scholarly journals Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Margherita Francescatto ◽  
Marina Lizio ◽  
Ingrid Philippens ◽  
Luba M. Pardo ◽  
Ronald Bontrop ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Transcription Start Site ◽  
Macaca Mulatta ◽  
Start Site ◽  
Transcription Start

scholarly journals Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Margherita Francescatto ◽  
Marina Lizio ◽  
Ingrid Philippens ◽  
Luba M. Pardo ◽  
Ronald Bontrop ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Transcription Start Site ◽  
Macaca Mulatta ◽  
Start Site ◽  
Transcription Start

scholarly journals Prosaposin: promoter analysis and central-nervous-system-preferential elements for expression in vivo

2000 ◽  
Vol 352 (2) ◽  
pp. 549-556 ◽  
Author(s):  
Ying SUN ◽  
Peng JIN ◽  
David P. WITTE ◽  
Gregory A. GRABOWSKI
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Transgenic Mice ◽  
Transcription Start Site ◽  
Luciferase Reporter ◽  
Start Site ◽  
Transcription Start ◽  
Α Subunit ◽  
Preferential Expression

The expression of prosaposin is temporally and spatially regulated at the transcriptional and post-translational levels. In vitro, the mouse prosaposin promoter contains functional RORE [retinoic acid-receptor-related orphan receptor α subunit (RORα)-binding element], Sp1 and U (unknown) sites within 310bp directly 5′ to the transcription start site and additional elements within 2400bp 5′ to the transcription start site. To elucidate promoter regions important to tissue-preferential expression in vivo, transgenic mice were created with 5′-flanking deletions of the prosaposin gene fused to a luciferase reporter. Nearly exclusive expression was observed in cerebrum, cerebellum and eyes of adult transgenic mice containing constructs with 234–310bp of 5ƀ-flanking DNA. This central nervous system (CNS) expression was due to the presence of RORE and overlapping Sp1 sites in this region. Internal deletion of RORE and the Sp1 cluster from the longer constructs with 2400bp of 5ƀ-flanking DNA significantly diminished expression in the CNS. The appearance of substantial visceral tissue (e.g. liver, spleen, lung, kidney, thymus and heart) expression was obtained with transgenic mice bearing constructs with 742–2400bp of 5ƀ-flanking DNA. The cellular localization of luciferase reporter-gene expression from these constructs corresponded closely with that for prosaposin. These results define important CNS and visceral regulatory regions in the promoter in vivo and may be sufficient to account for the majority of prosaposin's tissue-preferential expression.

The Role of XPB/Ssl2 dsDNA Translocase Processivity in Transcription Start-site Scanning

2021 ◽  
pp. 166813
Author(s):  
Eric J. Tomko ◽  
Olivia Luyties ◽  
Jenna K. Rimel ◽  
Chi-Lin Tsai ◽  
Jill O. Fuss ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start

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).

Mapping of the Human Renin Transcription Start Site: Evidence for a Single Functional Promoter

1988 ◽  
Vol 10 (6) ◽  
pp. 1313-1316
Author(s):  
Martin Paul ◽  
David W. Burt ◽  
Norifumi Nakamura ◽  
Richard E. Pratt ◽  
Victor J. Dzau
Keyword(s):  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start ◽  
Human Renin

scholarly journals Sequence of the 5′-flanking region and promoter activity of the human mucin gene MUC5B in different phenotypes of colon cancer cells

2000 ◽  
Vol 348 (3) ◽  
pp. 675-686 ◽  
Author(s):  
Isabelle VAN SEUNINGEN ◽  
Michaël PERRAIS ◽  
Pascal PIGNY ◽  
Nicole PORCHET ◽  
Jean-Pierre AUBERT
Keyword(s):  
Gene Expression ◽  
Transcription Start Site ◽  
Promoter Activity ◽  
Luciferase Reporter ◽  
Nuclear Factor ◽  
Start Site ◽  
Transcription Start ◽  
Mucin Gene ◽  
Intron 1 ◽  
Flanking Region

Control of gene expression in intestinal cells is poorly understood. Molecular mechanisms that regulate transcription of cellular genes are the foundation for understanding developmental and differentiation events. Mucin gene expression has been shown to be altered in many intestinal diseases and especially cancers of the gastrointestinal tract. Towards understanding the transcriptional regulation of a member of the 11p15.5 human mucin gene cluster, we have characterized 3.55 kb of the 5ʹ-flanking region of the human mucin gene MUC5B, including the promoter, the first two exons and the first intron. We report here the promoter activity of successively 5ʹ-truncated sections of 956 bases of this region by fusing it to the coding region of a luciferase reporter gene. The transcription start site was determined by primer-extension analysis. The region upstream of the transcription start site is characterized by the presence of a TATA box at bases -32/-26, DNA-binding elements for transcription factors c-Myc, N-Myc, Sp1 and nuclear factor ĸB as well as putative activator protein (AP)-1-, cAMP-response-element-binding protein (CREB)-, hepatocyte nuclear factor (HNF)-1-, HNF-3-, TGT3-, gut-enriched Krüppel factor (GKLF)-, thyroid transcription factor (TTF)-1- and glucocorticoid receptor element (GRE)-binding sites. Intron 1 of MUC5B was also characterized, it is 2511 nucleotides long and contains a DNA segment of 259 bp in which are clustered eight tandemly repeated GA boxes and a CACCC box that bind Sp1. AP-2α and GATA-1 nuclear factors were also shown to bind to their respective cognate elements in intron 1. In transfection studies the MUC5B promoter showed a cell-specific activity as it is very active in mucus-secreting LS174T cells, whereas it is inactive in Caco-2 enterocytes and HT-29 STD (standard) undifferentiated cells. Within the promoter, maximal transcription activity was found in a segment covering the first 223 bp upstream of the transcription start site. Finally, in co-transfection experiments a transactivating effect of Sp1 on to MUC5B promoter was seen in LS174T and Caco-2 cells.

scholarly journals MAPCap: A fast and quantitative transcription start site profiling protocol

2019 ◽  
Author(s):  
Vivek Bhardwaj ◽  
Giuseppe Semplicio ◽  
Niyazi Umut Erdogdu ