Browsing by Person "Liu, Chang"

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3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization
(2024) Liu, Pengfei; Vigneau, Jeromine; Craig, Rory J.; Barrera-Redondo, Josué; Avdievich, Elena; Martinho, Claudia; Borg, Michael; Haas, Fabian B.; Liu, Chang; Coelho, Susana M.; Liu, Pengfei; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Vigneau, Jeromine; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Craig, Rory J.; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Barrera-Redondo, Josué; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Avdievich, Elena; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Martinho, Claudia; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Borg, Michael; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Haas, Fabian B.; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Liu, Chang; Institute of Biology, University of Hohenheim, Stuttgart, Germany; Coelho, Susana M.; Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR) within the U and V chromosomes are insulated and span the centromeres and we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome’s 3D chromosomal folding.
Industrial chicory genome gives insights into the molecular timetable of anther development and male sterility
(2023) Waegneer, Evelien; Rombauts, Stephane; Baert, Joost; Dauchot, Nicolas; De Keyser, Annick; Eeckhaut, Tom; Haegeman, Annelies; Liu, Chang; Maudoux, Olivier; Notté, Christine; Staelens, Ariane; van der Veken, Jeroen; van Laere, Katrijn; Ruttink, Tom
Industrial chicory (Cichorium intybus var. sativum) is a biannual crop mostly cultivated for extraction of inulin, a fructose polymer used as a dietary fiber. F1 hybrid breeding is a promising breeding strategy in chicory but relies on stable male sterile lines to prevent self-pollination. Here, we report the assembly and annotation of a new industrial chicory reference genome. Additionally, we performed RNA-Seq on subsequent stages of flower bud development of a fertile line and two cytoplasmic male sterile (CMS) clones. Comparison of fertile and CMS flower bud transcriptomes combined with morphological microscopic analysis of anthers, provided a molecular understanding of anther development and identified key genes in a range of underlying processes, including tapetum development, sink establishment, pollen wall development and anther dehiscence. We also described the role of phytohormones in the regulation of these processes under normal fertile flower bud development. In parallel, we evaluated which processes are disturbed in CMS clones and could contribute to the male sterile phenotype. Taken together, this study provides a state-of-the-art industrial chicory reference genome, an annotated and curated candidate gene set related to anther development and male sterility as well as a detailed molecular timetable of flower bud development in fertile and CMS lines.
Mutations of PDS5 genes enhance TAD-like domain formation in Arabidopsis thaliana
(2024) Göbel, Anna-Maria; Zhou, Sida; Wang, Zhidan; Tzourtzou, Sofia; Himmelbach, Axel; Zheng, Shiwei; Pradillo, Mónica; Liu, Chang; Jiang, Hua; Göbel, Anna-Maria; Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany; Zhou, Sida; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany; Wang, Zhidan; Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany; Tzourtzou, Sofia; Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany; Himmelbach, Axel; Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany; Zheng, Shiwei; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany; Pradillo, Mónica; Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense, Madrid, Spain; Liu, Chang; Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, Stuttgart, Germany; Jiang, Hua; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
In eukaryotes, topologically associating domains (TADs) organize the genome into functional compartments. While TAD-like structures are common in mammals and many plants, they are challenging to detect in Arabidopsis thaliana. Here, we demonstrate that Arabidopsis PDS5 proteins play a negative role in TAD-like domain formation. Through Hi-C analysis, we show that mutations in PDS5 genes lead to the widespread emergence of enhanced TAD-like domains throughout the Arabidopsis genome, excluding pericentromeric regions. These domains exhibit increased chromatin insulation and enhanced chromatin interactions, without significant changes in gene expression or histone modifications. Our results suggest that PDS5 proteins are key regulators of genome architecture, influencing 3D chromatin organization independently of transcriptional activity. This study provides insights into the unique chromatin structure of Arabidopsis and the broader mechanisms governing plant genome folding.
Reactivation of the tRNASer/tRNATyr gene cluster in Arabidopsis thaliana root tips
(2025) Hummel, Guillaume; Kumari, Priyanka; Hua, Chenlei; Wang, Long; Mai, Yan-Xia; Wang, Nan; Shala, Negjmedin; Kaya, Emir Can; Molinier, Jean; Wang, Jia-Wei; Liu, Chang
Plants maintain redundant tRNA genes (tDNAs) in their nuclear genomes, but the significance, regulation, and functional roles of these genes remain poorly understood. A cluster of tandemly repeated tDNAs decoding serine and tyrosine (SYY cluster) is located on Arabidopsis (Arabidopsis thaliana) chromosome 1, intersecting constitutive heterochromatin and remaining transcriptionally silenced in most tissues. The natural conditions inducing their transcription remain unknown. Here, we elucidate the tissue-specific expression pattern of this cluster during seedling establishment. Our findings reveal that SYY cluster tRNAs are primarily produced in the root cap columella and adjacent root cap cells. Transcriptional reactivation of the SYY cluster occurs in these tissues despite high DNA methylation levels. Furthermore, we demonstrate that these cells accumulate high levels of a transgenic glycoprotein rich in serine, tyrosine, and proline, and that CRISPR/Cas9 deletion of the SYY cluster alters the accumulation and stability of the glycoprotein in these specific cells. Our work provides pioneering evidence of a developmental and cell-specific expression program for a plant tDNA. We offer insights into the putative role of specialized tDNAs in enhancing glycoprotein biosynthesis in protective tissues of the meristem.