scholarly journals Small RNAs Targeting Transcription Start Site Induce Heparanase Silencing through Interference with Transcription Initiation in Human Cancer Cells

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e31379 ◽  
Author(s):  
Guosong Jiang ◽  
Liduan Zheng ◽  
Jiarui Pu ◽  
Hong Mei ◽  
Jun Zhao ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Transcription Start Site ◽  
Small Rnas ◽  
Transcription Initiation ◽  
Human Cancer ◽  
Start Site ◽  
Transcription Start ◽  
Human Cancer Cells

scholarly journals Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

2016 ◽  
Vol 113 (21) ◽  
pp. E2899-E2905 ◽  
Author(s):  
Irina O. Vvedenskaya ◽  
Hanif Vahedian-Movahed ◽  
Yuanchao Zhang ◽  
Deanne M. Taylor ◽  
Richard H. Ebright ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Start Site ◽  
Transcription Initiation ◽  
Specific Protein ◽  
Start Site ◽  
Transcription Start ◽  
Transcription Bubble ◽  
Recognition Element

During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein–DNA interactions with the downstream part of the nontemplate strand of the transcription bubble (“core recognition element,” CRE). Here, we investigated whether sequence-specific RNAP–CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP–CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP–CRE interactions on TSS selection in vitro and in vivo for a library of 47 (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP–CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5′ merodiploid native-elongating-transcript sequencing, 5′ mNET-seq, we assessed effects of RNAP–CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP–CRE interactions determine TSS selection. Our findings establish RNAP–CRE interactions are a functional determinant of TSS selection. We propose that RNAP–CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).

scholarly journals Core Promoter-Dependent TFIIB Conformation and a Role for TFIIB Conformation in Transcription Start Site Selection

2002 ◽  
Vol 22 (19) ◽  
pp. 6697-6705 ◽  
Author(s):  
Jennifer A. Fairley ◽  
Rachel Evans ◽  
Nicola A. Hawkes ◽  
Stefan G. E. Roberts
Keyword(s):  
Transcription Start Site ◽  
Site Selection ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Initiation Site ◽  
Start Site ◽  
Wild Type ◽  
Transcription Start ◽  
General Transcription Factor ◽  
Selection Of

ABSTRACT The general transcription factor TFIIB plays a central role in the selection of the transcription initiation site. The mechanisms involved are not clear, however. In this study, we analyze core promoter features that are responsible for the susceptibility to mutations in TFIIB and cause a shift in the transcription start site. We show that TFIIB can modulate both the 5′ and 3′ parameters of transcription start site selection in a manner dependent upon the sequence of the initiator. Mutations in TFIIB that cause aberrant transcription start site selection concentrate in a region that plays a pivotal role in modulating TFIIB conformation. Using epitope-specific antibody probes, we show that a TFIIB mutant that causes aberrant transcription start site selection assembles at the promoter in a conformation different from that for wild-type TFIIB. In addition, we uncover a core promoter-dependent effect on TFIIB conformation and provide evidence for novel sequence-specific TFIIB promoter contacts.

scholarly journals Template activating factor-I epigenetically regulates the TERT transcription in human cancer cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kohsuke Kato ◽  
Atsushi Kawaguchi ◽  
Kyosuke Nagata
Keyword(s):  
Cancer Cells ◽  
Transcriptional Activation ◽  
Human Cancer ◽  
Tumor Development ◽  
Telomerase Activity ◽  
Transcription Start ◽  
Cpg Dinucleotides ◽  
Human Cancer Cells ◽  
Factor I ◽  
Repeat Dna

AbstractTelomere, the terminus of linear chromosome in eukaryotes, is composed of specific repeat DNA which is mainly synthesized by a protein complex called telomerase. The maintenance of telomere DNA is important for unlimited proliferative capacity of cancer cells. The telomerase activity is controlled by the expression level of telomerase reverse transcriptase (TERT), a catalytic unit of telomerase, in some species including human. Therefore, to reveal the regulatory mechanisms of the transcription of TERT gene is important for understanding the tumor development. We found that template activating factor-I (TAF-I), a multifunctional nuclear protein, is involved in the transcriptional activation of TERT for the maintenance of telomere DNA in HeLa cells. TAF-I maintains the histone H3 modifications involved in transcriptional activation and hypomethylated cytosines in CpG dinucleotides around the transcription start site (TSS) in the TERT gene locus. Collectively, TAF-I is involved in the maintenance of telomere DNA through the regulation of TERT transcription, then consequently the occurrence and/or recurrence of cancer cells.

