Specific regulation of Fos family transcription factors in thymocytes at two developmental checkpoints

ABSTRACT The Ets family transcription factor PU.1 is crucial for the regulation of hematopoietic development. Pu.1 is activated in hematopoietic stem cells and is expressed in mast cells, B cells, granulocytes, and macrophages but is switched off in T cells. Many of the transcription factors regulating Pu.1 have been identified, but little is known about how they organize Pu.1 chromatin in development. We analyzed the Pu.1 promoter and the upstream regulatory element (URE) using in vivo footprinting and chromatin immunoprecipitation assays. In B cells, Pu.1 was bound by a set of transcription factors different from that in myeloid cells and adopted alternative chromatin architectures. In T cells, Pu.1 chromatin at the URE was open and the same transcription factor binding sites were occupied as in B cells. The transcription factor RUNX1 was bound to the URE in precursor cells, but binding was down-regulated in maturing cells. In PU.1 knockout precursor cells, the Ets factor Fli-1 compensated for the lack of PU.1, and both proteins could occupy a subset of Pu.1 cis elements in PU.1-expressing cells. In addition, we identified novel URE-derived noncoding transcripts subject to tissue-specific regulation. Our results provide important insights into how overlapping, but different, sets of transcription factors program tissue-specific chromatin structures in the hematopoietic system.

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Specific regulation of mRNA cap methylation by the c-Myc and E2F1 transcription factors

Oncogene ◽

10.1038/onc.2008.463 ◽

2009 ◽

Vol 28 (9) ◽

pp. 1169-1175 ◽

Cited By ~ 46

Author(s):

M D Cole ◽

V H Cowling

Keyword(s):

Transcription Factors ◽

Specific Regulation

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Age-Specific Regulation of Drug-Processing Genes in Mouse Liver by Ligands of Xenobiotic-Sensing Transcription Factors

Drug Metabolism and Disposition ◽

10.1124/dmd.115.066639 ◽

2015 ◽

Vol 44 (7) ◽

pp. 1038-1049 ◽

Cited By ~ 16

Author(s):

C. Y. Li ◽

H. J. Renaud ◽

C. D. Klaassen ◽

J. Y. Cui

Keyword(s):

Transcription Factors ◽

Mouse Liver ◽

Specific Regulation

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Functional interaction of Oct transcription factors with the family of repeats in Epstein–Barr virus oriP

Journal of General Virology ◽

10.1099/vir.0.80620-0 ◽

2005 ◽

Vol 86 (5) ◽

pp. 1261-1267 ◽

Cited By ~ 13

Author(s):

J. Almqvist ◽

J. Zou ◽

Y. Linderson ◽

C. Borestrom ◽

E. Altiok ◽

...

Keyword(s):

Transcription Factors ◽

Epstein Barr Virus ◽

Mobility Shift ◽

Barr Virus ◽

Binding Factor ◽

The Family ◽

Epstein Barr ◽

Mobility Shift Assay ◽

Specific Regulation ◽

Cellular Transcription

The family of repeats (FR) is a major upstream enhancer of the Epstein–Barr virus (EBV) latent C promoter (Cp) that controls transcription of six different latent nuclear proteins following interaction with the EBV nuclear protein EBNA1. Here, it was shown that Cp could also be activated by octamer-binding factor (Oct) proteins. Physical binding to the FR by the cellular transcription factors Oct-1 and Oct-2 was demonstrated by using an electrophoretic mobility-shift assay. Furthermore, Oct-1 in combination with co-regulator Bob.1, or Oct-2 alone, could drive transcription of a heterologous thymidine kinase promoter linked to the FR in both B cells and epithelial cells. Cp controlled by the FR was also activated by binding of Oct-2 to the FR. This may have direct implications for B cell-specific regulation of Cp.

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A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana ‘Changchun’

Genes ◽

10.3390/genes11010015 ◽

2019 ◽

Vol 11 (1) ◽

pp. 15 ◽

Cited By ~ 1

Author(s):

