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Chia M.*, C. Li*, S. Marques, V. Pelechano, N.M. Luscombe and F.J. van Werven. Cell-state transitions feature widespread transcriptional control by alternative starts. Genome biology *equal contributions (in print)

Moretto F., N.E. Wood, M. Chia, C. Li, N.M. Luscombe, F.J. van Werven. Transcription levels of a long noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. Cell reports (in print)

Tam J., and F.J. van Werven. Regulated repression, and not activation, governs the cell fate promoter controlling yeast meiosis. Nature Communications. 10.1038/s41467-020-16107-w.

Neurohr G.E., R.L. Terry, J. Lengefeld, M. Bonney, G.P. Brittingham, F. Moretto, T.P. Miettinen, L. Pontano Vaites, L.M. Soares, J. Paulo, W. Harper, S. Buratowski, S. Manalis, F.J. van Werven, L.J. Holt, B. A. Amon. Excessive cell growth causes cytoplasm dilution. Cell. 2019;176(5):1083-1097.e18.

 Wu, A.C.K., H. Patel, M. Chia, F. Moretto, D. Frith, A.P. Snijders, F.J. van Werven. 2018. Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor. Molecular Cell. 20;72(6):942-954. 10.1016/j.molcel.2018.10.018.

Moretto, F., N.E. Wood, G. Kelly, A. Doncic and F.J. van Werven. 2018. A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast. Nature Communications. 10.1038/s41467-018-03213-z.

 Chia M., A. Tresenrider, J. Chen, G. Spedale, V. Jorgensen, E. Ünal* and F.J. van Werven*. 2017. Transcription of a 5’ extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter. Elife. 10.7554/eLife.27420. *co-corresponding authors.

Chen, J., A. Tresenrider, M. Chia, D.T. McSwiggen, G. Spedale, H. Liao, F.J. Van Werven* and E. Ünal*. 2017. Kinetochore inactivation by expression of a repressive mRNA. Elife. 10.7554/eLife.27417. *co-corresponding authors.

Moretto, F. and F.J. van Werven. 2016. Transcription of the mating-type-regulated lncRNA IRT1 is governed by TORC1 and PKA. Current Genetics. 10.1007/s00294-016-0639-6

Weidberg, H., F. Moretto, G. Spedale, A. Amon, F.J. van Werven. 2016. Nutrient control of yeast gametogenesis is mediated by TORC1, PKA and energy availability. PLOS Genetics. 12 (6): e1006075

Berchowitz, L.E., A.S. Gajadhar, F.J. van Werven, A.A. De Rosa, M.L. Samoylova, G.A. Brar, Y. Xu , C Xiao, B. Futcher, J.S. Weissman, F.M. White, A. Amon. 2013. A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Genes & Development. 27:2147-2163.

van Werven, F.J., G. Neuert, N. Hendrick, A. Lardenois, S. Buratowski,  A. van Oudenaarden, M. Primig and A. Amon. 2012. Transcription of two long non-coding RNAs mediates mating type control of gametogenesis in budding yeast. Cell. 50: 1170-81  

van Werven, F.J., and A. Amon. 2011. Regulation of entry into gametogenesis. Philos Trans R Soc Lond B Biol Sci. 366, 3521-3531

van Werven, F.J. H.A. van Teeffelen, F.C. Holstege and H.T. Timmers. 2009. Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nature Structural & Molecular Biology. 16: 1043 - 1048

van Werven, F.J., H. van Bakel, H.A. van Teeffelen, A.F. Altelaar, M. Groot Koerkamp, A.J. Heck, F.C. Holstege and H.T. Timmers. 2008. Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes & Development. 22: 2359-2369

van Bakel, H.*, F.J. van Werven*, M. Radonjic, M.O. Brok, D. van Leenen, F.C. Holstege, and H.T. Timmers. 2008. Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification. Nucleic Acids Res. 36: e21. * These authors contributed equally.

van Werven, F.J. and H.T. Timmers. 2006. The use of biotin tagging in Saccharomyces cerevisiae improves the sensitivity of chromatin immunoprecipitation. Nucleic Acids Res. 34: e33.

van Oevelen, C.J., H.A. van Teeffelen, F.J. van Werven, and H.T. Timmers. 2006. Snf1p-dependent Spt-Ada-Gcn5-acetyltransferase (SAGA) recruitment and chromatin remodeling activities on the HXT2 and HXT4 promoters. J Biol Chem. 281: 4523-4531.

Goto, D.B., M. Ogi, F. Kijima, T. Kumagai, F. van Werven, H. Onouchi, and S. Naito. 2002. A single-nucleotide mutation in a gene encoding S-adenosylmethionine synthetase is associated with methionine over-accumulation phenotype in Arabidopsis thaliana. Genes Genet Syst. 77: 89-95.