scholarly journals Computer Designed PRC2 Inhibitor, EBdCas9, Reveals Functional TATA Boxes in Distal Promoter Regions

2020 ◽  
Author(s):  
Shiri Levy ◽  
Logesh Somasundaram ◽  
Infencia Raj Xavier ◽  
Diego Ic-Mex ◽  
Sven Schmidt ◽  
...  
Keyword(s):  
Promoter Regions ◽  
Distal Promoter

scholarly journals Tissue-specific in vitro transcription from the mouse myelin basic protein promoter.

1989 ◽  
Vol 9 (7) ◽  
pp. 3122-3126 ◽  
Author(s):  
T Tamura ◽  
A Aoyama ◽  
T Inoue ◽  
M Miura ◽  
H Okano ◽  
...  
Keyword(s):  
Myelin Basic Protein ◽  
Basic Protein ◽  
In Vitro Transcription ◽  
Distal Region ◽  
Proximal Region ◽  
Promoter Regions ◽  
Nuclear Extracts ◽  
Brain Extracts ◽  
Distal Promoter

The mouse myelin basic protein promoter was transcribed in brain nuclear extracts. The distal promoter region from -253 to -54 directed preferential transcription in brain extracts, whereas the same region repressed transcription activity in liver extracts. Stimulation of transcription was observed when the distal region was located only in a native orientation. The proximal region downstream from -53 alone still directed preferential transcription. It is suggested that cooperative function by the two promoter regions may be required for higher specificity.

Functional analysis of chicken vimentin distal promoter regions in cultured lens cells

Gene ◽  
1993 ◽  
Vol 130 (2) ◽  
pp. 277-281 ◽  
Author(s):  
Christina M. Sax ◽  
Denise M. Stover ◽  
John G. Ilagan ◽  
Zendra E. Zehner ◽  
Joram Piatigorsky
Keyword(s):  
Functional Analysis ◽  
Promoter Regions ◽  
Lens Cells ◽  
Distal Promoter

scholarly journals A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila

PLoS Genetics ◽  
2021 ◽  
Vol 17 (6) ◽  
pp. e1009613
Author(s):  
Clara Poupault ◽  
Diane Choi ◽  
Khanh Lam-Kamath ◽  
Deepshe Dewett ◽  
Ansa Razzaq ◽  
...  
Keyword(s):  
Promoter Region ◽  
Core Promoter ◽  
Expression Patterns ◽  
Core Promoter Region ◽  
Promoter Regions ◽  
Specific Expression ◽  
General Activation ◽  
Different Color ◽  
Photoreceptor Neurons ◽  
Distal Promoter

Color vision in Drosophila melanogaster is based on the expression of five different color-sensing Rhodopsin proteins in distinct subtypes of photoreceptor neurons. Promoter regions of less than 300 base pairs are sufficient to reproduce the unique, photoreceptor subtype-specific rhodopsin expression patterns. The underlying cis-regulatory logic remains poorly understood, but it has been proposed that the rhodopsin promoters have a bipartite structure: the distal promoter region directs the highly restricted expression in a specific photoreceptor subtype, while the proximal core promoter region provides general activation in all photoreceptors. Here, we investigate whether the rhodopsin promoters exhibit a strict specialization of their distal (subtype specificity) and proximal (general activation) promoter regions, or if both promoter regions contribute to generating the photoreceptor subtype-specific expression pattern. To distinguish between these two models, we analyze the expression patterns of a set of hybrid promoters that combine the distal promoter region of one rhodopsin with the proximal core promoter region of another rhodopsin. We find that the function of the proximal core promoter regions extends beyond providing general activation: these regions play a previously underappreciated role in generating the non-overlapping expression patterns of the different rhodopsins. Therefore, cis-regulatory motifs in both the distal and the proximal core promoter regions recruit transcription factors that generate the unique rhodopsin patterns in a combinatorial manner. We compare this combinatorial regulatory logic to the regulatory logic of olfactory receptor genes and discuss potential implications for the evolution of rhodopsins.

