scholarly journals The Locus Control Region Activates Serpin Gene Expression through Recruitment of Liver-Specific Transcription Factors and RNA Polymerase II

2007 ◽  
Vol 27 (15) ◽  
pp. 5286-5295 ◽  
Author(s):  
Hui Zhao ◽  
Richard D. Friedman ◽  
R. E. K. Fournier
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase ◽  
Protease Inhibitor ◽  
Histone Acetylation ◽  
Rna Polymerase Ii ◽  
Control Region ◽  
Regulatory Region ◽  
Locus Control Region ◽  
Upstream Regulatory Region ◽  
Serpin Gene

ABSTRACT The human serine protease inhibitor (serpin) gene cluster at 14q32.1 comprises 11 serpin genes, many of which are expressed specifically in hepatic cells. Previous studies identified a locus control region (LCR) upstream of the human α1-antitrypsin (α1AT) gene that is required for gene activation, chromatin remodeling, and histone acetylation throughout the proximal serpin subcluster. Here we show that the LCR interacts with multiple liver-specific transcription factors, including hepatocyte nuclear factor 3β (HNF-3β), HNF-6α, CCAAT/enhancer binding protein alpha (C/EBPα), and C/EBPβ. RNA polymerase II is also recruited to the locus through the LCR. Nongenic transcription at both the LCR and an upstream regulatory region was detected, but the deletion of the LCR abolished transcription at both sites. The deletion of HNF-3 and HNF-6 binding sites within the LCR reduced histone acetylation at both the LCR and the upstream regulatory region and decreased the transcription of the α1AT, corticosteroid binding globulin, and protein Z-dependent protease inhibitor genes. These results suggest that the LCR activates genes in the proximal serpin subcluster by recruiting liver-specific transcription factors and components of the general transcription machinery to regulatory regions upstream of the α1AT gene.

scholarly journals Distinct Mechanisms Control RNA Polymerase II Recruitment to a Tissue-Specific Locus Control Region and a Downstream Promoter

2001 ◽  
Vol 8 (2) ◽  
pp. 465-471 ◽  
Author(s):  
Kirby D. Johnson ◽  
Heather M. Christensen ◽  
Bryan Zhao ◽  
Emery H. Bresnick
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Control Region ◽  
Locus Control Region ◽  
Tissue Specific ◽  
Specific Locus

scholarly journals Expression analysis of transcription factors in sugarcane during cold stress

2023 ◽  
Vol 83 ◽  
Author(s):  
S. U. Rehman ◽  
K. Muhammad ◽  
E. Novaes ◽  
Y. Que ◽  
A. Din ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Rna Polymerase ◽  
Cold Stress ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Regulatory Region ◽  
Transcription Factor Activity ◽  
Factor Activity ◽  
Upregulated Genes

Abstract Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

scholarly journals Highly Restricted Localization of RNA Polymerase II within a Locus Control Region of a Tissue-Specific Chromatin Domain

2003 ◽  
Vol 23 (18) ◽  
pp. 6484-6493 ◽  
Author(s):  
Kirby D. Johnson ◽  
Jeffrey A. Grass ◽  
Changwon Park ◽  
Hogune Im ◽  
Kyunghee Choi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Histone Modification ◽  
Rna Polymerase Ii ◽  
Control Region ◽  
Locus Control Region ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Pol Ii ◽  
Reading Frame ◽  
Hypersensitive Sites

