The RNA Polymerase II Transcriptional Machinery and Its Epigenetic Context

Barrero, María J.; Malik, Sohail

doi:10.1007/978-94-007-4525-4_11

Cited by 3 publications

(1 citation statement)

References 142 publications

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“…진핵세포 유전자 전사 (transcription) 과정은 genomic DNA 내 프로모터 부위에 RNA polymerase, 전사 인자들(transcription factors), activator, enhancer, repressor 등과 같은 transcription machinery 들이 결합함으로써 진행된다 [4]. 전사인자들은 DNA에 직접 작용하거나 RNA 중합효소의 결합력을 변화시켜 전사단계를 조절하는 등 RNA 합성을 증진 시키거나, 감소 시키는 역할을 수행한다 [1]. 따라서 유전자 발현을 연구하기 위해 프로모터 부위를 클로닝하여 luciferase 등과 같은 reporter 유전자 활성 등을 분석하는 실험들이 수행되고 있다 [10].…”

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Promoter Cloning of Human SETDB1 Gene Utilizing Bioinformatic Programs

Noh¹,

Kim

2014

Journal of Life Science

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Eukaryotic gene expression is an important process, which is initiated by several transcription factors and RNA polymerases that occupy the promoter region of genomic DNA. Although there are many experiments to identify the promoter region in a gene, it is time and labor consuming to finalize it. In this study, we utilized bioinformatic programs, including Ensembl, NCBI, and CpG plots, to identify the cloning promoter region in SETDB1 genomic DNA. We performed PCR amplification to obtain the SETDB1 promoter on an approximately 2 kb region upstream from the TSS named SETDB1-P1. The PCR product was ligated with TA cloning vectors, and we confirmed the insert size using restriction enzyme digestion. Sequentially, the insert was subcloned into a pGL3-luc vector to produce pGL3-SETDB1-P1-luc and then confirmed by DNA sequencing. We also obtained a fragmented PCR product called P2 and P3 and performed a luciferase assay using pGL3-SETDB1-P1-luc transfection. We found that several anticancer drugs, including taxol, 4-FU, and doxorubicin, decreased the promoter activity of SETDB1. We obtained consistent data on the regulation of SETDB1 gene expression after anticancer drug treatment using Western blot analysis and RT-PCR. Our results suggest that promoter cloning of the human SETDB1 gene utilizing bioinformatics is a very useful and timesaving approach to study gene expression.

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Promoter Cloning of Human SETDB1 Gene Utilizing Bioinformatic Programs

Noh¹,

Kim

2014

Journal of Life Science

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Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner

Abbas

Padmanabhan

Eng

2020

Human Molecular Genetics

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PTEN is implicated in a wide variety of pathophysiological conditions and traditionally studied in the context of the PIK3-AKT–mTOR axis. Recent studies from our group and others have reported a novel role of PTEN in the regulation of transcription at the genome-wide scale. This emerging role of PTEN on global transcriptional regulation is providing a better understanding of various diseases, including cancer. Since cancer progression is an energy-demanding process and PTEN is known to regulate metabolic processes, we sought to understand the role of PTEN in transcriptional regulation under metabolic stress, a condition often developing in the tumor microenvironment. In the present study, we demonstrate that PTEN modulates genome-wide RNA Polymerase II (Pol II) occupancy in cells undergoing glucose deprivation. The glucose-deprived PTEN null cells were found to continue global gene transcription, which may activate a survival mode. However, cells with constitutive PTEN expression slow transcription, an evolutionary mechanism that may save cellular energy and activate programmed cell death pathways, in the absence of glucose. Interestingly, alternative exon usage by PTEN null cells is increased under metabolic stress compared to PTEN expressing cells. Overall, our study demonstrates distinct mechanisms involved in PTEN-dependent genome-wide transcriptional control under metabolic stress. Our findings provide a new insight in understanding tumor pathology and how PTEN loss of function, whether by genetic or non-genetic mechanisms, can contribute to a favorable transcriptional program employed by tumor cells to escape apoptosis, hence developing more aggressive and metastatic phenotypes.

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Manipulation of plant RNA biology by geminiviruses

Wang

Lozano‐Durán²

2023

Journal of Experimental Botany

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Viruses are intracellular parasites that have evolved to effectively manipulate the cells they infect. As a result of the viral infection, multiple cellular processes are altered, suppressed, or redirected, partially due to the viral co-option of the host’s molecular machinery. RNA biology plays a central role in virus-host interactions, since it is at the basis of viral gene expression, splicing of viral transcripts, anti-viral RNA silencing and, at least in the case of RNA viruses, genome replication, and therefore is heavily targeted by viruses. The plant DNA geminiviruses, causal agents of devasting diseases in crops worldwide, are no exception, and RNA processing is tightly entrenched in their infection cycle. In this review, we will discuss the relevance of the manipulation of RNA biology by geminiviruses for a successful viral infection, the underlying molecular mechanisms, and posit some of the multiple remaining open questions in this field.

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The RNA Polymerase II Transcriptional Machinery and Its Epigenetic Context

Cited by 3 publications

References 142 publications

Promoter Cloning of Human SETDB1 Gene Utilizing Bioinformatic Programs

Promoter Cloning of Human SETDB1 Gene Utilizing Bioinformatic Programs

Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner

Manipulation of plant RNA biology by geminiviruses

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