GATA transcription factors as tissue-specific master regulators for induced responses

ABSTRACT In Saccharomyces cerevisiae, Avt4 exports neutral and basic amino acids from vacuoles. Previous studies have suggested that the GATA transcription factors, Gln3 and Gat1, which are key regulators that adapt cells in response to changes in amino acid status, are involved in the AVT4 transcription. Here, we show that mutations in the putative GATA-binding sites of the AVT4 promoter reduced AVT4 expression. Consistently, a chromatin immunoprecipitation (ChIP) assay revealed that Gat1-Myc13 binds to the AVT4 promoter. Previous microarray results were confirmed that gln3∆gat1∆ cells showed a decrease in expression of AVT1 and AVT7, which also encode vacuolar amino acid transporters. Additionally, ChIP analysis revealed that the AVT6 encoding vacuolar acidic amino acid exporter represents a new direct target of the GATA transcription factor. The broad effect of the GATA transcription factors on the expression of AVT transporters suggests that vacuolar amino acid transport is integrated into cellular amino acid homeostasis.

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B-GATA transcription factors – insights into their structure, regulation, and role in plant development

Frontiers in Plant Science ◽

10.3389/fpls.2015.00090 ◽

2015 ◽

Vol 6 ◽

Cited By ~ 46

Author(s):

Carina Behringer ◽

Claus Schwechheimer

Keyword(s):

Transcription Factors ◽

Plant Development ◽

Gata Transcription Factors ◽

Structure Regulation

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Neuroblastoma: Role of GATA Transcription Factors

Pediatric Cancer - Neuroblastoma ◽

10.1007/978-94-007-2418-1_14 ◽

2011 ◽

pp. 151-159

Author(s):

Victoria Hoene ◽

Christof Dame

Keyword(s):

Transcription Factors ◽

Gata Transcription Factors

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Molecular and biochemical analyses of avocado (Persea americana) reveal differences in the oil accumulation pattern between the mesocarp and seed during the fruit developmental period

10.21203/rs.3.rs-20746/v1 ◽

2020 ◽

Author(s):

Yu Ge ◽

Xiangshu Dong ◽

Yuanzheng Liu ◽

Ying Yang ◽

Rulin Zhan

Keyword(s):

Transcription Factors ◽

Fatty Acid ◽

Single Molecule ◽

Oil Production ◽

Developmental Period ◽

Persea Americana ◽

Oil Accumulation ◽

Accumulation Pattern ◽

Tissue Specific ◽

Non Coding Rnas

Abstract Background: The avocado (Persea americana) mesocarp and seed contain high-value oil with broad industrial applications. The oil contents in these two tissues vary considerably at maturity. Additionally, the molecular mechanism underlying the tissue-specific oil accumulation in the developing avocado mesocarp and seed remains unclear, which has hampered the exploration of the utility of avocado for oil production.Results: To clarify the mechanisms mediating the differences in oil contents and fatty acid compositions, the transcriptomes and oil bodies were compared between the oil-storing tissues during the fruit developmental period. The results revealed the increasing and fluctuating trends in the oil accumulation in the developing avocado mesocarp and seed, respectively. Additionally, striking differences in the lipid droplets between the mature mesocarp and seed were revealed in confocal microscopy images. Subsequently, the gene transcription profiles of the developing mesocarp and seed were characterized via a comprehensive transcriptome analysis involving second-generation sequencing and single-molecule real-time sequencing techniques. The tissue-specific transcription of lipid-related genes contributing to fatty acid synthesis, triacylglycerol assembly, and triacylglycerol storage was examined, with most of the lipid-related genes expressed at higher levels in the developing mesocarp than in the developing seed. A weighted gene co-expression network analysis uncovered 291 transcription factors that were commonly or uniquely correlated with the oil contents in the avocado mesocarp and seed. Moreover, 11 trans-acting and 79 cis-acting long non-coding RNAs were identified as common or unique to the developing avocado mesocarp and seed. These long non-coding RNAs may regulate the expression of 43 lipid-related genes. Finally, a network of genes associated with oil accumulation in the developing avocado mesocarp and seed was established.Conclusions: The results of this study further elucidate the tissue-specific oil biosynthesis and related regulatory network in the avocado mesocarp and seed. Furthermore, tissue-specific lipid-related genes, putative transcription factors, and putativelong non-coding RNAs affecting oil accumulation were identified. Our data may also be useful for characterizing tissue-specific oil accumulation at the transcriptomic level, thereby identifying candidate genes for improving the oil production of related plant species.

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Improved detection of tumor suppressor events in single-cell RNA-Seq data

npj Genomic Medicine ◽

10.1038/s41525-020-00151-y ◽

2020 ◽

Vol 5 (1) ◽

Author(s):

Andrew E. Teschendorff ◽

Ning Wang

Keyword(s):

Transcription Factors ◽

Tumor Suppressor ◽

Single Cell ◽

Cancer Cells ◽

Dropout Rate ◽

Lung Epithelial Cells ◽

Rna Seq ◽

Regulatory Activity ◽

Tissue Specific ◽

Early Tumor

Abstract Tissue-specific transcription factors are frequently inactivated in cancer. To fully dissect the heterogeneity of such tumor suppressor events requires single-cell resolution, yet this is challenging because of the high dropout rate. Here we propose a simple yet effective computational strategy called SCIRA to infer regulatory activity of tissue-specific transcription factors at single-cell resolution and use this tool to identify tumor suppressor events in single-cell RNA-Seq cancer studies. We demonstrate that tissue-specific transcription factors are preferentially inactivated in the corresponding cancer cells, suggesting that these are driver events. For many known or suspected tumor suppressors, SCIRA predicts inactivation in single cancer cells where differential expression does not, indicating that SCIRA improves the sensitivity to detect changes in regulatory activity. We identify NKX2-1 and TBX4 inactivation as early tumor suppressor events in normal non-ciliated lung epithelial cells from smokers. In summary, SCIRA can help chart the heterogeneity of tumor suppressor events at single-cell resolution.

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