Works (13)

Updated: February 27th, 2024 08:30

2023 article

Cell-type-specific PtrWOX4a and PtrVCS2 form a regulatory nexus with a histone modification system for stem cambium development in Populus trichocarpa

Dai, X., Zhai, R., Lin, J., Wang, Z., Meng, D., Li, M., … Li, W. (2023, January 9). Nature Plants, Vol. 9, pp. 96–111.

By: X. Dai*, R. Zhai*, J. Lin*, Z. Wang*, D. Meng*, M. Li*, Y. Mao*, B. Gao* ...

Contributors: X. Dai*, R. Zhai*, J. Lin*, Z. Wang*, D. Meng*, M. Li*, Y. Mao*, B. Gao* ...

MeSH headings : Cambium / genetics; Populus / genetics; Epigenesis, Genetic; Histone Code; Wood; Gene Expression Regulation, Plant
topics (OpenAlex): Plant Molecular Biology Research; Plant Gene Expression Analysis; Chromosomal and Genetic Variations
TL;DR: A regulatory system in which transcription factor and histone acetylation functions are coordinated for maintaining normal stem vascular cambium development for wood formation in Populus trichocarpa is revealed. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: January 23, 2023

2021 article

A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa

Yu, J., Zhou, C., Li, D., Li, S., Lin, Y.-C. J., Wang, J. P., … Li, W. (2021, October 22). Plant Communications, Vol. 1.

Contributors: J. Yu*, C. Zhou*, D. Li*, S. Li*, Y. Jimmy Lin*, J. Wang n, V. Chiang n, W. Li*

author keywords: tension wood; cellulose; lignin; transcriptional regulatory network; transcriptomics; chromatin immunoprecipitation sequencing
MeSH headings : Biomechanical Phenomena; Gene Expression Regulation, Plant / physiology; Gene Regulatory Networks / physiology; Genes, Plant / genetics; Genes, Plant / physiology; Laser Capture Microdissection; Populus / genetics; Populus / physiology; Wood / genetics; Wood / physiology; Xylem
topics (OpenAlex): Plant Gene Expression Analysis; Plant Molecular Biology Research; Plant biochemistry and biosynthesis
TL;DR: This work suggests that P trLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus by directly regulating 26 novel TW-responsive transcription factor genes. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: January 31, 2022

2021 article

Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa

Lin, C.-Y., Sun, Y., Song, J., Chen, H.-C., Shi, R., Yang, C., … Chiang, V. L. (2021, October 6). Frontiers in Plant Science, Vol. 12.

By: C. Lin n, Y. Sun*, J. Song n, H. Chen n, R. Shi n, C. Yang n, J. Liu n, S. Tunlaya-Anukit n ...

Contributors: C. Lin n, H. Chen n, R. Shi n, C. Yang n, J. Liu n, S. Tunlaya-Anukit n, Y. Lin n, R. Sederoff n ...

author keywords: protein interaction; monolignol biosynthesis; wood formation; Populus trichocarpa; BiFC; metabolic flux
topics (OpenAlex): Plant Gene Expression Analysis; Lignin and Wood Chemistry; Biofuel production and bioconversion
TL;DR: It is proposed that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: November 8, 2021

2021 article

Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood

Liu, B., Liu, J., Yu, J., Wang, Z., Sun, Y., Li, S., … Wang, J. P. (2021, January 28). PLANT PHYSIOLOGY, Vol. 186, pp. 250–269.

MeSH headings : Cell Wall / metabolism; Gene Expression Regulation, Plant; Populus / anatomy & histology; Populus / genetics; Transcription, Genetic; Wood / genetics; Wood / metabolism; Xylem / metabolism
topics (OpenAlex): Plant Molecular Biology Research; Plant Gene Expression Analysis; Plant Surface Properties and Treatments
TL;DR: A transcriptional regulatory network is established in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively in P. trichocarpa, to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: May 27, 2021

2019 article

A novel synthetic-genetic-array–based yeast one-hybrid system for high discovery rate and short processing time

Yeh, C.-S., Wang, Z., Miao, F., Ma, H., Kao, C.-T., Hsu, T.-S., … Lin, Y.-C. J. (2019, June 11). Genome Research, Vol. 29, pp. 1343–1351.

By: C. Yeh*, Z. Wang*, F. Miao*, H. Ma*, C. Kao*, T. Hsu*, J. Yu*, E. Hung* ...

Contributors: C. Yeh*, Z. Wang*, F. Miao*, H. Ma*, C. Kao*, T. Hsu*, J. Yu*, E. Hung* ...

MeSH headings : Animals; DNA / genetics; DNA / metabolism; Gene Expression Regulation; Gene Regulatory Networks; Genetic Markers; Humans; Meiosis; Microarray Analysis / instrumentation; Microarray Analysis / methods; Plasmids / chemistry; Plasmids / metabolism; Ploidies; Populus / cytology; Protein Binding; Protoplasts / cytology; Protoplasts / metabolism; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Time Factors; Transcription Factors / genetics; Transcription Factors / metabolism; Two-Hybrid System Techniques
topics (OpenAlex): Fungal and yeast genetics research; CRISPR and Genetic Engineering; Genomics and Chromatin Dynamics
TL;DR: A high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis that has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: September 16, 2019

2018 article

CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa

Yan, X., Liu, J., Kim, H., Liu, B., Huang, X., Yang, Z., … Chiang, V. L. (2018, October 2). New Phytologist, Vol. 222, pp. 244–260.

