References
Baker SE (2013) Fungi and industrial biotechnology – a special issue for an amazing kingdom. Ind Biotechnol 9:105–107
Blackwell M (2011) The fungi: 1, 2, 3 ... 5.1 million species? Am J Bot 98:426–438
Braunsdorf C et al (2016) Fungal sensing of host environment. Cell Microbiol 18:1188–1200
Buijs NA et al (2013) Advanced biofuel production by the yeast Saccharomyces cerevisiae. Curr Opin Chem Biol 17:480–488
Cairns TC et al (2018) How a fungus shapes biotechnology: 100 years of Aspergillus niger research. Fungal Biol and Biotechnol 5:13
de Vries RP et al (2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 18:28
Dupont J et al (2017) Fungi as a source of food. In: Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (eds) The fungal kingdom. ASM Press, Washington, DC, p 1063–1085
Eick D, Geyer M (2013) The RNA polymerase II carboxy-terminal domain (CTD) code. Chem Rev 113:8456–8490
Fisher MC et al (2012) Emerging fungal threats to animal, plant and ecosystem health. Nature 484:186–194
Geisberg JV et al (2014) Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell 156:812–824
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274(5287):546–567
Gruber-Dorninger C et al (2017) Emerging mycotoxins: beyond traditionally determined food contaminants. J Agric Food Chem 65:7052–7070
Gupta I et al (2014) Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Mol Syst Biol 10:719
Hawksworth DL, Lucking R (2017) Fungal diversity revisited: 2.2 to 3.8 million species. In: Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (eds) The fungal kingdom. ASM Press, Washington, DC, p 79–95
Hooks KB et al (2014) Intron evolution in Saccharomycetaceae. Genome Biol Evol 6:2543–2556
Khaldi N et al (2010) SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47:736–741
Köhler JR et al (2017) Fungi that infect humans. In: Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (eds) The fungal kingdom. ASM Press, Washington, DC, p 813–843
Leach MD et al (2016) Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nat Commun 7:11704
Maekawa S et al (2015) Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance. BMC Genomics 16:154
Mason PB, Struhl K (2005) Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell 17:831–840
Miller D et al (2018) Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen. PLoS Genet 14:e1007406
Mohan JE et al (2014) Mycorrhizal fungi mediation of terrestrial ecosystem responses to global change: mini-review. Fungal Ecol 10:3–19
Money NP (2016) Chapter 12 - fungi and biotechnology. In: Watkinson SC et al (eds) The Fungi, 3rd edn. Academic Press, Boston, pp 401–424
Proft M et al (2006) The stress-activated Hog1 kinase is a selective transcriptional elongation factor for genes responding to osmotic stress. Mol Cell 23:241–250
Stajich JE et al (2007) Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol 8:R223
Treseder KK, Lennon JT (2015) Fungal traits that drive ecosystem dynamics on land. Microbiol Mol Biol Rev 79:243
Veri AO et al (2018) Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space. PLoS Genet 14:e1007270
Wong KH, Struhl K (2011) The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein. Genes Dev 25:2525–2539
Wong KH et al (2013) Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7:Unit 7 11
Wong KH et al (2014) TFIIH phosphorylation of the Pol II CTD stimulates mediator dissociation from the preinitiation complex and promoter escape. Mol Cell 54:601–612
Xie JL et al (2017) The Candida albicans transcription factor Cas5 couples stress responses, drug resistance and cell cycle regulation. Nat Commun 8:499
Yang C, Stiller JW (2014) Evolutionary diversity and taxon-specific modifications of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci U S A 111:5920–5925
Acknowledgements
We thank members of the Wong lab for sharing their experience with PolII ChIP-seq and Prof. Michael J. Hynes and Prof. Richard B. Todd for comments and suggestions on the manuscript.
Funding
We acknowledge the Science and Technology Development Fund of Macau S.A.R (grant number: FDCT085/2014/A2), Research Services and Knowledge Transfer Office of the University of Macau (grant numbers: MYRG2015-00186-FHS and MYRG2016-00211-FHS), and the Faculty of Health Sciences for their funding supports.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
Kaeling Tan declares that she has no conflict of interest. Koon Ho Wong declares that he has no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This article is part of a Special Issue on ‘Big Data’ edited by Joshua WK Ho and Eleni Giannoulatou.
Rights and permissions
About this article
Cite this article
Tan, K., Wong, K.H. RNA polymerase II ChIP-seq—a powerful and highly affordable method for studying fungal genomics and physiology. Biophys Rev 11, 79–82 (2019). https://doi.org/10.1007/s12551-018-00497-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12551-018-00497-9