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1. Exploring plant cis‐regulatory elements at single‐cell resolution: overcoming biological and computational challenges to advance plant research

   https://doi.org/10.1111/tpj.16351  

   Mendieta, John Pablo; Sangra, Ankush; Yan, Haidong; Minow, Mark A. A.; Schmitz, Robert J. (June 2023, The Plant Journal)

   SUMMARY Cis‐regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with the inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall has limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Advances in single‐cell epigenomics have revolutionized the field of identifying cell‐type‐specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single‐cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single‐cell research, challenges, and common pitfalls in the analysis of plant single‐cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single‐cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes. 

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2. The changes in plant and soil C pools and their C : N stoichiometry control grassland N retention under elevated N inputs

   https://doi.org/10.1002/eap.2517  

   Yang, Sen; Liu, Weixing; Guo, Lulu; Wang, Chengzhang; Deng, Meifeng; Peng, Ziyang; Liu, Lingli (March 2022, Ecological Applications)
3. Expanding plant genome editing scope and profiles with CRISPR‐FrCas9 systems targeting palindromic TA sites

   https://doi.org/10.1111/pbi.14363  

   He, Yao; Han, Yangshuo; Ma, Yanqin; Liu, Shishi; Fan, Tingting; Liang, Yanling; Tang, Xu; Zheng, Xuelian; Wu, Yuechao; Zhang, Tao; et al (May 2024, Plant Biotechnology Journal)

   Summary CRISPR‐Cas9 is widely used for genome editing, but its PAM sequence requirements limit its efficiency. In this study, we exploreFaecalibaculum rodentiumCas9 (FrCas9) for plant genome editing, especially in rice. FrCas9 recognizes a concise 5′‐NNTA‐3′ PAM, targeting more abundant palindromic TA sites in plant genomes than the 5′‐NGG‐3′ PAM sites of the most popular SpCas9. FrCas9 shows cleavage activities at all tested 5′‐NNTA‐3′ PAM sites with editing outcomes sharing the same characteristics of a typical CRISPR‐Cas9 system. FrCas9 induces high‐efficiency targeted mutagenesis in stable rice lines, readily generating biallelic mutants with expected phenotypes. We augment FrCas9's ability to generate larger deletions through fusion with the exonuclease, TREX2. TREX2‐FrCas9 generates much larger deletions than FrCas9 without compromise in editing efficiency. We demonstrate TREX2‐FrCas9 as an efficient tool for genetic knockout of a microRNA gene. Furthermore, FrCas9‐derived cytosine base editors (CBEs) and adenine base editors (ABE) are developed to produce targeted C‐to‐T and A‐to‐G base edits in rice plants. Whole‐genome sequencing‐based off‐target analysis suggests that FrCas9 is a highly specific nuclease. Expression of TREX2‐FrCas9 in plants, however, causes detectable guide RNA‐independent off‐target mutations, mostly as single nucleotide variants (SNVs). Together, we have established an efficient CRISPR‐FrCas9 system for targeted mutagenesis, large deletions, C‐to‐T base editing, and A‐to‐G base editing in plants. The simple palindromic TA motif in the PAM makes the CRISPR‐FrCas9 system a promising tool for genome editing in plants with an expanded targeting scope. 

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4. Pan‐Arctic soil moisture control on tundra carbon sequestration and plant productivity

   https://doi.org/10.1111/gcb.16487  

   Zona, Donatella; Lafleur, Peter M.; Hufkens, Koen; Gioli, Beniamino; Bailey, Barbara; Burba, George; Euskirchen, Eugénie S.; Watts, Jennifer D.; Arndt, Kyle A.; Farina, Mary; et al (March 2023, Global Change Biology)
5. The plant response to high CO₂ levels is heritable and orchestrated by DNA methylation

   https://doi.org/10.1111/nph.18876  

   Panda, Kaushik; Mohanasundaram, Boominathan; Gutierrez, Jorge; McLain, Lauren; Castillo, S_Elizabeth; Sheng, Hudanyun; Casto, Anna; Gratacós, Gustavo; Chakrabarti, Ayan; Fahlgren, Noah; et al (March 2023, New Phytologist)

   Summary Plant responses to abiotic environmental challenges are known to have lasting effects on the plant beyond the initial stress exposure. Some of these lasting effects are transgenerational, affecting the next generation. The plant response to elevated carbon dioxide (CO₂) levels has been well studied. However, these investigations are typically limited to plants grown for a single generation in a high CO₂environment while transgenerational studies are rare.We aimed to determine transgenerational growth responses in plants after exposure to high CO₂by investigating the direct progeny when returned to baseline CO₂levels.We found that both the flowering plantArabidopsis thalianaand seedless nonvascular plantPhyscomitrium patenscontinue to display accelerated growth rates in the progeny of plants exposed to high CO₂. We used the model species Arabidopsis to dissect the molecular mechanism and found that DNA methylation pathways are necessary for heritability of this growth response.More specifically, the pathway of RNA‐directed DNA methylation is required to initiate methylation and the proteins CMT2 and CMT3 are needed for the transgenerational propagation of this DNA methylation to the progeny plants. Together, these two DNA methylation pathways establish and then maintain a cellular memory to high CO₂exposure. 

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