Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response

Mallik, Rwitie; Kundu, Anindya; Sachdev, Sonal; Biswas, Ruby; Dutta, Arkajyoti; Roy, Adrita; Mukhopadhyay, Jayanta; Bag, Sumit K.; Chaudhuri, Shubho

doi:10.1016/j.bbagrm.2020.194644

Cited by 8 publications

(10 citation statements)

References 52 publications

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“…AtHMGB11 preferably binds to AT-rich DNA and shows structural bias for supercoiled DNA (Roy et al, 2016). DNA binding and footprinting assays further identified A(A/C)-ATA-(A/T)(A/T) as AtHMGB15 binding motif (Mallik et al, 2020). Here, OsHMGB707 could bind several target DNA (Figure 8), and several of these target promoters contain CCAAT elements (data not shown).…”

Section: Oshmgb707 Encodes a Nuclear Dna Binding Proteinmentioning

confidence: 88%

“…The HMG protein is an abundant non-histone chromosomal protein that modulates chromatin/DNA configuration, regulates gene transcription, and participates in DNA damage repair and plant innate immunity (Agresti and Bianchi, 2003;Choi et al, 2016;Charbonnel et al, 2018). Several studies have shown that some HMG proteins modulate stress response in Arabidopsis (Kwak et al, 2007;Lildballe et al, 2008;Mallik et al, 2020). Here, OsHMGB707, a novel HMGB gene in rice, was isolated and characterized.…”

Section: Oshmgb707 Positively Regulates Rice Drought Tolerancementioning

confidence: 99%

“…For example, the overexpression of the HMGB gene ZmHMGB1 in maize inhibited root growth (Lichota et al, 2004). AtHMGB15 promoted pollen tube development in Arabidopsis (Xia et al, 2014) and regulated the expression of stress response genes under cold stress (Mallik et al, 2020). HMGB3 also participates in the activation of plant innate immunity (Choi et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Overexpression of OsHMGB707, a High Mobility Group Protein, Enhances Rice Drought Tolerance by Promoting Stress-Related Gene Expression

Chen

et al. 2021

Front. Plant Sci.

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Drought stress adversely affects crop growth and productivity worldwide. In response, plants have evolved several strategies in which numerous genes are induced to counter stress. High mobility group (HMG) proteins are the second most abundant family of chromosomal proteins. They play a crucial role in gene transcriptional regulation by modulating the chromatin/DNA structure. In this study, we isolated a novel HMG gene, OsHMGB707, one of the candidate genes localized in the quantitative trait loci (QTL) interval of rice drought tolerance, and examined its function on rice stress tolerance. The expression of OsHMGB707 was up-regulated by dehydration and high salt treatment. Its overexpression significantly enhanced drought tolerance in transgenic rice plants, whereas its knockdown through RNA interference (RNAi) did not affect the drought tolerance of the transgenic rice plants. Notably, OsHMGB707-GFP is localized in the cell nucleus, and OsHMGB707 is protein-bound to the synthetic four-way junction DNA. Several genes were up-regulated in OsHMGB707-overexpression (OE) rice lines compared to the wild-type rice varieties. Some of the genes encode stress-related proteins (e.g., DREB transcription factors, heat shock protein 20, and heat shock protein DnaJ). In summary, OsHMGB707 encodes a stress-responsive high mobility group protein and regulates rice drought tolerance by promoting the expression of stress-related genes.

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Section: Oshmgb707 Encodes a Nuclear Dna Binding Proteinmentioning

confidence: 88%

Section: Oshmgb707 Positively Regulates Rice Drought Tolerancementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Overexpression of OsHMGB707, a High Mobility Group Protein, Enhances Rice Drought Tolerance by Promoting Stress-Related Gene Expression

Chen

et al. 2021

Front. Plant Sci.

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“…Chromatin Immunoprecipitation (ChIP) assays were performed essentially as described before ( Coarfa et al, 2020 ; Hu et al, 2020 ; Jehanno et al, 2020 ; Maity et al, 2020 ; Mallik et al, 2020 ; Moon et al, 2020 ; Shen et al, 2020 ; Wang J. N. et al, 2020 ; Wang S. et al, 2020 ; Zhang et al, 2020 ; Zhao et al, 2020 ; Marti et al, 2021 ; Peng et al, 2021 ; Rashid et al, 2021 ). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde.…”

Section: Methodsmentioning

confidence: 99%

A KDM4-DBC1-SIRT1 Axis Contributes to TGF-b Induced Mesenchymal Transition of Intestinal Epithelial Cells

Chen

Dong

Shao

et al. 2021

Front. Cell Dev. Biol.