MOLECULAR CLONING OF THE HUMAN GENE FOR VON WILLEBRAND FACTOR AND IDENTIFICATION OF THE TRANSCRIPTION INITIATION SITE

1987 ◽  
Author(s):  
Corolyn J Collins ◽  
Richard B Levene ◽  
Christina P Ravera ◽  
Marker J Dombalagian ◽  
David M Livingston ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Start Site ◽  
Von Willebrand Factor ◽  
Transcription Initiation ◽  
Promoter Region ◽  
Start Site ◽  
Transcription Start ◽  
Von Willebrand's Disease ◽  
Von Willebrand ◽  
Willebrand Factor

Most patients with von Willebrand's disease appear to have a defect affecting the level of expression of the von Willebrand factor (vWf) gene. Thus, an understanding of the pathogenesis of von Willebrand's disease will require an analysis of the structure and function of the vWf gene in normals and in patients. To begin such analyses, we have screened a human genomic cosmid library with probes obtained from vWf cDNA and isolated a colinear segment spanning ≈175 kb in five overlapping clones. This segment extends ≈25 kb upstream and ≈5 kb downstream of the transcription start and stop sites for vWf mRNA, implying the vWf gene has a length of ≈150 kb. Within one of these clones, the vWf transcription initiation sites have been mapped. A portion of the promoter region has been sequenced, revealing a typical TATA box, a downstream CCAAT box, and a perfect downstream repeat of the 8 base pairs containing the major transcription start site. Primer extension analysis suggests that sequences contained within the downstream repeat of the transcription start site may be used as minor initiation sites in endothelial cells. Transfection studies are underway to evaluate the role of sequences within this promoter region in gene regulatory activity. Comparative restriction analyses of cloned and chromosomal DNA segments strongly suggests that no major alterations ocurred during cloning and that there is only one complete copy of the vWf gene in the human haploid genome. Similar analyses of DNA from vWf-expressing endothelial cells and non-expressing white blood cells suggests that no major rearrangements are associated with vWf gene expression. Finally, cross hybridization patterns among seven mammalian species suggests a strong conservation of genomic sequences encoding the plasma portion of vWf, but a lower degree of conservation of sequences encoding the N terminal region of provWf.

scholarly journals RNA Processing of Nitrogenase Transcripts in the Cyanobacterium Anabaena variabilis

2010 ◽  
Vol 192 (13) ◽  
pp. 3311-3320 ◽  
Author(s):  
Justin L. Ungerer ◽  
Brenda S. Pratte ◽  
Teresa Thiel
Keyword(s):  
Transcription Start Site ◽  
Transcription Initiation ◽  
De Novo ◽  
Start Site ◽  
Transcription Start ◽  
Stem Loop ◽  
Upstream Gene ◽  
Genes Encoding ◽  
Nitrogenase Genes ◽  
Cyanobacterium Anabaena

ABSTRACT Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence for a transcription start site just upstream of nifH1 and vnfH, promoter fragments that included these start sites did not drive the transcription of lacZ and, for nifH1, did not drive the expression of nifHDK1. Further analysis using larger regions upstream of nifH1 indicated that a promoter within nifU1 and a promoter upstream of nifB1 both contributed to expression of nifHDK1, with the nifB1 promoter contributing to most of the expression. Similarly, while the region upstream of vnfH, containing the putative transcription start site, did not drive expression of lacZ, the region that included the promoter for the upstream gene, ava4055, did. Characterization of the previously reported nifH1 and vnfH transcriptional start sites by 5′RACE (5′ rapid amplification of cDNA ends) revealed that these 5′ ends resulted from processing of larger transcripts rather than by de novo transcription initiation. The 5′ positions of both the vnfH and nifH1 transcripts lie at the base of a stem-loop structure that may serve to stabilize the nifHDK1 and vnfH specific transcripts compared to the transcripts for other genes in the operons providing the proper stoichiometry for the Nif proteins for nitrogenase synthesis.