By: X. Yan*, J. Liu n, H. Kim*, B. Liu*, X. Huang*, Z. Yang n, Y. Lin*, H. Chen n ...

Contributors: X. Yan*, J. Liu n, H. Kim*, B. Liu*, X. Huang*, Z. Yang n, Y. Lin*, H. Chen n ...

author keywords: co-immunoprecipitation; enzyme activity; monolignol biosynthetic pathway; nuclear magnetic resonance (NMR); Populus trichocarpa; stem-differentiating xylem protein
MeSH headings : Aldehyde Oxidoreductases / genetics; Aldehyde Oxidoreductases / metabolism; Down-Regulation / genetics; Gene Expression Regulation, Plant; Lignin / metabolism; Magnetic Resonance Spectroscopy; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Populus / genetics; Populus / metabolism; RNA Interference; Recombinant Proteins / metabolism; Xylem / metabolism
topics (OpenAlex): Plant Gene Expression Analysis; Lignin and Wood Chemistry; Biofuel production and bioconversion
TL;DR: Evidence is provided for the formation of PtrCAD1/PtrCCR2 protein complexes in monolignol biosynthesis in planta, and biomolecular fluorescence complementation and pull-down/co-immunoprecipitation experiments supported a hypothesis of P Tr trichocarpa heterodimer formation. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 17, 2018

2017 article

Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa

Shi, R., Wang, J. P., Lin, Y.-C., Li, Q., Sun, Y.-H., Chen, H., … Chiang, V. L. (2017, January 12). Planta, Vol. 245, pp. 927–938.

By: R. Shi n, J. Wang n, Y. Lin n, Q. Li*, Y. Sun*, H. Chen n, R. Sederoff n, V. Chiang*

Contributors: R. Shi n, J. Wang n, Y. Lin n, Q. Li*, Y. Sun*, H. Chen n, R. Sederoff n, V. Chiang*

author keywords: Wood formation; Transcriptome; Fiber cells; Vessel elements; Cell wall biosynthesis; Co-expression network
MeSH headings : Cell Wall / metabolism; Cellulose / metabolism; Cluster Analysis; Gene Expression Regulation, Plant; Lignin / metabolism; Molecular Sequence Annotation; Organ Specificity; Phloem / genetics; Phloem / growth & development; Plant Leaves / genetics; Plant Leaves / growth & development; Plant Proteins / genetics; Populus / genetics; Populus / growth & development; Sequence Analysis, RNA; Transcription Factors / genetics; Transcriptome; Wood / genetics; Wood / growth & development; Xylem / genetics; Xylem / growth & development
topics (OpenAlex): Plant Gene Expression Analysis; Wood and Agarwood Research; Fermentation and Sensory Analysis
TL;DR: The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2015 journal article

Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis

Proceedings of the National Academy of Sciences, 112(27), 8481–8486.

By: J. Wang n, L. Chuang n, P. Loziuk n, H. Chen n, Y. Lin n, R. Shi n, G. Qu*, D. Muddiman n, R. Sederoff n, V. Chiang n

Contributors: J. Wang n, L. Chuang n, P. Loziuk n, H. Chen n, Y. Lin n, R. Shi n, G. Qu*, D. Muddiman n, R. Sederoff n, V. Chiang n

author keywords: AldOMT; COMT; lignin; phosphoproteomics; phosphoregulation
MeSH headings : Acrolein / analogs & derivatives; Acrolein / metabolism; Amino Acid Sequence; Binding Sites / genetics; Biocatalysis; Catechols / metabolism; Chromatography, Liquid; Electrophoresis, Polyacrylamide Gel; Green Fluorescent Proteins / genetics; Green Fluorescent Proteins / metabolism; Isoenzymes / genetics; Isoenzymes / metabolism; Lignin / biosynthesis; Methyltransferases / genetics; Methyltransferases / metabolism; Microscopy, Confocal; Molecular Sequence Data; Mutation; Phosphoproteins / metabolism; Phosphorylation; Plant Proteins / genetics; Plant Proteins / metabolism; Populus / enzymology; Populus / genetics; Populus / metabolism; Proteomics / methods; Protoplasts / enzymology; Protoplasts / metabolism; Sequence Homology, Amino Acid; Tandem Mass Spectrometry
topics (OpenAlex): Plant Gene Expression Analysis; Biofuel production and bioconversion; Horticultural and Viticultural Research
TL;DR: It is shown that reversible monophosphorylation at Ser123 or Ser125 acts as an on/off switch for the activity of 5-hydroxyconiferaldehyde O-methyltransferase 2 (PtrAldOMT2), an enzyme central to monolignol biosynthesis for lignification in stem-differentiating xylem of Populus trichocarpa. (via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018

2014 article

A robust chromatin immunoprecipitation protocol for studying transcription factor–DNA interactions and histone modifications in wood-forming tissue

Li, W., Lin, Y.-C., Li, Q., Shi, R., Lin, C.-Y., Chen, H., … Chiang, V. L. (2014, August 21). Nature Protocols.

