A Framework for Accessible Cluster-Enabled Epistatic Analysis

Author(s):  
Alex Upton ◽  
Johan Karlsson ◽  
Oswaldo Trelles ◽  
Miguel Hernandez ◽  
Juan Elvira
Keyword(s):  
Development ◽  
1998 ◽  
Vol 125 (7) ◽  
pp. 1161-1171 ◽  
Author(s):  
D.B. Szymanski ◽  
R.A. Jilk ◽  
S.M. Pollock ◽  
M.D. Marks

More than twenty genes are required for the correct initiation, spacing, and morphogenesis of trichomes in Arabidopsis. The initial selection of trichome precursors requires the activity of both the GLABROUS1 (GL1) and TRANSPARENT TESTA GLABROUS (TTG) genes. The GLABRA2 (GL2) gene is required for subsequent phases of trichome morphogenesis such as cell expansion, branching, and maturation of the trichome cell wall. Previous studies have shown that GL2 is a member of the homeodomain class of transcription factors. Here we report a detailed analysis of GL2 expression in the shoot using anti-GL2 antibodies and the GUS reporter gene fused to the GL2 promoter. The GL2 expression profile in the shoot is complex, and involves spatial and temporal variation in developing leaves and trichomes. Two separate promoter domains that are expressed in trichomes were identified. GL2, like GL1, is expressed in developing trichomes and in cells surrounding trichomes during early stages of trichome development. Unlike GL1, GL2 expression persists in mature trichomes. It was found that while GL1 and TTG were not required for the initiation of GL2 expression in the non-trichome cells, the presence of a functional GL1 or TTG gene was able to increase GL2 expression in these cells compared to ttg gl1 plants. The hypothesis that GL1 regulates aspects of GL2 expression is consistent with epistatic analysis of gl1 and gl2 and the expression patterns of GL1 and GL2. In support of this hypothesis, it was found that ectopic expression of GL1 in the presence of ectopic expression of the maize R gene, which can bypass the requirement for TTG, can ectopically activate GL2 transcription.


2017 ◽  
Vol 62 ◽  
pp. 312-319
Author(s):  
Alex Upton ◽  
Miguel Blanca ◽  
José Antonio Cornejo-García ◽  
James Richard Perkins
Keyword(s):  

2015 ◽  
Vol 51 ◽  
pp. 725-734 ◽  
Author(s):  
Alex Upton ◽  
Oswaldo Trelles ◽  
James Perkins

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 493 ◽  
Author(s):  
Cory Batenchuk ◽  
Lioudmila Tepliakova ◽  
Mads Kærn

Author(s):  
Shijie Liu ◽  
Waqar Majeed ◽  
Pranas Grigaitis ◽  
Matthew J. Betts ◽  
Leslie K. Climer ◽  
...  

2014 ◽  
Vol 10 ◽  
pp. P95-P96
Author(s):  
Jingwen Yan ◽  
Sungeun Kim ◽  
Kwangsik T. Nho ◽  
Shannon Leigh Risacher ◽  
Jason Moore ◽  
...  

1995 ◽  
Vol 15 (10) ◽  
pp. 5246-5257 ◽  
Author(s):  
Z S Zhao ◽  
T Leung ◽  
E Manser ◽  
L Lim

Pheromone signalling in Saccharomyces cerevisiae is mediated by the STE4-STE18 G-protein beta gamma subunits. A possible target for the subunits is Ste20p, whose structural homolog, the serine/threonine kinase PAK, is activated by GTP-binding p21s Cdc42 and Rac1. The putative Cdc42p-binding domain of Ste20p, expressed as a fusion protein, binds human and yeast GTP-binding Cdc42p. Cdc42p is required for alpha-factor-induced activation of FUS1.cdc24ts strains defective for Cdc42p GDP/GTP exchange show no pheromone induction at restrictive temperatures but are partially rescued by overexpression of Cdc42p, which is potentiated by Cdc42p12V mutants. Epistatic analysis indicates that CDC24 and CDC42 lie between STE4 and STE20 in the pathway. The two-hybrid system revealed that Ste4p interacts with Cdc24p. We propose that Cdc42p plays a pivotal role both in polarization of the cytoskeleton and in pheromone signalling.


2014 ◽  
Vol 35 (4) ◽  
pp. 699-715 ◽  
Author(s):  
Takayuki Sekimoto ◽  
Tsukasa Oda ◽  
Kiminori Kurashima ◽  
Fumio Hanaoka ◽  
Takayuki Yamashita

DNA rereplication is a major form of aberrant replication that causes genomic instabilities, such as gene amplification. However, little is known about which DNA polymerases are involved in the process. Here, we report that low-fidelity Y-family polymerases (Y-Pols), Pol η, Pol ι, Pol κ, and REV1, significantly contribute to DNA synthesis during rereplication, while the replicative polymerases, Pol δ and Pol ε, play an important role in rereplication, as expected. When rereplication was induced by depletion of geminin, these polymerases were recruited to rereplication sites in human cell lines. This finding was supported by RNA interference (RNAi)-mediated knockdown of the polymerases, which suppressed rereplication induced by geminin depletion. Interestingly, epistatic analysis indicated that Y-Pols collaborate in a common pathway, independently of replicative polymerases. We also provide evidence for a catalytic role for Pol η and the involvement of Pol η and Pol κ in cyclin E-induced rereplication. Collectively, our findings indicate that, unlike normal S-phase replication, rereplication induced by geminin depletion and oncogene activation requires significant contributions of both Y-Pols and replicative polymerases. These findings offer important mechanistic insights into cancer genomic instability.


Sign in / Sign up

Export Citation Format

Share Document