Automated and customizable quantitative image analysis of whole Caenorhabditis elegans germlines.

Szczegóły
Abstrakt

Tytuł:: Automated and customizable quantitative image analysis of whole Caenorhabditis elegans germlines.
Autorzy:: Toraason E; Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Adler VL; Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Kurhanewicz NA; Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
DiNardo A; Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Saunders AM; Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Cahoon CK; Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Libuda DE; Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Źródło:: Genetics [Genetics] 2021 Mar 31; Vol. 217 (3).
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Austin, Tex. [etc.]
MeSH Terms:: Germ Cells/*metabolism
Gonads/*cytology
Image Processing, Computer-Assisted/*methods
Animals ; Caenorhabditis elegans ; Caenorhabditis elegans Proteins/metabolism ; DNA Breaks, Double-Stranded ; DNA-Binding Proteins/metabolism ; Germ Cells/cytology ; Gonads/metabolism ; Meiosis ; Microscopy, Fluorescence/methods ; Rad51 Recombinase/metabolism
References:: Cell. 2012 Mar 30;149(1):75-87. (PMID: 22464324)
PLoS Genet. 2009 Aug;5(8):e1000611. (PMID: 19696886)
Genetics. 2019 Oct;213(2):395-409. (PMID: 31431470)
PLoS Genet. 2008 Oct;4(10):e1000235. (PMID: 18949042)
Genes Dev. 2002 Sep 15;16(18):2428-42. (PMID: 12231631)
WormBook. 2005 Sep 01;:1-4. (PMID: 18050415)
Genetics. 2014 Sep;198(1):193-207. (PMID: 25053665)
Genetics. 2000 Oct;156(2):617-30. (PMID: 11014811)
PLoS Biol. 2012;10(8):e1001378. (PMID: 22927794)
PLoS Genet. 2012;8(8):e1002880. (PMID: 22912597)
Genetics. 2019 Dec;213(4):1145-1188. (PMID: 31796552)
Genetics. 2016 Nov;204(3):999-1013. (PMID: 27605052)
Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12805-10. (PMID: 21768382)
Genes Dev. 2001 Jul 1;15(13):1674-87. (PMID: 11445542)
Chromosoma. 2011 Feb;120(1):1-21. (PMID: 21052706)
Cell. 2018 Jun 14;173(7):1678-1691.e16. (PMID: 29754818)
PLoS Genet. 2013;9(8):e1003674. (PMID: 23950729)
Dev Dyn. 2000 May;218(1):2-22. (PMID: 10822256)
Mol Cell Biol. 2004 Sep;24(18):7998-8006. (PMID: 15340062)
PLoS Genet. 2010 Jul 22;6(7):e1001028. (PMID: 20661436)
Elife. 2016 Oct 05;5:. (PMID: 27705743)
Bioinformatics. 2009 Jun 1;25(11):1463-5. (PMID: 19346324)
Chromosome Res. 2007;15(5):607-21. (PMID: 17674149)
Cell. 2009 Oct 2;139(1):73-86. (PMID: 19781752)
Mol Biol Cell. 2019 Jul 1;30(14):1757-1769. (PMID: 31067147)
Dev Cell. 2003 Sep;5(3):463-74. (PMID: 12967565)
Mol Cell. 2018 May 17;70(4):639-649.e6. (PMID: 29775580)
Genetics. 2020 Oct;216(2):359-379. (PMID: 32796008)
Chromosoma. 2019 Sep;128(3):199-214. (PMID: 30826870)
Nat Struct Mol Biol. 2019 Mar;26(3):220-226. (PMID: 30833787)
Cell. 1998 Sep 4;94(5):635-45. (PMID: 9741628)
Nature. 2013 Oct 31;502(7473):703-6. (PMID: 24107990)
Nature. 2018 May;557(7707):679-683. (PMID: 29769721)
Elife. 2016 Feb 27;5:e12039. (PMID: 26920220)
Genes Dev. 2008 Oct 15;22(20):2886-901. (PMID: 18923085)
Dev Biol. 2007 Aug 1;308(1):206-21. (PMID: 17599823)
WormBook. 2017 May 4;2017:1-43. (PMID: 26694509)
Genes Dev. 2009 Aug 1;23(15):1763-78. (PMID: 19574299)
Science. 2011 Dec 2;334(6060):1286-9. (PMID: 22144627)
J Mol Biol. 2018 Nov 2;430(23):4702-4710. (PMID: 30096346)
Mol Gen Genet. 1998 Nov;260(2-3):289-94. (PMID: 9862483)
PLoS Genet. 2013;9(8):e1003679. (PMID: 23990794)
G3 (Bethesda). 2020 Oct 5;10(10):3719-3728. (PMID: 32763952)
Proc Natl Acad Sci U S A. 1982 Mar;79(5):1558-62. (PMID: 7041123)
Dev Cell. 2019 Sep 23;50(6):716-728.e6. (PMID: 31402283)
Grant Information:: F32 GM130006 United States GM NIGMS NIH HHS; P40 OD010440 United States OD NIH HHS; R35 GM128890 United States GM NIGMS NIH HHS; T32 GM007413 United States GM NIGMS NIH HHS
Contributed Indexing:: Keywords: C. elegans; DNA repair; P granules; germ cells; germline; gonad; image analysis; meiosis; microscopy; worms
Substance Nomenclature:: 0 (COSA-1 protein, C elegans)
0 (Caenorhabditis elegans Proteins)
0 (DNA-Binding Proteins)
0 (MSH-5 protein, C elegans)
EC 2.7.7.- (Rad51 Recombinase)
EC 2.7.7.- (rad-51 protein, C elegans)
Entry Date(s):: Date Created: 20210327 Date Completed: 20210901 Latest Revision: 20240211
Update Code:: 20240211
PubMed Central ID:: PMC8045727
DOI:: 10.1093/genetics/iyab010
PMID:: 33772283
: Czasopismo naukowe

Arranged in a spatial-temporal gradient for germ cell development, the adult germline of Caenorhabditis elegans is an excellent system for understanding the generation, differentiation, function, and maintenance of germ cells. Imaging whole C. elegans germlines along the distal-proximal axis enables powerful cytological analyses of germ cell nuclei as they progress from the pre-meiotic tip through all the stages of meiotic prophase I. To enable high-content image analysis of whole C. elegans gonads, we developed a custom algorithm and pipelines to function with image processing software that enables: (1) quantification of cytological features at single nucleus resolution from immunofluorescence images; and (2) assessment of these individual nuclei based on their position within the germline. We show the capability of our quantitative image analysis approach by analyzing multiple cytological features of meiotic nuclei in whole C. elegans germlines. First, we quantify double-strand DNA breaks (DSBs) per nucleus by analyzing DNA-associated foci of the recombinase RAD-51 at single-nucleus resolution in the context of whole germline progression. Second, we quantify the DSBs that are licensed for crossover repair by analyzing foci of MSH-5 and COSA-1 when they associate with the synaptonemal complex during meiotic prophase progression. Finally, we quantify P-granule composition across the whole germline by analyzing the colocalization of PGL-1 and ZNFX-1 foci. Our image analysis pipeline is an adaptable and useful method for researchers spanning multiple fields using the C. elegans germline as a model system.
(© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

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