Genome-Wide Identification of Direct Targets of the TTG1–bHLH–MYB Complex in Regulating Trichome Formation and Flavonoid Accumulation in Arabidopsis Thaliana

Extensive studies have shown that the MBW complex consisting of three kinds of regulatory proteins, MYB and basic helix–loop–helix (bHLH) transcription factors and a WD40 repeat protein, TRANSPARENT TESTA GLABRA1 (TTG1), acts in concert to promote trichome formation and flavonoid accumulation in Arabidopsis thaliana. TTG1 functions as an essential activator in these two biological processes. However, direct downstream targets of the TTG1-dependent MBW complex have not yet been obtained in the two biological processes at the genome-wide level in A. thaliana. In the present study, we found, through RNA sequencing and quantitative real-time PCR analysis, that a great number of regulatory and structural genes involved in both trichome formation and flavonoid accumulation are significantly downregulated in the young shoots and expanding true leaves of ttg1-13 plants. Post-translational activation of a TTG1-glucocorticoid receptor fusion protein and chromatin immunoprecipitation assays demonstrated that these downregulated genes are directly or indirectly targeted by the TTG1-dependent MBW complex in vivo during trichome formation and flavonoid accumulation. These findings further extend our understanding of the role of TTG1-dependent MBW complex in the regulation of trichome formation and flavonoid accumulation in A. thaliana.

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Genome-wide identification of the tea plant bHLH transcription factor family and discovery of candidate regulators of trichome formation

Scientific Reports ◽

10.1038/s41598-021-90205-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Renjian Liu ◽

Yuyuan Wang ◽

Song Tang ◽

Jiarong Cai ◽

Shaoqun Liu ◽

...

Keyword(s):

Transcriptional Activation ◽

Expression Patterns ◽

Tea Plant ◽

Bhlh Transcription Factor ◽

Phylogenetic Tree Analysis ◽

Helix Loop Helix ◽

Trichome Formation ◽

Genome Wide ◽

Tea Plants ◽

Bhlh Transcription Factors

AbstractLeaf trichomes play vital roles in plant resistance and the quality of tea. Basic helix-loop-helix (bHLH) transcription factors (TFs) play an important role in regulating plant development and growth. In this study, a total of 134 CsbHLH proteins were identified in the Camellia sinensis var. sinensis (CSS) genome. They were divided into 17 subgroups according to the Arabidopsis thaliana classification. Phylogenetic tree analysis indicated that members of subgroups IIIc-I and IIIc-II might be associated with trichome formation. The expression patterns of CsbHLH116, CsbHLH133, CsbHLH060, CsbHLH028, CsbHLH024, CsbHLH112 and CsbHLH053 from clusters 1, 3 and 5 were similar to the trichome distribution in tea plants. CsbHLH024 and CsbHLH133 were located in the cell nucleus and possessed transcriptional activation ability. They could interact with CsTTG1, which is a regulator of tea trichome formation. This study provides useful information for further research on the function of CsbHLHs in trichome formation.

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Genome-Wide Identification of Tea Plant bHLH Transcription Factor Family and Discovery of Candidate Regulator for Trichome Formation

10.21203/rs.3.rs-148784/v1 ◽

2021 ◽

Author(s):

Renjian Liu ◽

Yuyuan Wang ◽

Song Tang ◽

Jiarong Cai ◽

Shaoqun Liu ◽

...

Keyword(s):

Transcriptional Activation ◽

Expression Patterns ◽

Tea Plant ◽

Bhlh Transcription Factor ◽

Phylogenetic Tree Analysis ◽

Helix Loop Helix ◽

Trichome Formation ◽

Genome Wide ◽

Tea Plants ◽

Bhlh Transcription Factors

Abstract Leaf trichomes play vital roles in plant resistance and tea quality. Basic helix-loop-helix (bHLH) transcription factors (TFs) play an important role in regulating plant development and growth. However, it is poorly understood whether bHLH TFs are associated with trichome formation in tea plant. In this study, a total of 134 CsbHLH proteins were identified in the Camellia sinensis var. sinensis (CSS) genome. All identified proteins were divided into 19 subgroups according to the Arabidopsis thaliana classification. Phylogenetic tree analysis indicated that the members of group IIIc-I and group IIIc-II might be associated with trichome formation. Expression analysis showed that the candidate genes associated with trichome formation in tea plant were primarily located in cluster 1, cluster 3 and cluster 5. The expression patterns of CsbHLH116, CsbHLH133, CsbHLH060, CsbHLH028, CsbHLH024, CsbHLH112 and CsbHLH053 from these clusters were similar to the trichome distribution in tea plants. Notably, CsbHLH024 and CsbHLH133 were highly expressed in the young tissues of different cultivars. CsbHLH024 and CsbHLH133 possessed transcriptional activation ability and could interact with CsTTG1, a regulator of tea trichome formation. This study provides useful information for further research on the function of CsbHLHs in the regulation of trichome formation.

