MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor

Schlereth, Alexandra; Möller, Barbara; Li, Weilin; Kientz, Marika; Flipse, Jacky; Rademacher, Eike H.; Schmid, Markus; Jürgens, Gerd; Weijers, Dolf

doi:10.1038/nature08836

Cited by 530 publications

(686 citation statements)

References 36 publications

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“…MONOPTEROS and GNL1 operate in embryo and vascular development 45,46 ; TOADSTOOL 2 operates in meristem maintenance 47 , and the Arabidopsis WRKY2 protein acts in zygote polarization in embryo development 48 . Additionally, WRKY2 has a role in pollen development 49 and growth arrest induced by ABA during seed germination 50 .…”

Section: Selective Sweeps Reveal Coordinated Local Adaptationmentioning

confidence: 99%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

237

253

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Forest ecosystems maintain a large share of Northern Hemisphere biodiversity. Boreal forests comprise roughly 30% of global forest area 1 and contain the highest tree density among climate zones 2 . Moreover, boreal regions are undergoing extensive climate change. Annual temperature increases exceeding 1.5 °C are projected to result in a warming of 4-11 °C by the end of this century, with little concomitant increase in precipitation 1 . At this pace, climate zones will shift northward at a greater speed than trees can migrate 3 . To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes. Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch.Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightlylinked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.A full list of affiliations appears at the end of the paper.

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Section: Selective Sweeps Reveal Coordinated Local Adaptationmentioning

confidence: 99%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

237

253

View full text Add to dashboard Cite

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“…To evaluate the in vivo relevance of our spacing model, we identified a set of 69 ARF5 target genes that rapidly respond to ARF5-specific repression with IAA19/BODENLOS and auxin treatments (Schlereth et al, 2010). 64% of these ARF5 targets contained a DAP-seq peak in their promoter, 3-fold enrichment over expectation ( Figure S5F; p < 1 × 10 −10 ).…”

Section: Cooperative Binding Of Arf Homodimers At Phased Motif Repeatsmentioning

confidence: 99%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

369

482

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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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“…The initiation of the root meristem requires two or more apical MONOPTEROS (MP)-dependent signals that reach the uppermost suspensor cell during the early-globular stage to establish its hypophyseal cell fate and to trigger its asymmetric division (Weijers et al, 2006;Schlereth et al, 2010). One of these signals seems to be auxin, because disruption of the auxin response by inhibiting MP function in the embryo downregulates PIN1 expression and presumably limits auxin transport to the basal pole (Weijers et al, 2006;Ploense et al, 2009).…”

Section: Gnom Mediates Apical-basal Auxin Fluxmentioning

confidence: 99%

Coordination of apical and basal embryo development revealed by tissue-specific GNOM functions

et al. 2011

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SUMMARYFlowering-plant embryogenesis generates the basic body organization, including the apical and basal stem cell niches, i.e. shoot and root meristems, the major tissue layers and the cotyledon(s). gnom mutant embryos fail to initiate the root meristem at the early-globular stage and the cotyledon primordia at the late globular/transition stage. Tissue-specific GNOM expression in the gnom mutant embryo revealed that both apical and basal embryo organization depend on GNOM provascular expression and a functioning apical-basal auxin flux: GNOM provascular expression in gnom mutant background resulted in non-cell-autonomous reconstitution of apical and basal tissues which could be linked to changes in auxin responses in those tissues, stressing the importance of apical-basal auxin flow for overall embryo organization. Although reconstitution of apical-basal auxin flux in gnom results in the formation of single cotyledons (monocots), only additional GNOM epidermal expression is able to induce wild-type apical patterning. We conclude that provascular expression of GNOM is vital for both apical and basal tissue organization, and that epidermal GNOM expression is required for radial-to-bilateral symmetry transition of the embryo. We propose GNOM-dependent auxin sinks as a means to generate auxin gradients across tissues.

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MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor

Cited by 530 publications

References 36 publications

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

Coordination of apical and basal embryo development revealed by tissue-specific GNOM functions

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