Advertisement

Mapping a Transcriptome-Guided Arabidopsis SAM Interactome

  • Muhammad Naseem
  • Ozge Osmanoglu
  • Jibran Iqbal
  • Fares M. Howari
  • Fatima A. AlRemeithi
  • Martin Kaltdorf
  • Thomas DandekarEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2094)

Abstract

The advent of multi-OMICS approaches has a significant impact on the investigation of biological processes occurring in plants. RNA-SEQ, cellular proteomics, and metabolomics have added a considerable ease in studying the dynamics of stem cell niches. New cell sorting approaches coupled with the labeling of stem cell population specific marker genes are highly instrumental in enriching distinct cellular populations for various types of analysis. One more promising field of OMICS is the mapping of cellular interactomes. The plant stem cells research is barely profited from this newly emerging field of OMICS. Generation of stem cell/niche-specific interactome is a time-consuming and labor-intensive task. Here, we describe a method on how to assemble a SAM-based interactome after using the available generic Arabidopsis interactomes. To define the context of SAM in a generic interactome, we used SAM cell population transcriptome datasets. Our step-by-step protocol can easily be adopted for other stem cell niches such as RAM and lateral meristems keeping in view the availability of transcriptome datasets for cellular populations of these niches.

Key words

SAM RAM Transcriptome OMICs Interactomes 

Notes

Acknowledgment

We thank the German Research Foundation (DFG) for funding (TR124/B1) to TD and start-up grant (R18045) and RIF-grant by Zayed University to MN and UAE Space Agency grant (EU1804) to FMH.

References

  1. 1.
    Naseem M, Srivastava M, Dandekar T (2014) Stem-cell-triggered immunity safeguards cytokinin enriched plant shoot apexes from pathogen infection. Front Plant Sci 5:588.  https://doi.org/10.3389/fpls.2014.00588CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Aichinger E, Kornet N, Friedrich T, Laux T (2012) Plant stem cell niches. Annu Rev Plant Biol 63:615–636.  https://doi.org/10.1146/annurev-arplant-042811-105555CrossRefPubMedGoogle Scholar
  3. 3.
    Hwang I, Sheen J, Müller B (2012) Cytokinin signaling networks. Ann Rev Plant Biol 63:353–380.  https://doi.org/10.1146/annurev-arplant-042811-105503CrossRefGoogle Scholar
  4. 4.
    Perales M, Reddy GV (2012) Stem cell maintenance in shoot apical meristems. Curr Opin Plant Biol 15:10–16.  https://doi.org/10.1016/j.pbi.2011.10.008CrossRefPubMedGoogle Scholar
  5. 5.
    Song X-F, Yu D-L, Xu T-T et al (2012) Contributions of individual amino acid residues to the endogenous CLV3 function in shoot apical meristem maintenance in arabidopsis. Mol Plant 5:515–523.  https://doi.org/10.1093/mp/ssr120CrossRefPubMedGoogle Scholar
  6. 6.
    Yadav RK, Tavakkoli M, Xie M et al (2014) A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche. Development 141:2735–2744.  https://doi.org/10.1242/dev.106104CrossRefPubMedGoogle Scholar
  7. 7.
    Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210.  https://doi.org/10.1093/nar/30.1.207CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Barrett T, Wilhite SE, Ledoux P et al (2013) NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res 41:D991–D995.  https://doi.org/10.1093/nar/gks1193CrossRefGoogle Scholar
  9. 9.
    Shannon P, Markiel A, Ozier O et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504.  https://doi.org/10.1101/gr.1239303CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Alcaraz N, Pauling J, Batra R et al (2014) KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. BMC Syst Biol 8:99.  https://doi.org/10.1186/s12918-014-0099-xCrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Muhammad Naseem
    • 1
    • 2
  • Ozge Osmanoglu
    • 2
  • Jibran Iqbal
    • 1
  • Fares M. Howari
    • 1
  • Fatima A. AlRemeithi
    • 1
  • Martin Kaltdorf
    • 2
  • Thomas Dandekar
    • 2
    Email author
  1. 1.Department of Life and Environmental SciencesCollege of Natural and Health Sciences, Zayed UniversityAbu DhabiUAE
  2. 2.Department of Bioinformatics, BiocenterUniversity of WuerzburgWuerzburgGermany

Personalised recommendations