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TCF12 controls oligodendroglial cell proliferation and regulates signaling pathways conserved in gliomas

10.1101/2021.07.26.453859 ◽

2021 ◽

Author(s):

Sofia Archontidi ◽

Corentine Marie ◽

Beata Gyorgy ◽

Justine Guegan ◽

Marc Sanson ◽

...

Keyword(s):

Biological Processes ◽

Oligodendrocyte Differentiation ◽

Gene Encoding ◽

Genome Wide ◽

Diffuse Gliomas ◽

Mrna And Protein Expression ◽

Oligodendrocyte Precursor ◽

Oligodendrocyte Development ◽

Chromatin Profiling

Diffuse gliomas are primary brain tumors originating from the transformation of glial cells. In particular, oligodendrocyte precursor cells constitute the major tumor-amplifying population in the gliomagenic process. We previously identified the TCF12 gene, encoding a transcription factor of the E protein family, as being recurrently mutated in oligodendrogliomas. In this study, we sought to understand the function of TCF12 in oligodendroglial cells, the glioma lineage of origin. We first describe TCF12 mRNA and protein expression pattern in oligodendroglial development in the mouse brain. Second, by TCF12 genome wide chromatin profiling in oligodendroglial cells, we show that TCF12 binds active promoters of genes involved in proliferation, translation/ribosomes, and pathways involved in oligodendrocyte development and cancer. Finally, we perform OPC-specific Tcf12 inactivation in vivo and demonstrate by immunofluorescence and transcriptomic analyses that TCF12 is transiently required for OPC proliferation but dispensable for oligodendrocyte differentiation. We further show that Tcf12 inactivation results in deregulation of biological processes that are also altered in oligodendrogliomas. Together, our data suggest that TCF12 directly regulates transcriptional programs in oligodendroglia development that are relevant in a glioma context.

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CLIP and RNA interactome studies to unravel genome-wide RNA-protein interactions in vivo in Arabidopsis thaliana

Methods ◽

10.1016/j.ymeth.2019.09.005 ◽

2020 ◽

Vol 178 ◽

pp. 63-71 ◽

Cited By ~ 1

Author(s):

Tino Köster ◽

Marlene Reichel ◽

Dorothee Staiger

Keyword(s):

Arabidopsis Thaliana ◽

Protein Interactions ◽

Genome Wide

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Cloning, purification and preliminary X-ray data analysis of the human ID2 homodimer

Acta Crystallographica Section F Structural Biology and Crystallization Communications ◽

10.1107/s174430911203895x ◽

2012 ◽

Vol 68 (11) ◽

pp. 1354-1358 ◽

Cited By ~ 3

Author(s):

Marie V. Wong ◽

Paaventhan Palasingam ◽

Prasanna R. Kolatkar

Keyword(s):

Dna Binding ◽

Potassium Acetate ◽

Class Iii ◽

Data Set ◽

Cell Parameters ◽

Helix Loop Helix ◽

Id Protein ◽

Bhlh Transcription Factors

The ID proteins are named for their role as inhibitors of DNA binding and differentiation. They contain a helix–loop–helix (HLH) domain but lack a basic DNA-binding domain. In complex with basic HLH (bHLH) transcription factors, gene expression is regulated by DNA-binding inactivation. Although the HLH domain is highly conserved and shares a similar topology, the IDs preferentially bind class I bHLH-group members such as E47 (TCF3) but not the class III bHLH member Myc. A structure of an ID protein could potentially shed light on its mechanism. Owing to their short half-livesin vivoand reportedin vitroinstability, this paper describes the strategies that went into expressing sufficient soluble and stable ID2 to finally obtain diffraction-quality crystals. A 2.1 Å resolution data set was collected from a crystal belonging to space groupP3121 with unit-cell parametersa=b= 51.622,c= 111.474 Å, α = β = 90, γ = 120° that was obtained by hanging-drop vapour diffusion in a precipitant solution consisting of 0.1 MMES pH 6.5, 2.0 Mpotassium acetate. The solvent content was consistent with the presence of one or two molecules in the asymmetric unit.

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Early specification of sensory neuron fate revealed by expression and function of neurogenins in the chick embryo

Development ◽

10.1242/dev.126.8.1715 ◽

1999 ◽

Vol 126 (8) ◽

pp. 1715-1728 ◽

Cited By ~ 27

Author(s):

S.E. Perez ◽

S. Rebelo ◽

D.J. Anderson

Keyword(s):

Neural Crest ◽

Sensory Neuron ◽

Ectopic Expression ◽

Neural Crest Cells ◽

Sensory Ganglia ◽

Helix Loop Helix ◽

Autonomic Neurons ◽

And Function ◽

Bhlh Transcription Factors

The generation of sensory and autonomic neurons from the neural crest requires the functions of two classes of basic helix-loop-helix (bHLH) transcription factors, the Neurogenins (NGNs) and MASH-1, respectively (Fode, C., Gradwohl, G., Morin, X., Dierich, A., LeMeur, M., Goridis, C. and Guillemot, F. (1998) Neuron 20, 483–494; Guillemot, F., Lo, L.-C., Johnson, J. E., Auerbach, A., Anderson, D. J. and Joyner, A. L. (1993) Cell 75, 463–476; Ma, Q., Chen, Z. F., Barrantes, I. B., de la Pompa, J. L. and Anderson, D. J. (1998 Neuron 20, 469–482). We have cloned two chick NGNs and found that they are expressed in a subset of neural crest cells early in their migration. Ectopic expression of the NGNs in vivo biases migrating neural crest cells to localize in the sensory ganglia, and induces the expression of sensory neuron-appropriate markers in non-sensory crest derivatives. Surprisingly, the NGNs can also induce the expression of multiple pan-neuronal and sensory-specific markers in the dermomyotome, a mesodermal derivative. Taken together, these data suggest that a subset of neural crest cells may already be specified for a sensory neuron fate early in migration, as a consequence of NGN expression.