Promoter-targeted double-stranded small RNAs activate PAWR gene expression in human cancer cells

2013 ◽  
Vol 45 (7) ◽  
pp. 1338-1346 ◽  
Author(s):  
Kai Yang ◽  
Jie Shen ◽  
Yan-Qi Xie ◽  
Yi-Wei Lin ◽  
Jie Qin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cancer Cells ◽  
Small Rnas ◽  
Human Cancer ◽  
Human Cancer Cells

scholarly journals Transcription start site-associated small RNAs in the PTEN gene

2017 ◽  
Vol 114 (49) ◽  
pp. E10510-E10511 ◽  
Author(s):  
Ji-Long Liu ◽  
Wen-Qian Zhang ◽  
Ming-Yu Huang
Keyword(s):  
Transcription Start Site ◽  
Small Rnas ◽  
Pten Gene ◽  
Start Site ◽  
Transcription Start

scholarly journals The histone variant macroH2A1.1 regulates gene expression by direct association with their transcription start site

2020 ◽  
Author(s):  
Ludmila Recoules ◽  
Alexandre Heurteau ◽  
Flavien Raynal ◽  
Fatima Moutahir ◽  
Fabienne Bejjani ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Cells ◽  
Transcription Start Site ◽  
Breast Cancer Cells ◽  
Molecular Mechanisms ◽  
Histone Variants ◽  
Histone Variant ◽  
Start Site ◽  
Transcription Start

AbstractThe histone variant macroH2A1 (mH2A1) is involved in cellular growth, differentiation and reprogramming, but the underlying molecular mechanisms are a matter of debate. Different roles of mH2A1 in gene expression may relate to functional differences of its two splicing isoforms, mH2A1.1 and mH2A1.2. Here, we map for the first time genome-wide localization of endogenous mH2A1.1 and link the distribution of mH2A1.1 to control of gene expression in human breast cancer cells. In addition to localization shared with mH2A1.2 to facultative heterochromatin, mH2A1.1 specifically associates with regulatory elements required for gene activation, super-enhancers and promoters of highly expressed genes. Depending on the recruitment profile of mH2A1.1 to these elements, selective depletion of mH2A1.1 up- or downregulates its target genes. mH2A1.1 represses transcription when its binding is spread over the entire gene and promoter, and activates transcription when its binding is strictly confined to the transcription start site (TSS). Notably, RNA Polymerase II was frequently in pause at mH2A1.1-activated genes. Functionally, mH2A1.1-dependent regulation of a subset of paused genes impedes mammary tumor cell migration. Molecular mechanisms of mH2A1.1 function at the TSS uncovered by our study define an intriguing new mode of transcription regulation in cancer cells.Author SummaryControl of gene expression driving cellular functions from differentiation to epistasis and causing, when dysfunctional, uncountable diseases, relies on modifications of chromatin structure. One key element enabling chromatin plasticity is the replacement of canonical histones by histone variants. Among histone variants macroH2A1 (mH2A) is an extraordinary H2A variant possessing a large non-histone domain placed outside of the nucleosome. Two splicing isoforms, mH2A1.1 and mH2A1.2, are produced, but these are rarely studied separately because they only differ in a 30 amino acid region and are difficult to distinguish experimentally, which likely explains contradictory functions reported in the literature. Here, we take advantage of a mH2A1.1 specific antibody to generate the first genome-wide chromatin-associated map of this histone variant in the invasive breast cancer cells line MDA-MB231. We confirm that mH2A1.1, like mH2A1.2, is enriched at facultative heterochromatin in agreement with its reported role as a repressor. However, we discovered that unlike its splicing isoform, mH2A1.1 specifically binds to super-enhancers and the transcription start site of highly transcribed genes. mH2A1.1 is necessary for regulating transcription of these genes. At the cellular level, we demonstrate that mH2A1.1 inhibits migration capacity of highly metastatic breast cancer cells. Our study characterizes for the first time binding profiles of mH2A1.1 that are linked to regulation of gene expression, thereby providing a new molecular mechanisms which govern the plasticity of human tumor cells.

scholarly journals Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster

2017 ◽  
Author(s):  
Michael P. Meers ◽  
Karen Adelman ◽  
Robert J. Duronio ◽  
Brian D. Strahl ◽  
Daniel J. McKay ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Transcription Initiation ◽  
Local Density ◽  
Global Analysis ◽  
Regulatory Elements ◽  
Start Site ◽  
Transcription Start ◽  
Vast Number ◽  
Animal Development ◽  
Divergent Transcription

AbstractBackgroundHigh-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis.ResultsThe data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for “enhancer RNAs” (eRNAs) in defining transcriptional programs that are important for animal development.ConclusionsHigh-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low-stability RNAs. Global analysis of transcription initiation patterns in a developing organism reveals a vast number of novel initiation events that identify potential eRNAs as well as other non-coding transcripts critical for animal development.

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