MeSH headings : Base Sequence; Chromatin Immunoprecipitation / methods; DNA / metabolism; DNA Fragmentation; Histones / metabolism; Immunoprecipitation; Molecular Sequence Data; Populus / cytology; Populus / metabolism; Sequence Analysis, DNA; Transcription Factors / metabolism; Wood / cytology; Xylem / genetics; Xylem / metabolism
topics (OpenAlex): Plant Molecular Biology Research; Genomics and Chromatin Dynamics; Plant Gene Expression Analysis
TL;DR: This protocol is the only working ChIP system for wood-forming tissue and uses stem-differentiating xylem to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2014 article

A simple improved-throughput xylem protoplast system for studying wood formation

Lin, Y.-C., Li, W., Chen, H., Li, Q., Sun, Y.-H., Shi, R., … Chiang, V. L. (2014, August 21). Nature Protocols, Vol. 9, pp. 2194–2205.

By: Y. Lin n, W. Li n, H. Chen n, Q. Li n, Y. Sun*, R. Shi n, C. Lin n, J. Wang n ...

Contributors: Y. Lin n, W. Li n, H. Chen n, Q. Li n, Y. Sun*, R. Shi n, C. Lin n, J. Wang n ...

MeSH headings : Cell Wall / metabolism; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Green Fluorescent Proteins; Populus / cytology; Populus / growth & development; Protoplasts / metabolism; Transfection / methods; Wood / cytology; Wood / growth & development; Xylem / chemistry
topics (OpenAlex): Plant Molecular Biology Research; Plant Reproductive Biology; Plant Gene Expression Analysis
TL;DR: A protocol for the isolation and transfection of protoplasts from wood-forming tissue, the stem-differentiating xylem (SDX), in the model woody plant Populus trichocarpa is presented. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 article

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

Lin, Y.-C., Li, W., Sun, Y.-H., Kumari, S., Wei, H., Li, Q., … Chiang, V. L. (2013, November 1). The Plant Cell.

MeSH headings : Algorithms; Cell Wall / genetics; Chromatin Immunoprecipitation; Gene Expression Regulation, Plant; Gene Ontology; Gene Regulatory Networks; High-Throughput Nucleotide Sequencing; Models, Genetic; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Polymerase Chain Reaction / methods; Populus / genetics; Populus / metabolism; Protoplasts; Reproducibility of Results; Transcription Factors / genetics; Transcription Factors / metabolism; Transfection; Wood / genetics; Wood / metabolism; Xylem / cytology; Xylem / genetics
topics (OpenAlex): Plant Gene Expression Analysis; Plant Molecular Biology Research; Plant biochemistry and biosynthesis
TL;DR: A genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)–directed hierarchical gene regulatory networks (hGRNs) in wood formation is developed and may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2012 article

Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC–MS/MS based protein quantification and metabolic flux analysis

Wang, J. P., Shuford, C. M., Li, Q., Song, J., Lin, Y.-C., Sun, Y.-H., … Chiang, V. L. (2012, May 24). Planta, Vol. 236, p. 795–808.

By: J. Wang n, C. Shuford n, Q. Li n, J. Song n, Y. Lin n, Y. Sun n, H. Chen n, C. Williams n ...

Contributors: J. Wang n, C. Shuford n, Q. Li n, J. Song n, Y. Lin n, Y. Sun n, H. Chen n, C. Williams n ...

author keywords: Lignin; Syringyl lignin; Angiosperm; Kinetics; Subcellular localization
MeSH headings : Cloning, Molecular; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Hydroxylation; Kinetics; Lignin / analysis; Lignin / biosynthesis; Mixed Function Oxygenases / metabolism; Plants, Genetically Modified; Populus / metabolism; Xylem / enzymology; Yeasts / metabolism
topics (OpenAlex): Plant Gene Expression Analysis; Fermentation and Sensory Analysis; Biochemical and biochemical processes
TL;DR: The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis. (via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2012 article

Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa

Li, Q., Lin, Y.-C., Sun, Y.-H., Song, J., Chen, H., Zhang, X.-H., … Chiang, V. L. (2012, August 22). Proceedings of the National Academy of Sciences.

MeSH headings : Blotting, Western; Cloning, Molecular; DNA Primers / genetics; Dimerization; Electrophoresis, Polyacrylamide Gel; Gene Regulatory Networks / genetics; Homeostasis / physiology; Models, Biological; Plasmids / genetics; Populus / genetics; Protein Isoforms / genetics; Protein Transport; Real-Time Polymerase Chain Reaction; Transcription Factors / genetics
topics (OpenAlex): Plant Molecular Biology Research; Plant Gene Expression Analysis; Photosynthetic Processes and Mechanisms
TL;DR: A stem-differentiating xylem (SDX)-specific alternative SND1 splice variant, PtrSND1-A2IR, that acts as a dominant negative of S ND1 transcriptional network genes in Populus trichocarpa is discovered and may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

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