = December 2008 | pmid = 19111665 | pmc = 4556649 | doi = 10.1016/j.molcel.2008.12.005 }}</ref><ref>{{cite journal | vauthors = Xu X, Rochette PJ, Feyissa EA, Su TV, Liu Y | title = MCM10 mediates RECQ4 association with MCM2-7 helicase complex during DNA replication | journal = The EMBO Journal | volume = 28 | issue = 19 | pages = 3005–3014 | date = October 2009 | pmid = 19696745 | pmc = 2760112 | doi = 10.1038/emboj.2009.235 }}</ref>

[[DNA damage]] response: Cell-free extracts have been instrumental to unravel the signaling pathways activated in response to DNA double-strand breaks (ATM), replication fork stalling (ATR) or DNA interstrand crosslinks (FA proteins and ATR). Notably, several mechanisms and components of these signal transduction pathways were first identified in ''Xenopus''.<ref name="Checkpoint signaling from a single"/><ref>{{cite journal | vauthors = Räschle M, Knipscheer P, Knipsheer P, Enoiu M, Angelov T, Sun J, Griffith JD, Ellenberger TE, Schärer OD, Walter JC | display-authors = 6 | title = Mechanism of replication-coupled DNA interstrand crosslink repair | journal = Cell | volume = 134 | issue = 6 | pages = 969–980 | date = September 2008 | pmid = 18805090 | pmc = 2748255 | doi = 10.1016/j.cell.2008.08.030 | author-link9 = Orlando D. Schärer }}</ref><ref>{{cite journal | vauthors = MacDougall CA, Byun TS, Van C, Yee MC, Cimprich KA | title = The structural determinants of checkpoint activation | journal = Genes & Development | volume = 21 | issue = 8 | pages = 898–903 | date = April 2007 | pmid = 17437996 | pmc = 1847708 | doi = 10.1101/gad.1522607 }}</ref>

[[Apoptosis]]:  ''Xenopus'' oocytes provide a tractable model for biochemical studies of apoptosis.  Recently, oocytes were used recently to study the biochemical mechanisms of caspase-2 activation;  importantly, this mechanism turns out to be conserved in mammals.<ref>{{cite journal | vauthors = Nutt LK, Buchakjian MR, Gan E, Darbandi R, Yoon SY, Wu JQ, Miyamoto YJ, Gibbons JA, Gibbon JA, Andersen JL, Freel CD, Tang W, He C, Kurokawa M, Wang Y, Margolis SS, Fissore RA, Kornbluth S | display-authors = 6 | title = Metabolic control of oocyte apoptosis mediated by 14-3-3zeta-regulated dephosphorylation of caspase-2 | journal = Developmental Cell | volume = 16 | issue = 6 | pages = 856–866 | date = June 2009 | pmid = 19531356 | pmc = 2698816 | doi = 10.1016/j.devcel.2009.04.005 }}</ref>

[[Regenerative medicine]]:  In recent years, tremendous interest in developmental biology has been stoked by the promise of regenerative medicine.  ''Xenopus'' has played a role here, as well.  For example,  expression of seven transcription factors in pluripotent ''Xenopus'' cells rendered those cells able to develop into functional eyes when implanted into ''Xenopus'' embryos, providing potential insights into the repair of retinal degeneration or damage.<ref>{{cite journal | vauthors = Viczian AS, Solessio EC, Lyou Y, Zuber ME | title = Generation of functional eyes from pluripotent cells | journal = PLOS Biology | volume = 7 | issue = 8 | pages = e1000174 | date = August 2009 | pmid = 19688031 | pmc = 2716519 | doi = 10.1371/journal.pbio.1000174 | doi-access = free }}</ref>  In a vastly different study, ''Xenopus'' embryos was used to study the effects of tissue tension on morphogenesis,<ref>{{cite journal | vauthors = Dzamba BJ, Jakab KR, Marsden M, Schwartz MA, DeSimone DW | title = Cadherin adhesion, tissue tension, and noncanonical Wnt signaling regulate fibronectin matrix organization | journal = Developmental Cell | volume = 16 | issue = 3 | pages = 421–432 | date = March 2009 | pmid = 19289087 | pmc = 2682918 | doi = 10.1016/j.devcel.2009.01.008 }}</ref> an issue that will be critical for ''in vitro'' tissue engineering. ''Xenopus'' species are important model organisms for the study of spinal cord regeneration, because while capable of regeneration in their larval stages, ''Xenopus'' lose this capacity in early metamorphosis.<ref>{{cite journal | vauthors = Beattie MS, Bresnahan JC, Lopate G | title = Metamorphosis alters the response to spinal cord transection in Xenopus laevis frogs | journal = Journal of Neurobiology | volume = 21 | issue = 7 | pages = 1108–1122 | date = October 1990 | pmid = 2258724 | doi = 10.1002/neu.480210714 }}</ref>

[[Physiology]]:  The directional beating of multiciliated cells is essential to development and homeostasis in the central nervous system, the airway, and the oviduct.  The multiciliated cells of the ''Xenopus'' epidermis have recently been developed as the first ''in vivo'' test-bed for live-cell studies of such ciliated tissues, and these studies have provided important insights into the biomechanical and molecular control of directional beating.<ref>{{cite journal | vauthors = Park TJ, Mitchell BJ, Abitua PB, Kintner C, Wallingford JB | title = Dishevelled controls apical docking and planar polarization of basal bodies in ciliated epithelial cells | journal = Nature Genetics | volume = 40 | issue = 7 | pages = 871–879 | date = July 2008 | pmid = 18552847 | pmc = 2771675 | doi = 10.1038/ng.104 }}</ref><ref>{{cite journal | vauthors = Mitchell B, Jacobs R, Li J, Chien S, Kintner C | title = A positive feedback mechanism governs the polarity and motion of motile cilia | journal = Nature | volume = 447 | issue = 7140 | pages = 97–101 | date = May 2007 | pmid = 17450123 | doi = 10.1038/nature05771 | s2cid = 4415593 | bibcode = 2007Natur.447...97M }}</ref>

[[Actin]]: Another result from cell-free ''Xenopus'' oocyte extracts has been improved understanding of actin.<ref name="Noireaux-Liu-2020" />