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Intestinal fibrosis is one of the common pathophysiological processes in inflammatory bowel diseases (IBDs). Previously it has been demonstrated that epithelial-mesenchymal transition (EMT) can contribute to the development of intestinal fibrosis. Here we report that conditional ablation of SIRT1, a class III lysine deacetylase, in intestinal epithelial cells exacerbated 2, 4, 6-trinitro-benzene sulfonic acid (TNBS) induced intestinal fibrosis in mice. SIRT1 activity, but not SIRT1 expression, was down-regulated during EMT likely due to up-regulation of its inhibitor deleted in breast cancer 1 (DBC1). TGF-β augmented the recruitment of KDM4A, a histone H3K9 demethylase, to the DBC1 promoter in cultured intestinal epithelial cells (IEC-6) leading to DBC1 trans-activation. KDM4A depletion or inhibition abrogated DBC1 induction by TGF-β and normalized SIRT1 activity. In addition, KDM4A deficiency attenuated TGF-β induced EMT in IEC-6 cells. In conclusion, our data identify a KDM4-DBC1-SIRT1 pathway that regulates EMT to contribute to intestinal fibrosis.

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“…Chromatin immunoprecipitation (ChIP) assays were performed essentially as described before (Coarfa et al, 2020;Hu et al, 2020;Jehanno et al, 2020;Maity et al, 2020;Mallik et al, 2020;Moon et al, 2020;Shen et al, 2020;Wang et al, 2020a,b;Zhang et al, 2020;Zhao et al, 2020;Marti et al, 2021;Peng et al, 2021;Rashid et al, 2021). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde.…”

Section: Chromatin Immunoprecipitationmentioning

confidence: 99%

Choline Kinase Alpha Is a Novel Transcriptional Target of the Brg1 in Hepatocyte: Implication in Liver Regeneration

Kong

Dong

et al. 2021

Front. Cell Dev. Biol.

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Liver regeneration is a key compensatory process in response to liver injury serving to contain damages and to rescue liver functions. Hepatocytes, having temporarily exited the cell cycle after embryogenesis, resume proliferation to regenerate the injured liver parenchyma. In the present study we investigated the transcriptional regulation of choline kinase alpha (Chka) in hepatocytes in the context of liver regeneration. We report that Chka expression was significantly up-regulated in the regenerating livers in the partial hepatectomy (PHx) model and the acetaminophen (APAP) injection model. In addition, treatment with hepatocyte growth factor (HGF), a strong pro-proliferative cue, stimulated Chka expression in primary hepatocytes. Chka depletion attenuated HGF-induced proliferation of hepatocytes as evidenced by quantitative PCR and Western blotting measurements of pro-proliferative genes as well as EdU incorporation into replicating DNA. Of interest, deletion of Brahma-related gene 1 (Brg1), a chromatin remodeling protein, attenuated Chka induction in the regenerating livers in mice and in cultured hepatocytes. Further analysis revealed that Brg1 interacted with hypoxia-inducible factor 1 alpha (HIF-1α) to directly bind to the Chka promoter and activate Chka transcription. Finally, examination of human acute liver failure (ALF) specimens identified a positive correlation between Chka expression and Brg1 expression. In conclusion, our data suggest that Brg1-dependent trans-activation of Chka expression may contribute to liver regeneration.

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Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response

Cited by 8 publications

References 52 publications

Overexpression of OsHMGB707, a High Mobility Group Protein, Enhances Rice Drought Tolerance by Promoting Stress-Related Gene Expression

Overexpression of OsHMGB707, a High Mobility Group Protein, Enhances Rice Drought Tolerance by Promoting Stress-Related Gene Expression

A KDM4-DBC1-SIRT1 Axis Contributes to TGF-b Induced Mesenchymal Transition of Intestinal Epithelial Cells

Choline Kinase Alpha Is a Novel Transcriptional Target of the Brg1 in Hepatocyte: Implication in Liver Regeneration

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