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  • 1
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    Online Resource
    A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data (2023)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    b3kat_BV048521203
    Format: 1 Online-Ressource
    Edition: [Zweitveröffentlichung]
    Language: English
    DOI: 10.18452/25808
    URN: urn:nbn:de:kobv:11-110-18452/26480-2
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    HU Berlin
  • 2
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    Online Resource
    Single-nucleus RNA sequencing of plant tissues using a nanowell‐based system (2021)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_25253
    Format: 1 Online-Ressource (11 Seiten)
    ISSN: 0960-7412 , 0960-7412
    Content: Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nucleus isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as an alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nucleus isolation method by using different plant materials from different species. The potential of our single-nucleus RNA sequencing method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors regulating this process, and predicted potential target genes of these transcription factors. Our nucleus isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
    Content: Peer Reviewed
    In: Oxford [u.a.] : Wiley-Blackwell, 108,3, Seiten 859-869, 0960-7412
    Language: English
    DOI: 10.1111/tpj.15458
    DOI: 10.18452/24579
    URN: urn:nbn:de:kobv:11-110-18452/25253-5
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  • 3
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    The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors (2021)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_25221
    Format: 1 Online-Ressource (13 Seiten)
    Content: The MADS transcription factors (TF) are an ancient eukaryotic protein family. In plants, the family is divided into two main lineages. Here, we demonstrate that DNA binding in both lineages absolutely requires a short amino acid sequence C-terminal to the MADS domain (M domain) called the Intervening domain (I domain) that was previously defined only in type II lineage MADS. Structural elucidation of the MI domains from the floral regulator, SEPALLATA3 (SEP3), shows a conserved fold with the I domain acting to stabilise the M domain. Using the floral organ identity MADS TFs, SEP3, APETALA1 (AP1) and AGAMOUS (AG), domain swapping demonstrate that the I domain alters genome-wide DNA-binding specificity and dimerisation specificity. Introducing AG carrying the I domain of AP1 in the Arabidopsis ap1 mutant resulted in strong complementation and restoration of first and second whorl organs. Taken together, these data demonstrate that the I domain acts as an integral part of the DNA-binding domain and significantly contributes to the functional identity of the MADS TF.
    Content: Peer Reviewed
    Note: This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin.
    In: London : Nature Publishing Group UK, 12
    Language: English
    DOI: 10.18452/24549
    DOI: 10.1038/s41467-021-24978-w
    URN: urn:nbn:de:kobv:11-110-18452/25221-6
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  • 4
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    Online Resource
    The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation (2020)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_23242
    Format: 1 Online-Ressource (14 Seiten)
    Content: Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon.
    Content: Peer Reviewed
    Note: This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin.
    In: Basel : Molecular Diversity Preservation International, 21,16
    Language: English
    DOI: 10.18452/22629
    DOI: 10.3390/ijms21165633
    URN: urn:nbn:de:kobv:11-110-18452/23242-2
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  • 5
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    Online Resource
    Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation (2018)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_20381
    Format: 1 Online-Ressource (14 Seiten)
    Content: Chloroplasts (and other plastids) harbor their own genetic material, with a bacterial-like gene-expression systems. Chloroplast RNA metabolism is complex and is predominantly mediated by nuclear-encoded RNA-binding proteins. In addition to these nuclear factors, the chloroplast-encoded intron maturase MatK has been suggested to perform as a splicing factor for a subset of chloroplast introns. MatK is essential for plant cell survival in tobacco, and thus null mutants have not yet been isolated. We therefore attempted to over-express MatK from a neutral site in the chloroplast, placing it under the control of a theophylline-inducible riboswitch. This ectopic insertion of MatK lead to a variegated cotyledons phenotype. The addition of the inducer theophylline exacerbated the phenotype in a concentration-dependent manner. The extent of variegation was further modulated by light, sucrose and spectinomycin, suggesting that the function of MatK is intertwined with photosynthesis and plastid translation. Inhibiting translation in the transplastomic lines has a profound effect on the accumulation of several chloroplast mRNAs, including the accumulation of an RNA antisense to rpl33, a gene coding for an essential chloroplast ribosomal protein. Our study further supports the idea that MatK expression needs to be tightly regulated to prevent detrimental effects and establishes another link between leaf variegation and chloroplast translation.
    Content: Peer Reviewed
    Note: This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin.
