Cell cycle control across the eukaryotic kingdom

Harashima, Hirofumi; Dißmeyer, Nico; Schnittger, Arp

doi:10.1016/j.tcb.2013.03.002

Cited by 327 publications

(252 citation statements)

References 105 publications

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“…For the entire set of 327 TFs that had sufficient motif instances for quantification, mC-all inhibition was seen for 72% (234) of TFs, weak to no binding inhibition for 24% (79), while 4.3% (14) preferentially bound methylated motifs ( Figure 7F). Interestingly, E2F family member DEL2, with specific roles in DNA replication, preferentially bound to methylated motifs, suggesting a possible relationship between this epigenetic mark and central regulators of cell division (Harashima et al, 2013).…”

Section: The Epicistromementioning

confidence: 99%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

356

461

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SUMMARYThe cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TFspecific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.

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Section: The Epicistromementioning

confidence: 99%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

356

461

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“…Another obvious difference between plants and other well‐studied eukaryotes is the presence of a large groups of cyclins, for example, more than 30 cyclins in Arabidopsis , most of which are still uncharacterized (Harashima et al , 2013). Very little is known about the regulation of these cyclins but remarkably, previous studies have revealed that CYCB1;1 is upregulated during various treatments of DNA damage‐inducing agents or in mutants affected in chromatin organization, DNA metabolism, and/or repair such as fasciata 1 ( fas1 ), jing he sheng 1 ( jhs1 ), and dna replication factor c1 ( rfc1 ) (Chen et al , 2003; Culligan et al , 2004; Endo et al , 2006; Liu et al , 2010; Adachi et al , 2011; Jia et al , 2016).…”

Section: Introductionmentioning

confidence: 99%

The plant‐specific CDKB 1‐ CYCB 1 complex mediates homologous recombination repair in Arabidopsis

et al. 2016

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Upon DNA damage, cyclin‐dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology‐dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant‐specific B1‐type CDKs (CDKB1s) and the class of B1‐type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1‐CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1;1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell‐cycle activity is blocked after DNA damage, CDKB1‐CYCB1 complexes are specifically activated to mediate HR.

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“…The mitotic cell cycle is characterized by a round of DNA replication (S phase) followed by mitosis and cytokinesis (M phase), which are separated by two gap phases (G1 and G2) (Inzé, 2005). Cyclin-dependent kinases (CDKs) and their cyclin partners regulate the G1/S and G2/M phase transitions as well as progression through, and exit from, the mitotic cell cycle (Menges et al, 2002;Beemster et al, 2005;Inzé and De Veylder, 2006;Berckmans and De Veylder, 2009;Harashima et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Potential Involvement of Cell Cycle-Related Genes in the Arrest of Stamen Development of Female Flowers During Sex Expression in Cucumber (<i>Cucumis sativus</i> L.)

Yamasaki

Yamakuchi

Yamanaka

et al. 2017

Environmental Control in Biology

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These physiological phenomena were confirmed at the molecular level. Two genes (CS-ACS1G and CS-ACS2) which encode a key enzyme in the ethylene biosynthesis pathway, 1-aminocyclopropane-1-carboxylic acid (ACC) synthase, were identified as being related to sex expression in cucumber plants. The CS-ACS1G gene, which exists in gynoecious cucumber plants but not in monoecious cucumber plants, was closely linked to the F gene (Trebitsh et al., 1997 Monoecious cucumber (Cucumis sativus L.) produces male and female flowers on the same plant, but application of ethylene promotes expression of female flowers. In the early bisexual stage, all flower buds contain primordia for both stamens and pistils and sexual differences are established by the selective arrest of sexual organ primordia. The expression of six cell cycle-related genes [Cs Cyclin A (CsCycA), CsCycB, CsCycD3; 1, CsCycD3; 2, Cs Cyclin-dependent kinase A CsCDKA), and CsCDKB] was analyzed in male and female flower buds to investigate cell cycle activity in sexual organs. CsCycA was expressed specifically in the area containing arrested stamen primordia (ACASP) in female flower buds, but was barely detected in male flower buds. Expression of the other five genes was detected in the ACASP but not in pistils of female flower buds. Expression of all six genes was elevated transiently following the application of 2-chloroethylphosphonic acid (ethephon), an ethylene-releasing agent, to the shoot apices. The correlation of expression of these genes with the formation of female flowers suggests they play a role in the arrest of stamens of female flowers in monoecious cucumber plants.

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Cell cycle control across the eukaryotic kingdom

Cited by 327 publications

References 105 publications

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

The plant‐specific CDKB 1‐ CYCB 1 complex mediates homologous recombination repair in Arabidopsis

Potential Involvement of Cell Cycle-Related Genes in the Arrest of Stamen Development of Female Flowers During Sex Expression in Cucumber (<i>Cucumis sativus</i> L.)

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