@article{lei_comprehensive_2025,
	title = {Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits},
	issn = {2160-1836},
	url = {https://doi.org/10.1093/g3journal/jkaf140},
	doi = {10.1093/g3journal/jkaf140},
	abstract = {By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.},
	urldate = {2025-07-25},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Lei, Mengyu and Si, Huan and Zhu, Mingjia and Han, Yu and Liu, Wei and Dai, Yifei and Ji, Yan and Liu, Zhengwen and Hao, Fan and Hao, Ran and Zhao, Jiarui and Ye, Guoyou and Zan, Yanjun},
	month = jul,
	year = {2025},
	pages = {jkaf140},
}

By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.

@article{boussardon_comparative_2025,
	title = {Comparative {Study} of the {Mitochondrial} {Proteome} {From} {Mesophyll}, {Vascular}, and {Guard} {Cells} in {Response} to {Carbon} {Starvation}},
	volume = {177},
	copyright = {© 2025 The Author(s). 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.70465},
	doi = {10.1111/ppl.70465},
	abstract = {A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.},
	language = {en},
	number = {5},
	urldate = {2025-09-05},
	journal = {Physiologia Plantarum},
	author = {Boussardon, Clément and Hussain, Shah and Keech, Olivier},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70465},
	keywords = {cell-specific, glutamate, mitochondria, proteome, translation},
	pages = {e70465},
}

A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.

@article{rosenkranz_cis-_2025,
	title = {Cis- and trans-action of the cold-induced {lncRNAs}, {SVALKA} and {SVALNA}, regulate {CBF1} and {CBF3} in {Arabidopsis}},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00568-5},
	doi = {10.1038/s44319-025-00568-5},
	abstract = {Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.},
	urldate = {2025-09-05},
	journal = {EMBO reports},
	author = {Rosenkranz, Isabell and Mermet, Sarah and Zacharaki, Vasiliki and Kindgren, Peter},
	month = sep,
	year = {2025},
	note = {Num Pages: 18
Publisher: John Wiley \& Sons, Ltd},
	keywords = {Arabidopsis, Cold Response, Epigenetic Regulation, Long Non-coding RNAs},
	pages = {1--18},
}

Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.

@article{meyer_expanded_2025,
	title = {The {Expanded} {LYR} {Motif}-{Containing} {Protein} {Family} in {Archaeplastida}},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70482},
	doi = {10.1111/ppl.70482},
	abstract = {The LYR motif (LYRM)-containing proteins are small eukaryote-specific proteins that have been defined based on the presence of a Lys-Tyr-Arg amino acid motif and a conserved triplet of α-helices. Twelve LYRM proteins were described in humans. They are involved in core mitochondrial processes as subunits or assembly/stabilising factors of mitochondrial complexes. Their function depends on their ability to interact with the acylated form of acyl-carrier proteins (mtACPs), which places these proteins as direct contributors to two intertwined functional processes, energy metabolism and mitochondrial biogenesis. To gain insight into LYRM proteins in Archaeplastida, we first analyzed the Arabidopsis thaliana genome and then a set of organisms representing the different groups of the Archaeplastida clade. This analysis revealed the existence of 17 classes encompassing 10 of the 12 LYRM classes found in humans. Eleven classes exist in Arabidopsis, and six additional classes are present in some organisms but not in Arabidopsis, thus expanding previous observations. Subsequent data mining based on literature, gene expression, and in silico analyses allowed us to speculate about the possible molecular function of some currently uncharacterised LYRMs in plants. Altogether, this study revealed the diversification of the LYRM protein family in Archaeplastida and more globally among eukaryotes, in which the LYRM-mtACP associations represent central molecular systems to regulate mitochondrial biogenesis upon fluctuating growth conditions.},
	language = {en},
	number = {5},
	urldate = {2025-09-05},
	journal = {Physiologia Plantarum},
	author = {Meyer, Etienne H. and Lopez-Lopez, Alicia and Keech, Olivier and Rouhier, Nicolas},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70482},
	keywords = {Archaeplastida, LYR-motif containing proteins, classification, mitochondria},
	pages = {e70482},
}