284 IDENTIFICATION AND CHARACTERIZATION OF THE 5′-FLANKING REGION OF THREE MOUSE MATERNAL GENES (HISTONE H1OO, NUCLEOPLASMIN 2, AND ZYGOTE ARREST 1): TRANSCRIPTIONAL ACTIVITY IN MOUSE OOCYTES

2007 ◽  
Vol 19 (1) ◽  
pp. 257
Author(s):  
K. Tsunemoto ◽  
K. Matsumoto ◽  
M. Anzai ◽  
M. Hayakumo ◽  
T. Amano ◽  
...  
Keyword(s):  
Binding Sites ◽  
Transcriptional Activity ◽  
Luciferase Activity ◽  
Transcription Start ◽  
Promoter Regions ◽  
Promoter Sequences ◽  
E Box ◽  
Flanking Region ◽  
High Level ◽  
Distal Promoter

Maternal transcripts that accumulate during oocyte growth are involved in the meiotic maturation, the initiation of the first mitosis, and the later pre-implantation development. Although the conserved E-box sequences in promoter region of some maternal genes (for example, Zp3 and Gdf-9), which are important in regulating gene transcripts as binding sites of transcriptional factors, may play a role in the oocyte-specific expression in ovary, the molecular mechanism that regulates the expression of the maternal genes is still not known. In this study, we have focused on the transcriptional activity of promoter regions to clarify the molecular mechanism of transcriptional regulation of these maternal genes [Histone H1oo (H1oo), Nucleoplasmin 2 (Npm2), and Zygote arrest 1 (Zar1)]. First, we observed the expression of firefly luciferase expression vectors under promoter regions of 3 maternal genes in oocytes isolated from 10- to 12-day-old mice, which is mainly NSN-type, transcriptionally active form (Bouniol-Baly et al. 1999 Biol. Reprod. 60, 580–587). Transcriptional activities of H1oo (-3975), Npm2 (-2610), and Zar1 (-5187) promoters were detected in oocytes, the relative luciferase activities being an average of 70, 130, and 12, respectively. On the other hand, these promoter activities were not detected in embryos at the 2-cell stage. Furthermore, deletion analysis of promoter elements (E-boxes) of H1oo and Npm2 was done by microinjecting deletion constructs into oocytes. In the H1oo promoter, deletion of sequences between -3975 and -72 bp from the transcription start site resulted in one-third of the level obtained in the full H1oo (-3975) promoter. In addition, deletion of sequence -68 bp resulted in no detection of luciferase activity. These findings indicate that the putative distal promoter sequences exist at the 52-flanking region (-3975 to -759) of the H1oo gene and that the region (-314 to -68) including the E-box region (-72) may be required for high-level transcriptional activity of the H1oo promoter. In the Npm2 promoter, deletion of sequences between -2610 and -180 bp from the transcription start site resulted in one-third of the level of wild-type activity of the Npm2 (-2610) promoter. In addition, deletion of sequence -101 bp resulted in no detection of luciferase activity. These findings also indicate that 3 putative distal promoter sequences exist at the 52-flanking region (-2610 to -210) of the Npm2 gene and that the region (-210 to -101) that includes the E-box region (-180) is crucial for high-level transcriptional activity of the Npm2 promoter. In conclusion, the E-box may be a key regulatory region for the expression of two of the maternal genes (H1oo and Npm2) examined. Currently, we are attempting to identify the transcriptional factor binding sites by DNase I footprint analysis and gel mobility shift assay.

Isolation and characterization of a 28-kDa HMG-like protein that binds to A/T-rich distal promoter regions of zein genes

Plant Science ◽  
1998 ◽  
Vol 135 (1) ◽  
pp. 31-38 ◽  
Author(s):  
Pedro Guillén ◽  
Rosa M Debón ◽  
Klaus D Grasser ◽  
Peter Harrsch ◽  
Rudi Grimm ◽  
...  
Keyword(s):  
Promoter Regions ◽  
Isolation And Characterization ◽  
Distal Promoter ◽  
Zein Genes

scholarly journals C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle

Cells ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 145
Author(s):  
Ji Hae Lee ◽  
Jee Young Sung ◽  
Eun Kyung Choi ◽  
Hyun-Kyoung Yoon ◽  
Bo Ram Kang ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Cellular Proliferation ◽  
Normal Lung ◽  
Promoter Regions ◽  
Cycle Progression ◽  
Histone Deacetylase 2 ◽  
Enhancer Binding Protein ◽  
M Phase ◽  
Distal Promoter

