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1. Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis

   https://doi.org/10.1073/pnas.1807621116  

   Kirkbride, Ryan C. ; Lu, Jie ; Zhang, Changqing ; Mosher, Rebecca A. ; Baulcombe, David C. ; Chen, Z. Jeffrey ( February 2019 , Proceedings of the National Academy of Sciences)

   Arabidopsisseed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through theNRPD1-mediated pathway. To investigate their biological functions, we characterized siRNAs in the endosperm and seed coat that were separated by laser-capture microdissection (LCM) in reciprocal genetic crosses with annrpd1mutant. We also monitored the spatial-temporal activity of theNRPD1-mediated pathway on seed development using the AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches, we identified four distinct groups of siRNA loci dependent on or independent of the maternalNRPD1allele in the endosperm or seed coat. A group of maternally expressedNRPD1-siRNA loci targets endosperm-preferred genes,more »including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using translational promoter:AGL::GUS constructs as sensors, we demonstrate that spatial and temporal expression patterns of these genes in the endosperm are regulated by theNRPD1-mediated pathway irrespective of complete silencing (AGL91) or incomplete silencing (AGL40) of these target genes. Moreover, altered expression of these siRNA-targeted genes affects seed size. We propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.

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2. POPOVICH , encoding a C2H2 zinc-finger transcription factor, plays a central role in the development of a key innovation, floral nectar spurs, in Aquilegia

   https://doi.org/10.1073/pnas.2006912117  

   Ballerini, Evangeline S. ; Min, Ya ; Edwards, Molly B. ; Kramer, Elena M. ; Hodges, Scott A. ( August 2020 , Proceedings of the National Academy of Sciences)

   The evolution of novel features, such as eyes or wings, that allow organisms to exploit their environment in new ways can lead to increased diversification rates. Therefore, understanding the genetic and developmental mechanisms involved in the origin of these key innovations has long been of interest to evolutionary biologists. In flowering plants, floral nectar spurs are a prime example of a key innovation, with the independent evolution of spurs associated with increased diversification rates in multiple angiosperm lineages due to their ability to promote reproductive isolation via pollinator specialization. As none of the traditional plant model taxa have nectar spurs,more »little is known about the genetic and developmental basis of this trait. Nectar spurs are a defining feature of the columbine genusAquilegia(Ranunculaceae), a lineage that has experienced a relatively recent and rapid radiation. We use a combination of genetic mapping, gene expression analyses, and functional assays to identify a gene crucial for nectar spur development,POPOVICH(POP), which encodes a C2H2 zinc-finger transcription factor.POPplays a central role in regulating cell proliferation in theAquilegiapetal during the early phase (phase I) of spur development and also appears to be necessary for the subsequent development of nectaries. The identification ofPOPopens up numerous avenues for continued scientific exploration, including further elucidating of the genetic pathway of which it is a part, determining its role in the initial evolution of theAquilegianectar spur, and examining its potential role in the subsequent evolution of diverse spur morphologies across the genus.

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3. Cantil: a previously unreported organ in wild-type Arabidopsis regulated by FT, ERECTA and heterotrimeric G proteins

   https://doi.org/10.1242/dev.195545  

   Gookin, Timothy E. ; Assmann, Sarah M. ( June 2021 , Development)

   ABSTRACT We describe a previously unreported macroscopic Arabidopsis organ, the cantil, named for its ‘cantilever’ function of holding the pedicel at a distance from the stem. Cantil development is strongest at the first nodes after the vegetative to reproductive inflorescence transition; cantil magnitude and frequency decrease acropetally. Cantils develop in wild-type Arabidopsis accessions (e.g. Col-0, Ws and Di-G) as a consequence of delayed flowering in short days; cantil formation is observed in long days when flowering is delayed by null mutation of the floral regulator FLOWERING LOCUS T. The receptor-like kinase ERECTA is a global positive regulator of cantil formation;more »therefore, cantils never form in the Arabidopsis strain Ler. ERECTA functions genetically upstream of heterotrimeric G proteins. Cantil expressivity is repressed by the specific heterotrimeric complex subunits GPA1, AGB1 and AGG3, which also play independent roles: GPA1 suppresses distal spurs at cantil termini, while AGB1 and AGG3 suppress ectopic epidermal rippling. These G protein mutant traits are recapitulated in long-day flowering gpa1-3 ft-10 plants, demonstrating that cantils, spurs and ectopic rippling occur as a function of delayed phase transition, rather than as a function of photoperiod per se.« less
4. IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains

   https://doi.org/10.1073/pnas.2010003118  

   Kamei, Masayuki ; Ameri, Abigail J. ; Ferraro, Aileen R. ; Bar-Peled, Yael ; Zhao, Fangzhou ; Ethridge, Christina L. ; Lail, Kathleen ; Amirebrahimi, Mojgan ; Lipzen, Anna ; Ng, Vivian ; et al ( January 2021 , Proceedings of the National Academy of Sciences)

   Polycomb Group (PcG) proteins are part of an epigenetic cell memory system that plays essential roles in multicellular development, stem cell biology, X chromosome inactivation, and cancer. In animals, plants, and many fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to assemble transcriptionally repressed facultative heterochromatin. PRC2 is structurally and functionally conserved in the model fungusNeurospora crassa, and recent work in this organism has generated insights into PRC2 control and function. To identify components of the facultative heterochromatin pathway, we performed a targeted screen ofNeurosporadeletion strains lacking individual ATP-dependent chromatin remodeling enzymes. We foundmore »theNeurosporahomolog of IMITATION SWITCH (ISW) is critical for normal transcriptional repression, nucleosome organization, and establishment of typical histone methylation patterns in facultative heterochromatin domains. We also found that stable interaction between PRC2 and chromatin depends on ISW. A functional ISW ATPase domain is required for gene repression and normal H3K27 methylation. ISW homologs interact with accessory proteins to form multiple complexes with distinct functions. Using proteomics and molecular approaches, we identified three distinctNeurosporaISW-containing complexes. A triple mutant lacking three ISW accessory factors and disrupting multiple ISW complexes led to widespread up-regulation of PRC2 target genes and altered H3K27 methylation patterns, similar to an ISW-deficient strain. Taken together, our data show that ISW is a key component of the facultative heterochromatin pathway inNeurospora, and that distinct ISW complexes perform an apparently overlapping role to regulate chromatin structure and gene repression at PRC2 target domains.

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5. Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

   https://doi.org/10.1038/s41438-021-00606-y  

   Hyden, Brennan ; Carlson, Craig H. ; Gouker, Fred E. ; Schmutz, Jeremy ; Barry, Kerrie ; Lipzen, Anna ; Sharma, Aditi ; Sandor, Laura ; Tuskan, Gerald A. ; Feng, Guanqiao ; et al ( August 2021 , Horticulture Research)

   Sex dimorphism and gene expression were studied in developing catkins in 159 F₂individuals from the bioenergy cropSalix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suitemore »of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination inSalix purpureais likely different from that observed in the related genusPopulus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

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