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Quantitative proteomics reveals extensive lysine ubiquitination in the Arabidopsis root proteome and uncovers novel transcription factor stability states

10.1101/2021.01.07.425780 ◽

2021 ◽

Author(s):

Gaoyuan Song ◽

Damilola Olatunji ◽

Christian Montes ◽

Natalie M Clark ◽

Yunting Pu ◽

...

Keyword(s):

Posttranslational Modification ◽

Site Directed Mutagenesis ◽

Biological Processes ◽

Protein Activity ◽

Helix Loop Helix ◽

Primary Roots ◽

Lysine Residues ◽

Ubiquitin Proteasome ◽

The Stability

Protein activity, abundance, and stability can be regulated by posttranslational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function and yet we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich peptides containing the di-glycine (diGly) remnant of ubiquitin and coupled that with isobaric labeling to enable quantification, from up to 16-multiplexed samples, for plant tissues. Collectively, we identified 7,130 diGly-modified lysine residues sites arising from 3,178 proteins in Arabidopsis primary roots. These data include ubiquitin proteasome dependent ubiquitination events as well as ubiquitination events associated with auxin treatment. Gene Ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and root morphogenesis. We determined the ubiquitinated lysine residues that directly regulate the stability of the transcription factors CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) using site directed mutagenesis and in vivo degradation assays. These comprehensive site-level ubiquitinome profiles provide a wealth of data for future studies related to modulation of biological processes mediated by this posttranslational modification in plants.

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Identification and Characterization of the Basic Helix-Loop-Helix Transcription Factor Family in Pinus massoniana

Forests ◽

10.3390/f11121292 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1292

Author(s):

Yu Chen ◽

Peihuang Zhu ◽

Fan Wu ◽

Xiaofeng Wang ◽

Jinfeng Zhang ◽

...

Keyword(s):

Transcription Factor ◽

Pinus Massoniana ◽

Pcr Analysis ◽

Bhlh Protein ◽

Transcription Factor Family ◽

Masson Pine ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Bhlh Genes ◽

Bhlh Transcription Factors

The basic helix-loop-helix (bHLH) protein transcription factor family is the most widely distributed transcription factor family in eukaryotes. Members of this family play important roles in secondary metabolic biosynthesis, signal transduction, and plant resistance. Research on the bHLH family in animals is more extensive than that in plants, and members of the family in plants are classified according to the classification criteria for those in animals. To date, no research on the bHLH gene family in Pinus massoniana (Masson pine) has been reported. In this study, we identified 88 bHLH genes from four transcriptomes of Masson pine and performed bioinformatics analysis. These genes were divided into 10 groups in total. RT-PCR analysis revealed that the expression levels of the six genes increased under abiotic stress and hormone treatments. These findings will facilitate further studies on the functions of bHLH transcription factors.

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Homo- and heterodimerization of bHLH transcription factors balance stemness and bipotential differentiation

10.1101/685347 ◽

2019 ◽

Author(s):

Aleix Puig-Barbé ◽

Joaquín de Navascués

Keyword(s):

Stem Cells ◽

Transcription Factors ◽

Adult Stem Cells ◽

Cell Types ◽

E Proteins ◽

Self Renewal ◽

Helix Loop Helix ◽

Mechanism Of Interaction ◽

Bhlh Transcription Factors

ABSTRACTMultipotent adult stem cells must balance self-renewal with differentiation into various mature cell types. How this activity is molecularly regulated is poorly understood. By using genetic and molecular analyses in vivo, we show that a small network of basic Helix-Loop-Helix (bHLH) transcription factors controls both stemness and bi-potential differentiation in the Drosophila adult intestine. We find that homodimers of Daughterless (Da, homolog to mammalian E proteins) maintain the self-renewal of intestinal stem cells and antagonise the activity of heterodimers of Da and Scute (Sc, homolog to ASCL and known to promote intestinal secretory differentiation). We find a novel role for the HLH factor Extramacrochaetae (Emc, homolog to Id proteins), titrating Da and Sc to promote absorptive differentiation. We further show that Emc prevents committed absorptive progenitors from de-differentiating, revealing the plasticity of these cells. This mechanism of interaction partner-switching enables the active maintenance of stemness, but primes stem cells for differentiation along two alternative fates. Such regulatory logic could be recapitulated in other bipotent stem cell systems.

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