ABSTRACT RNA polymerase II (Pol II) can associate with regulatory elements far from promoters. For the murine β-globin locus, Pol II binds the β-globin locus control region (LCR) far upstream of the β-globin promoters, independent of recruitment to and activation of the βmajor promoter. We describe here an analysis of where Pol II resides within the LCR, how it is recruited to the LCR, and the functional consequences of recruitment. High-resolution analysis of the distribution of Pol II revealed that Pol II binding within the LCR is restricted to the hypersensitive sites. Blocking elongation eliminated the synthesis of genic and extragenic transcripts and eliminated Pol II from the βmajor open reading frame. However, the elongation blockade did not redistribute Pol II at the hypersensitive sites, suggesting that Pol II is recruited to these sites. The distribution of Pol II did not strictly correlate with the distributions of histone acetylation and methylation. As Pol II associates with histone-modifying enzymes, Pol II tracking might be critical for establishing and maintaining broad histone modification patterns. However, blocking elongation did not disrupt the histone modification pattern of the β-globin locus, indicating that Pol II tracking is not required to maintain the pattern.

scholarly journals Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II

1997 ◽  
Vol 110 (15) ◽  
pp. 1781-1791 ◽  
Author(s):  
M.A. Grande ◽  
I. van der Kraan ◽  
L. de Jong ◽  
R. van Driel
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Glucocorticoid Receptors ◽  
Cultured Cells ◽  
Spatial Relationship ◽  
Immunofluorescence Labelling ◽  
Transcription Sites ◽  
Nuclear Domains

We have investigated the spatial relationship between sites containing newly synthesized RNA and domains containing proteins involved in transcription, such as RNA polymerase II and the transcription factors TFIIH, Oct1, BRG1, E2F-1 and glucocorticoid receptors, using dual immunofluorescence labelling followed by confocal microscopy on cultured cells. As expected, a high degree of colocalisation between the RNA polymerase II and sites containing newly synthesised RNA was observed. Like the newly synthesised RNA and the RNA polymerase II, we found that all the transcription factors that we studied are distributed more or less homogeneously throughout the nucleoplasm, occupying numerous small domains. In addition to these small domains, TFIIH was found concentrated in coiled bodies and Oct1 in a single large domain of about 1.5 microm in 30% of the cells in an asynchronous HeLa cell culture. Remarkably, we found little or no relationship between the spatial distribution of the glucocorticoid receptor, Oct1 and E2F-1 on the one hand and RNA polymerase II and transcription sites on the other hand. In contrast, a significant but incomplete overlap was observed between the spatial distributions of transcription sites and BRG1 and TFIIH. These results indicate that many of the transcription factor-rich nuclear domains are not actively involved in transcription. They may represent incomplete transcription initiation complexes, inhibitory complexes, or storage sites.

Co-dependent recruitment of Ino80p and Snf2p is required for yeast CUP1 activation

2014 ◽  
Vol 92 (1) ◽  
pp. 69-75 ◽  
Author(s):  
Roshini N. Wimalarathna ◽  
Po Yun Pan ◽  
Chang-Hui Shen
Keyword(s):  
Rna Polymerase ◽  
Histone Acetylation ◽  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Copper Toxicity ◽  
Yeast Cells ◽  
Chromatin Remodelers ◽  
Insight Into ◽  
Cup1 Promoter

In yeast, Ace1p-dependent induction of CUP1 is responsible for protecting cells from copper toxicity. Although the mechanism of yeast CUP1 induction has been studied intensively, it is still uncertain which chromatin remodelers are involved in CUP1 transcriptional activation. Here, we show that yeast cells are inviable in the presence of copper when either chromatin remodeler, Ino80p or Snf2p, is not present. This inviability is due to the lack of CUP1 expression in ino80Δ and snf2Δ cells. Subsequently, we observe that both Ino80p and Snf2p are present at the promoter and they are responsible for recruiting chromatin remodeling activity to the CUP1 promoter under induced conditions. These results suggest that they directly participate in CUP1 transcriptional activation. Furthermore, the codependent recruitment of both INO80 and SWI/SNF depends on the presence of the transcriptional activator, Ace1p. We also demonstrate that both remodelers are required to recruit RNA polymerase II and targeted histone acetylation, indicating that remodelers are recruited to the CUP1 promoter before RNA polymerase II and histone acetylases. These observations provide evidence for the mechanism of CUP1 induction. As such, we propose a model that describes novel insight into the order of events in CUP1 activation.

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