The CCAAT/enhancer-binding protein β (C/EBPβ) is a transcription factor that regulates cellular proliferation, differentiation, apoptosis and tumorigenesis. Although the pro-oncogenic roles of C/EBPβ have been implicated in various human cancers, how it contributes to tumorigenesis or tumor progression has not been determined. Immunohistochemistry with human non-small cell lung cancer (NSCLC) tissues revealed that higher levels of C/EBPβ protein were expressed compared to normal lung tissues. Knockdown of C/EBPβ by siRNA reduced the proliferative capacity of NSCLC cells by delaying the G2/M transition in the cell cycle. In C/EBPβ-knockdown cells, a prolonged increase in phosphorylation of cyclin dependent kinase 1 at tyrosine 15 (Y15-pCDK1) was displayed with simultaneously increased Wee1 and decreased Cdc25B expression. Chromatin immunoprecipitation (ChIP) analysis showed that C/EBPβ bound to distal promoter regions of WEE1 and repressed WEE1 transcription through its interaction with histone deacetylase 2. Treatment of C/EBPβ-knockdown cells with a Wee1 inhibitor induced a decrease in Y15-pCDK1 and recovered cells from G2/M arrest. In the xenograft tumors, the depletion of C/EBPβ significantly reduced tumor growth. Taken together, these results indicate that Wee1 is a novel transcription target of C/EBPβ that is required for the G2/M phase of cell cycle progression, ultimately regulating proliferation of NSCLC cells.

scholarly journals C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle

2019 ◽  
Author(s):  
Ji Hae Lee ◽  
Jeeyoung Sung ◽  
Eun Kyung Choi ◽  
Hyun-Kyoung Yoon ◽  
Boram Kang ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Cellular Proliferation ◽  
Normal Lung ◽  
Promoter Regions ◽  
Cycle Progression ◽  
Histone Deacetylase 2 ◽  
Enhancer Binding Protein ◽  
M Phase ◽  
Distal Promoter

The CCAAT/enhancer-binding protein β (C/EBPβ) is a transcription factor that regulates cellular proliferation, differentiation, apoptosis and tumorigenesis. Although the pro-oncogenic roles of C/EBPβ have been implicated in various human cancers, how it contributes to tumorigenesis or tumor progression has not been determined. Immunohistochemistry with human non-small cell lung cancer (NSCLC) tissues revealed that higher levels of C/EBPβ protein are expressed compared to normal lung tissues. Knockdown of C/EBPβ by siRNA reduced the proliferative capacity of NSCLC cells by delaying G2/M transition of the cell cycle. In C/EBPβ-knockdown cells, a prolonged increase in phosphorylation of cyclin dependent kinase 1 at tyrosine 15 (Y15-pCDK1) was displayed with increased Wee1 and decreased Cdc25B expression, simultaneously. ChIP analysis showed that C/EBPβ bound to distal promoter regions of WEE1 and repressed WEE1 transcription through the interaction with histone deacetylase 2. Treatment of C/EBPβ-knockdown cells with a Wee1 inhibitor induced a decrease in Y15-pCDK1 and recovered cells from G2/M arrest. In the xenograft tumors, the depletion of C/EBPβ significantly reduced tumor growth. Taken together, these results indicate that Wee1 is a novel transcription target of C/EBPβ that is required for the G2/M phase of cell cycle progression, ultimately regulating proliferation of NSCLC cells.

scholarly journals Integrating RNA-seq and assay for transposase-accessible chromatin by sequencing (ATAC-seq) predicts functionally-relevant chromatin regions

2021 ◽  
Author(s):  
Collin B Merrill ◽  
Austin B Montgomery ◽  
Miguel A Pabon ◽  
Aylin R Rodan ◽  
Adrian Rothenfluh
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Transcriptional Response ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Data Types ◽  
Promoter Regions ◽  
Next Generation Sequencing Technology ◽  
Distal Promoter ◽  
Accessible Chromatin

Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for epigenomic investigations. Integrating epigenomic and transcriptomic data has the potential to reveal the chromatin-mediated mechanisms regulating transcription. However, integrating these two data types remains challenging. We used the insulin signaling pathway as a model to investigate chromatin regions and gene expression changes using ATAC- and RNA-seq in insulin-treated Drosophila S2 cells. We show that insulin causes widespread changes in chromatin accessibility and gene expression. Then, we attempted to integrate ATAC- and RNA-seq data to predict functionally-relevant chromatin regions that control the transcriptional response to insulin. We show that using differential chromatin accessibility can predict functionally-relevant genome regions, but that stratifying differentially-accessible chromatin regions by annotated feature type provides a better prediction of whether a chromatin region regulates gene expression. In particular, our data demonstrate a strong correlation between chromatin regions annotated to distal promoters (1-2 kb from the transcription start site). To test this prediction, we cloned candidate distal promoter regions upstream of luciferase and validated the functional relevance of these chromatin regions. Our data show that distal promoter regions selected by correlations with RNA-seq are more likely to control gene expression. Thus, correlating ATAC- and RNA-seq data can home in on functionally-relevant chromatin regions.

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