@article{meena_antisense_2024,
	title = {Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in {Arabidopsis}},
	volume = {36},
	issn = {1532-298X},
	doi = {10.1093/plcell/koae160},
	abstract = {Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the poly(A) signal of genes (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady-state RNA techniques to identify biologically relevant players in stress responses.},
	language = {eng},
	number = {9},
	journal = {The Plant Cell},
	author = {Meena, Shiv Kumar and Quevedo, Marti and Nardeli, Sarah Muniz and Verez, Clément and Bhat, Susheel Sagar and Zacharaki, Vasiliki and Kindgren, Peter},
	month = sep,
	year = {2024},
	pmid = {38801743},
	pmcid = {PMC11371176},
	keywords = {Arabidopsis, Arabidopsis Proteins, Cold Temperature, Cold-Shock Response, Gene Expression Regulation, Plant, RNA, Antisense, RNA, Messenger, Stress, Physiological, Transcription Factors, Transcription, Genetic},
	pages = {3467--3482},
}

Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the poly(A) signal of genes (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady-state RNA techniques to identify biologically relevant players in stress responses.

@article{nanda__2024,
	title = {: {A} new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection},
	volume = {176},
	copyright = {© 2024 The Authors. Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14306},
	doi = {10.1111/ppl.14306},
	abstract = {Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.},
	language = {en},
	number = {2},
	urldate = {2024-09-04},
	journal = {Physiologia Plantarum},
	author = {Nanda, Sanchali and Shutova, Tatyana and Cainzos, Maximiliano and Hu, Chen and Sasbrink, Bart and Bag, Pushan and Blanken, Tristian den and Buijs, Ronald and Gracht, Lex van der and Hendriks, Frans and Lambrev, Petar and Limburg, Rob and Mascoli, Vincenzo and Nawrocki, Wojciech J and Reus, Michael and Parmessar, Ramon and Singerling, Björn and Stokkum, Ivo H M and Jansson, Stefan and Holzwarth, Alfred R.},
	month = aug,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14306},
	pages = {e14306},
}

Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.

@article{luomaranta_systems_2024,
	title = {Systems genetic analysis of lignin biosynthesis in \textit{{Populus} tremula}},
	volume = {243},
	issn = {0028-646X, 1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.19993},
	doi = {10.1111/nph.19993},
	abstract = {Summary
            
              
                
                  
                    The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural ‘SwAsp’ population of aspen (
                    Populus tremula
                    ) trees.
                  
                
                
                  We analyzed gene expression by RNA sequencing (RNA‐seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis‐GC‐MS in mature wood of 268 trees from 99 genotypes.
                
                
                  
                    Abundant variation was observed for lignin content and composition, and genome‐wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top‐ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co‐expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin‐biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL‐CoA O‐METHYLTRANSFERASE 3.
                    PHENYLALANINE AMMONIA LYASE 3
                    was co‐expressed with
                    HOMEOBOX PROTEIN 5
                    (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees.
                  
                
                
                  The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees´ responses to external cues such as mechanical stimulus and nutrient availability.},
	language = {en},
	number = {6},
	urldate = {2024-08-30},
	journal = {New Phytologist},
	author = {Luomaranta, Mikko and Grones, Carolin and Choudhary, Shruti and Milhinhos, Ana and Kalman, Teitur Ahlgren and Nilsson, Ove and Robinson, Kathryn M. and Street, Nathaniel R. and Tuominen, Hannele},
	month = sep,
	year = {2024},
	keywords = {GWAS, HD-Zip III, Populus, aspen, eQTL, lignin biosynthesis, wood formation},
	pages = {2157--2174},
}

Summary The genetic control underlying natural variation in lignin content and composition in trees is not fully understood. We performed a systems genetic analysis to uncover the genetic regulation of lignin biosynthesis in a natural ‘SwAsp’ population of aspen ( Populus tremula ) trees. We analyzed gene expression by RNA sequencing (RNA‐seq) in differentiating xylem tissues, and lignin content and composition using Pyrolysis‐GC‐MS in mature wood of 268 trees from 99 genotypes. Abundant variation was observed for lignin content and composition, and genome‐wide association study identified proteins in the pentose phosphate pathway and arabinogalactan protein glycosylation among the top‐ranked genes that are associated with these traits. Variation in gene expression and the associated genetic polymorphism was revealed through the identification of 312 705 local and 292 003 distant expression quantitative trait loci (eQTL). A co‐expression network analysis suggested modularization of lignin biosynthesis and novel functions for the lignin‐biosynthetic CINNAMYL ALCOHOL DEHYDROGENASE 2 and CAFFEOYL‐CoA O‐METHYLTRANSFERASE 3. PHENYLALANINE AMMONIA LYASE 3 was co‐expressed with HOMEOBOX PROTEIN 5 (HB5), and the role of HB5 in stimulating lignification was demonstrated in transgenic trees. The systems genetic approach allowed linking natural variation in lignin biosynthesis to trees´ responses to external cues such as mechanical stimulus and nutrient availability.

@article{sivan_unraveling_2024,
	title = {Unraveling the unique structural motifs of glucuronoxylan from hybrid aspen wood},
	volume = {343},
	issn = {01448617},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S014486172400660X},
	doi = {10.1016/j.carbpol.2024.122434},
	language = {en},
	urldate = {2024-08-30},
	journal = {Carbohydrate Polymers},
	author = {Sivan, Pramod and Heinonen, Emilia and Escudero, Louis and Gandla, Madhavi Latha and Jiménez-Quero, Amparo and Jönsson, Leif J. and Mellerowicz, Ewa J. and Vilaplana, Francisco},
	month = nov,
	year = {2024},
	pages = {122434},
}

@article{jaillais_guidelines_2024,
	title = {Guidelines for naming and studying plasma membrane domains in plants},
	volume = {10},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-024-01742-8},
	doi = {10.1038/s41477-024-01742-8},
	language = {en},
	number = {8},
	urldate = {2024-08-30},
	journal = {Nature Plants},
	author = {Jaillais, Yvon and Bayer, Emmanuelle and Bergmann, Dominique C. and Botella, Miguel A. and Boutté, Yohann and Bozkurt, Tolga O. and Caillaud, Marie-Cecile and Germain, Véronique and Grossmann, Guido and Heilmann, Ingo and Hemsley, Piers A. and Kirchhelle, Charlotte and Martinière, Alexandre and Miao, Yansong and Mongrand, Sebastien and Müller, Sabine and Noack, Lise C. and Oda, Yoshihisa and Ott, Thomas and Pan, Xue and Pleskot, Roman and Potocky, Martin and Robert, Stéphanie and Rodriguez, Clara Sanchez and Simon-Plas, Françoise and Russinova, Eugenia and Van Damme, Daniel and Van Norman, Jaimie M. and Weijers, Dolf and Yalovsky, Shaul and Yang, Zhenbiao and Zelazny, Enric and Gronnier, Julien},
	month = aug,
	year = {2024},
	pages = {1172--1183},
}