The LYR motif (LYRM)-containing proteins are small eukaryote-specific proteins that have been defined based on the presence of a Lys-Tyr-Arg amino acid motif and a conserved triplet of α-helices. Twelve LYRM proteins were described in humans. They are involved in core mitochondrial processes as subunits or assembly/stabilising factors of mitochondrial complexes. Their function depends on their ability to interact with the acylated form of acyl-carrier proteins (mtACPs), which places these proteins as direct contributors to two intertwined functional processes, energy metabolism and mitochondrial biogenesis. To gain insight into LYRM proteins in Archaeplastida, we first analyzed the Arabidopsis thaliana genome and then a set of organisms representing the different groups of the Archaeplastida clade. This analysis revealed the existence of 17 classes encompassing 10 of the 12 LYRM classes found in humans. Eleven classes exist in Arabidopsis, and six additional classes are present in some organisms but not in Arabidopsis, thus expanding previous observations. Subsequent data mining based on literature, gene expression, and in silico analyses allowed us to speculate about the possible molecular function of some currently uncharacterised LYRMs in plants. Altogether, this study revealed the diversification of the LYRM protein family in Archaeplastida and more globally among eukaryotes, in which the LYRM-mtACP associations represent central molecular systems to regulate mitochondrial biogenesis upon fluctuating growth conditions.

@article{zhang_phytochrome_2025,
	title = {Phytochrome {B} and phytochrome-interacting-factor4 modulate tree seasonal growth in cold environments},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-63391-5},
	doi = {10.1038/s41467-025-63391-5},
	abstract = {Plants that live at high latitudes and altitudes must adapt to growth in cold environments. Trees survive freezing winter conditions by ceasing growth and forming protective winter buds at the end of the growing season. To optimize growth and adaptation, the timing of growth cessation and bud set is critical. Like the well-studied Populus species (poplars, aspens, cottonwoods), many trees respond to the shortening photoperiods of fall to induce growth cessation. Temperature also has a role in this process, but the mechanism is unknown. Here, we show that the PHYTOCHROME B (PHYB)-PHYTOCHROME INTERACTING FACTOR4 (PIF4) module controls the interplay between photoperiod cues and temperature to prevent premature growth cessation and bud set at cooler temperatures. PHYB is essential for the ability of aspen trees to maintain growth under lower temperatures in permissive long days. This is mediated through PIF4, which promotes growth cessation, specifically in response to low temperatures rather than to changes in photoperiod. PIF4 can directly bind to the promoter region of the vegetative growth marker gene FLOWERING LOCUS T2 (FT2). In contrast to annual plants, it does so to suppress its transcription. Furthermore, lower temperatures can suppress PIF4 function at the transcriptional and protein levels to prevent premature growth cessation. These data show how poplar trees balance the antagonistic roles of PHYB and PIF4 to optimise the timing of growth cessation and bud set in cold environments, and this has been achieved with contrasting mechanisms compared to the annual plant model.},
	language = {en},
	number = {1},
	urldate = {2025-09-05},
	journal = {Nature Communications},
	author = {Zhang, Bo and Lee, Keh Chien and Romañach, Laura García and Ding, Jihua and Marcon, Alice and Nilsson, Ove},
	month = aug,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Abiotic, Light responses, Plant molecular biology, Plant morphogenesis},
	pages = {8114},
}

Plants that live at high latitudes and altitudes must adapt to growth in cold environments. Trees survive freezing winter conditions by ceasing growth and forming protective winter buds at the end of the growing season. To optimize growth and adaptation, the timing of growth cessation and bud set is critical. Like the well-studied Populus species (poplars, aspens, cottonwoods), many trees respond to the shortening photoperiods of fall to induce growth cessation. Temperature also has a role in this process, but the mechanism is unknown. Here, we show that the PHYTOCHROME B (PHYB)-PHYTOCHROME INTERACTING FACTOR4 (PIF4) module controls the interplay between photoperiod cues and temperature to prevent premature growth cessation and bud set at cooler temperatures. PHYB is essential for the ability of aspen trees to maintain growth under lower temperatures in permissive long days. This is mediated through PIF4, which promotes growth cessation, specifically in response to low temperatures rather than to changes in photoperiod. PIF4 can directly bind to the promoter region of the vegetative growth marker gene FLOWERING LOCUS T2 (FT2). In contrast to annual plants, it does so to suppress its transcription. Furthermore, lower temperatures can suppress PIF4 function at the transcriptional and protein levels to prevent premature growth cessation. These data show how poplar trees balance the antagonistic roles of PHYB and PIF4 to optimise the timing of growth cessation and bud set in cold environments, and this has been achieved with contrasting mechanisms compared to the annual plant model.