SOG1 activator and MYB3R repressors regulate a complex DNA damage network in
            <i>Arabidopsis</i>

Bourbousse, Clara; Vegesna, Neeraja; Law, Julie A.

doi:10.1073/pnas.1810582115

Cited by 123 publications

(213 citation statements)

References 106 publications

(208 reference statements)

Supporting

Mentioning

186

Contrasting

Order By: Relevance

“…Briefly, 6-d-old PIF7-HA (Galvao et al, 2019) seedlings grown in LD at 21°C were either kept at 21°C or shifted at ZT2 to 28°C for 2 h before harvesting in liquid nitrogen. Chromatin extraction was performed as described previously (Bourbousse et al, 2018) except that samples were crosslinked only with formaldehyde. Immunoprecipitation was performed as described previously (Gendrel et al, 2005) using an anti-HA antibody (Santa Cruz Biotechnology, Inc., Dallas, TX, USA; sc-7392 X).…”

Section: Chip-qpcrmentioning

confidence: 99%

PHYTOCHROME INTERACTING FACTOR 7 is important for early responses to elevated temperature in Arabidopsis seedlings

et al. 2019

View full text Add to dashboard Cite

Summary In response to elevated ambient temperature Arabidopsis thaliana seedlings display a thermomorphogenic response that includes elongation of hypocotyls and petioles. Phytochrome B and cryptochrome 1 are two photoreceptors also playing a role in thermomorphogenesis. Downstream of both environmental sensors PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is essential to trigger this response at least in part through the production of the growth promoting hormone auxin. Using a genetic approach, we identified PHYTOCHROME INTERACTING FACTOR 7 (PIF7) as a novel player for thermomorphogenesis and compared the phenotypes of pif7 and pif4 mutants. We investigated the role of PIF7 during temperature‐regulated gene expression and the regulation of PIF7 transcript and protein by temperature. Furthermore, pif7 and pif4 loss‐of‐function mutants were similarly unresponsive to increased temperature. This included hypocotyl elongation and induction of genes encoding auxin biosynthetic or signalling proteins. PIF7 bound to the promoters of auxin biosynthesis and signalling genes. In response to temperature elevation PIF7 transcripts decreased while PIF7 protein levels increased rapidly. Our results reveal the importance of PIF7 for thermomorphogenesis and indicate that PIF7 and PIF4 likely depend on each other possibly by forming heterodimers. Elevated temperature rapidly enhances PIF7 protein accumulation, which may contribute to the thermomorphogenic response.

show abstract

Section: Chip-qpcrmentioning

confidence: 99%

PHYTOCHROME INTERACTING FACTOR 7 is important for early responses to elevated temperature in Arabidopsis seedlings

et al. 2019

View full text Add to dashboard Cite

show abstract

“…One of the key findings in this study is that DNA damage induces the cytokinin biosynthesis genes IPT1, IPT3, IPT5, IPT7, LOG7 and CYP735A2. Since these genes are not among the SOG1 target genes previously identified by ChIP-seq analyses 11,12 , downstream transcription factor(s) are likely involved in their induction. The promoter:GUS lines showed that IPT1 expression increased in zeocin-treated roots, while IPT3 and IPT5 were induced in cotyledons and shoot apices, respectively ( Fig.…”

Section: Discussionmentioning

confidence: 97%

DNA damage inhibits root growth by enhancing cytokinin biosynthesis inArabidopsis thaliana