Zheng Jiang ◽

Liyong Sun ◽

Qiang Wei ◽

Ye Ju ◽

Xuan Zou ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Molecular Basis ◽

Woody Plants ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Flower Buds ◽

Flowering Initiation ◽

Specific Regulation ◽

Flowering Process

Magnolia × soulangeana ‘Changchun’ are trees that bloom in spring and summer respectively after flower bud differentiation. Here, we use phenological and morphological observation and RNA-seq technology to study the molecular basis of flowering initiation in ‘Changchun’. During the process of flowering initiation in spring and summer, the growth of expanded flower buds increased significantly, and their shape was obviously enlarged, which indicated that flowering was initiated. A total of 168,120 expressed genes were identified in spring and summer dormant and expanded flower buds, of which 11,687 genes showed significantly differential expression between spring and summer dormant and expanded flower buds. These differentially expressed genes (DEGs) were mainly involved in plant hormone signal transduction, metabolic processes, cellular components, binding, and catalytic activity. Analysis of differential gene expression patterns revealed that gibberellin signaling, and some transcription factors were closely involved in the regulation of spring and summer flowering initiation in ‘Changchun’. A qRT-PCR (quantitative Real Time Polymerase Chain Reaction) analysis showed that BGISEQ-500 sequencing platform could truly reflect gene expression patterns. It also verified that GID1B (GIBBERELLIN INSENSITIVE DWARF1 B), GID1C, SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8), and GASA (GIBBERELLIC ACID-STIMULATED ARABIDOPSIS) family genes were expressed at high levels, while the expression of SPY (SPINDLY) was low during spring and summer flowering initiation. Meanwhile, the up- and down-regulated expression of, respectively, AGL6 (AGAMOUS-LIKE 6) and DREB3 (DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 3), AG15, and CDF1 (CYCLIC DOF FACTOR 1) might also be involved in the specific regulation of spring and summer flowering initiation. Obviously, flowering initiation is an important stage of the flowering process in woody plants, involving the specific regulation of relevant genes and transcription factors. This study provides a new perspective for the regulation of the flowering process in perennial woody plants.

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The Regulation of Target Genes by Co-occupancy of Transcription Factors, c-Myc and Mxi1 with Max in the Mouse Cell Line

Current Bioinformatics ◽

10.2174/1574893614666191106103633 ◽

2020 ◽

Vol 15 (6) ◽

pp. 581-588

Author(s):

Hui Wang ◽

Yuan Liu ◽

Hua Guan ◽

Guo-Liang Fan

Keyword(s):

Transcription Factors ◽

Cancer Cells ◽

Target Genes ◽

Gene Expression Regulation ◽

Regulatory Region ◽

Mouse Cell ◽

Regulatory Function ◽

Regulation Of Transcription ◽

Specific Regulation ◽

Synergistic Relationship

Background: The regulatory function of transcription factors on genes is not only related to the location of binding genes and its related functions, but is also related to the methods of binding. Objective: It is necessary to study the regulation effects in different binding methods on target genes. Methods: In this study, we provided a reliable theoretical basis for studying gene expression regulation of co-binding transcription factors and further revealed the specific regulation of transcription factor co-binding in cancer cells. Results: Transcription factors tend to combine with other transcription factors in the regulatory region to form a competitive or synergistic relationship to regulate target genes accurately. Conclusion: We found that up-regulated genes in cancer cells were involved in the regulation of their own immune system related to the normal cells.

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Tissue-specific regulation by transcription factors

Transcription Factors ◽

10.4324/9780203450406-15 ◽

2003 ◽

pp. 247-272

Keyword(s):

Transcription Factors ◽

Tissue Specific ◽

Specific Regulation

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Epigenetic Regulation of the Dendritic Cell Marker Gene MADDAM /ADAM19.

Blood ◽

10.1182/blood.v104.11.4187.4187 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4187-4187

Author(s):

Marina Kreutz ◽

Achim Ehrnsperger ◽

Michael Rehli ◽

Reinhard Andreesen

Keyword(s):

Transcription Factors ◽

Dendritic Cell ◽

Binding Sites ◽

Cpg Island ◽

Trichostatin A ◽

Proximal Promoter ◽

Cell Type ◽

Reporter Activity ◽

Cell Type Specific ◽

Specific Regulation

Abstract MADDAM (Metalloprotease And Disintegrin Dendritic Cell Antigen Marker, ADAM19), a human metalloprotease belonging to the ADAM-family, is strongly expressed during in vitro differentiation of monocytes into dendritic cells (DC), whereas differentiation of monocytes into macrophages (MAC) is associated with a loss of MADDAM transcription. To investigate the mechanisms underlying this cell-type specific expression pattern we defined the transcriptional start site and the proximal promoter of the MADDAM gene. Gene bank analysis of the CpG island promoter and first intron revealed putative binding sites for several transcription factors, including VDR, NF-kB and Sp1-family factors. EMSA demonstrated binding of Sp1, Sp3, NF-kB and VDR to their putative binding sites in the proximal promoter region and mutation of these elements led to a decreased reporter activity of the proximal promoter in luciferase assays. A minimal promoter construct of 150-bp showed weak reporter activity in primary monocyte-derived MAC and a threefold higher activity in monocyte-derived DC, indicating that differential binding of transcription factors contributes to the cell-type specific regulation of MADDAM. Transfection of monocytic THP-1 cells with the 150-bp fragment also resulted in significant reporter activity, despite the lack of endogenous MADDAM expression. Interestingly, Trichostatin A (TSA), a known inhibitor of histone deacetylation, lead to a dose dependent induction of MADDAM mRNA in THP-1 cells. Chromatin immunoprecipitation (ChIP) assays demonstrate increased levels of acetylated histones H3 and H4 in DC as compared to MAC, indicating an important role of histone acetylation in the cell-type specific regulation of the MADDAM gene.

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