A. Francis Stewart - Selected Publications#

Overall citations: 25345. H-index: 82 (data from Google Scholar). Corresponding author of all ten papers listed below.

1 . Logie C and Stewart AF (1995) Ligand-regulated site-specific recombination. Proc. Natl. Acad. Sci. USA 92, 5940-5944. 210 citations. This paper initiated the now widely used ligand inducible gene switch based on site specific recombinase - estrogen receptor fusion proteins, now predominantly in mammalian application as tamoxifen induction of CreERT2.

2. Zhang Y, Buchholz F, Muyrers JPP and Stewart AF (1998) A new logic for DNA engineering using recombination in E. coli. Nature Genetics, 20, 123-128. 1307 citations. This paper initiated the recombinant DNA methodology termed 'recombineering'.

3. Aasland R, Gibson TJ and Stewart AF (1995) The PHD finger: implications for chromatin-mediated transcriptional regulation.TIBS 20, 56-59. 987 citations. This paper identified a new zinc finger that appeared to be exclusively in nuclear proteins, and was subsequently shown to bind methylated histone 3 lysine 4 epitopes and exclusively present in epigenetic regulators.

4. Ringrose L, Chabanis S, Angrand P-O, Woodroofe C and Stewart AF. (1999) Quantitative comparison of DNA looping in vitro and in vivo: Chromatin increases effective DNA flexibility at short distances. EMBO J., 23, 6630-6641. 164 citations. The first measurement of the flexibility of active chromatin in a living cell revealed that it is twice as flexible as naked DNA, (whether due to the action of chromatin remodeling machines, loop extrusion and/or RNA Polymerase II is under investigation).

5. Roguev A, Schaft D, Shevchenko A, Pijnappel WWM, Wilm M, Aasland R and Stewart AF (2001) The S. cerevisiae Set1 complex includes an Ash2-like protein and methylates histone 3 lysine 4. EMBO J. 20, 7137-7148. 558 citations. This paper described the first H3K4 methyltransferase protein complex, which was the first linkage between H3K4 methylation and trithorax-Group action. This complex is highly conserved in eukaryotes and remains at the center of epigenetic research and Stewart lab activity.

6. Rostovskaya M, Fu J, Obst M, Baer I, Weidlich S, Wang H, Smith AJH, Anastassiadis K and Stewart AF. (2012) Transposon mediated BAC transgenesis in human ES cells. Nucleic Acids Res. 40, e150. 100 citations. Overturned the long held opinion that transposons are limited to small cargoes and established the premier method for transgenesis with large transgenes.

7. Denissov S, Hofemeister H, Marks H, Kranz A, Ciotta G, Singh S, Anastassiadis K, Stunnenberg HG and Stewart AF. (2014) Mll2 is required for H3K4 trimethylation of bivalent promoters in ES cells whereas Mll1 is redundant. Development, 141, 526-37. 163 citations. This paper reported the surprising discovery that one H3K4 methyltransfrase, Mll2, is responsible for the deposition of H3K4 trimethylation on bivalent promoters. The paper also revealed the first evidence that the paralogs, Mll1 and Mll2 are engaged in functional overlap and back-up during differentiation.

8. Ander M, Subramaniam S, Fahmy K, Stewart AF and Schäffer E (2015) A single strand annealing protein clamps DNA to detect and secure homology. PLoS Biol. 13(8):e1002213. 11 citations. Single molecule optical tweezer experiments enhanced a new model for SSAP action (proposed in Erler ..Stewart (2009) JMB 391, 586-98) to initiate homologous recombination by forming a very stable SSAP dimer on 20bp annealed DNA as a nucleating clamp to drive further annealing by SSAP polymerisation.

9. Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF (2019) The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes and Development, 33: 550-564. In contrast to opposition as logic suggests, in yeast the H3K4 methyltransferase and demethylase co-operate to ensure symmetrical H3K4 trimethylation on promoter nucleosomes. Remarkable insight into epigenetic detailing and also the action of histone demethylases.

10. Ashokkumar D, Zhang Q, Much C, Bledau AS, Naumann R, Alexopoulou D, Dahl A, Goveas N, Fu J, Anastassiadis K, Stewart AF and Kranz A (2020) MLL4 is required after implantation whereas MLL3 becomes essential during late gestation. Development, 147: dev186999. This paper completes the Stewart lab program to examine the functions of all six H3K4 methyltransferases in mouse development. It describes the zygotic null phenotypes of the paralogs and important cancer genes, Mll3 and Mll4, as well as reporting Mll4, but not Mll3, haploinsufficiency as sex distorted fetal exencephaly and neonatal/adult Kabuki Syndrome.