Takahashi

Inagaki

Nishimura

et al. 2020

Preprint

View full text Add to dashboard Cite

Plant root growth is influenced by external factors to adapt to changing environmental conditions. However, the mechanisms by which environmental stresses affect root growth remain elusive. Here we found that DNA double-strand breaks (DSBs) induce the expression of genes for the synthesis of cytokinin hormones and enhance the accumulation of cytokinins in the Arabidopsis root tip. This is a programmed response to DSBs through the DNA damage signaling pathway. Our data showed that activation of cytokinin signalling suppresses the expression of PIN-FORMED genes that encode efflux carriers of another plant hormone, auxin, thereby disturbing downward auxin flow and causing cell cycle retardation in the G2 phase.Elevated cytokinin signalling also promotes an early transition from cell division to endoreplication, resulting in a reduction of the root meristem size. We propose that in response to DNA stress, plants inhibit root growth by orchestrating hormone biosynthesis and signalling.Plant roots play a crucial role in water and nutrient uptake, anchorage to soil, and sensing the rhizosphere environment 1 . Since these functions have a substantial impact on overall plant growth, root development is precisely controlled in response to changing underground conditions. Environmental stresses usually inhibit root growth; salinity, oxidation or heat stress severely retards root growth. Previous studies demonstrated that high boron or aluminium stress, which causes DNA damage, leads to delay or cessation of cell division, thereby suppressing root growth 2,3 . This is an active response to DNA damage that is governed by the cell cycle checkpoint mechanism, in which cell cycle progression is arrested at a specific stage to ensure DNA repair or to provoke cell death in severe cases 4 . As do other eukaryotes, plants possess two protein kinases, ATAXIA TELANGIECTASIA MUTATED (ATM) and ATM AND RAD3-RELATED (ATR), that sense DNA damage and trigger cell cycle checkpoints 5,6 . ATM is activated by DNA double-strand breaks (DSBs), whereas ATR primarily senses single-strand DNA and replication stress caused by DNA replication fork blocking. In animals and fungi, DNA damage signals are transmitted to Checkpoint-1 (CHK1) and CHK2 kinases, and ATM, ATR, CHK1 and CHK2 phosphorylate and activate the tumour suppressor protein p53 7 .However, orthologues of CHK and p53 are missing in plants; instead, the plant-specific NAC-type transcription factor, named SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), plays a central role in transmitting the signal from ATM and ATR 8 . SOG1 is phosphorylated and activated by ATM and ATR 9,10 , and binds to the sequence CTT[N] 7 AAG to induce the expression of target genes involved in DNA repair, cell cycle arrest and stem cell death 11,12 .In Arabidopsis roots, cells actively divide and proliferate in the meristematic zone (MZ) in the tip region. After several rounds of cell division, cells stop dividing and start endoreplication, in which DNA replication is repeated without mitosis or cytokinesis.Endoreplicating c...

show abstract

“…ChIP-qPCR analyses were performed with an anti-H3K4me3 antibody and with antihistone H3 to normalize levels to nucleosome occupancy. H3K4me3/H3 levels are given as percentages of IP/input input relative to the mean signals over two housekeeping genes (At4g23100 and At4g22330) with no change in expression and in H3K4me3 level during the transition [96]. Error bars correspond to standard deviations from two replicates.…”

Section: S2lb Associates With Highly Transcribed Genes and Is Requirementioning

confidence: 99%

“…Profiling of S2Lb-GFP and MYC-SDG2 was performed using anti-GFP (Life Technologies #11122) and anti-MYC (Ozyme #71D10) antibodies, respectively, and two crosslink steps. As recently described [96], samples were cross-linked first with 1.5 mM ethylene glycol bis(succinimidyl succinate) for 20 min and then with 1% formaldehyde for 10 min at room temperature. Cross-linking was stopped by adding 1.7 mL of 2 M glycine and incubating for 10 min.…”

Section: Chip-qpcr Chip-sequencing and Chip Bioinformaticsmentioning

confidence: 99%

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in histone H3 Lys-4 trimethylation independently from histone H2B monoubiquitination

Fiorucci

Bourbousse

Concia

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in S. cerevisiae, where a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with Set1), in Arabidopsis thaliana this activity involves multiple histone methyltransferases (HMTs). Among these, the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. S2Lb co-purifies with the AtCOMPASS core subunit WDR5 from a highmolecular weight complex, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. Notwithstanding, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2 or H3 Lys-4 trimethylation, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been coopted by the plant-specific SDG2 HMT and mediates H3K4me3 deposition through an H2Bub-independent pathway in Arabidopsis.

show abstract

SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis

Cited by 123 publications

References 106 publications

PHYTOCHROME INTERACTING FACTOR 7 is important for early responses to elevated temperature in Arabidopsis seedlings

PHYTOCHROME INTERACTING FACTOR 7 is important for early responses to elevated temperature in Arabidopsis seedlings

DNA damage inhibits root growth by enhancing cytokinin biosynthesis inArabidopsis thaliana

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in histone H3 Lys-4 trimethylation independently from histone H2B monoubiquitination

Contact Info

Product

Resources

About