    In: Lausanne : Frontiers Media, 9
    Language: English
    DOI: 10.18452/19611
    DOI: 10.3389/fpls.2018.01453
    URN: urn:nbn:de:kobv:11-110-18452/20381-8
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  • 6
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    Cell identity specification in plants: lessons from flower development (2021)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_28770
    Format: 1 Online-Ressource (16 Seiten)
    Content: Multicellular organisms display a fascinating complexity of cellular identities and patterns of diversification. The concept of ‘cell type’ aims to describe and categorize this complexity. In this review, we discuss the traditional concept of cell types and highlight the impact of single-cell technologies and spatial omics on the understanding of cellular differentiation in plants. We summarize and compare position-based and lineage-based mechanisms of cell identity specification using flower development as a model system. More than understanding ontogenetic origins of differentiated cells, an important question in plant science is to understand their position- and developmental stage-specific heterogeneity. Combinatorial action and crosstalk of external and internal signals is the key to cellular heterogeneity, often converging on transcription factors that orchestrate gene expression programs.
    Content: Peer Reviewed
    In: Oxford : Oxford Univ. Press, 72,12, Seiten 4202-4217
    Language: English
    DOI: 10.18452/28125
    DOI: 10.1093/jxb/erab110
    URN: urn:nbn:de:kobv:11-110-18452/28770-4
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  • 7
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    Arabidopsis BBX14 is involved in high light acclimation and seedling development (2023)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_29218
    Format: 1 Online-Ressource (18 Seiten)
    ISSN: 0960-7412 , 0960-7412
    Content: The development of photosynthetically competent seedlings requires both light and retrograde biogenic signaling pathways. The transcription factor GLK1 functions at the interface between these pathways and receives input from the biogenic signal integrator GUN1. BBX14 was previously identified, together with GLK1, in a core module that mediates the response to high light (HL) levels and biogenic signals, which was studied by using inhibitors of chloroplast development. Our chromatin immunoprecipitation-Seq experiments revealed that BBX14 is a direct target of GLK1, and RNA-Seq analysis suggests that BBX14 may function as a regulator of the circadian clock. In addition, BBX14 plays a role in chlorophyll biosynthesis during early onset of light. Knockout of BBX14 results in a long hypocotyl phenotype dependent on a retrograde signal. Furthermore, the expression of BBX14 and BBX15 during biogenic signaling requires GUN1. Investigation of the role of BBX14 and BBX15 in GUN-type biogenic (gun) signaling showed that the overexpression of BBX14 or BBX15 caused de-repression of CA1 mRNA levels, when seedlings were grown on norflurazon. Notably, transcripts of the LHCB1.2 marker are not de-repressed. Furthermore, BBX14 is required to acclimate plants to HL stress. We propose that BBX14 is an integrator of biogenic signals and that BBX14 is a nuclear target of retrograde signals downstream of the GUN1/GLK1 module. However, we do not classify BBX14 or BBX15 overexpressors as gun mutants based on a critical evaluation of our results and those reported in the literature. Finally, we discuss a classification system necessary for the declaration of new gun mutants.
    Content: Peer Reviewed
    In: Oxford [u.a.] : Wiley-Blackwell, 118,1, Seiten 141-158, 0960-7412
    Language: English
    DOI: 10.18452/28597
    DOI: 10.1111/tpj.16597
    URN: urn:nbn:de:kobv:11-110-18452/29218-9
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  • 8
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    Online Resource
    A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data (2022)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_26480
    Format: 1 Online-Ressource (11 Seiten)
    Content: Cellular heterogeneity in growth and differentiation results in organ patterning. Single-cell transcriptomics allows characterization of gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during this methodology. To recover the original location of cells in the developing organ is essential to link gene activity with cellular identity and function in plants. Here, we propose a method to reconstruct genome-wide gene expression patterns of individual cells in a 3D flower meristem by combining single-nuclei RNA-seq with microcopy-based 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the method is used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com.
    Content: Peer Reviewed
    Note: This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin.
    In: [London] : Nature Publishing Group UK, 13
    Language: English
    DOI: 10.18452/25808
    DOI: 10.1038/s41467-022-30177-y
    URN: urn:nbn:de:kobv:11-110-18452/26480-2
    URL: Volltext  (kostenfrei)
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    HU Berlin
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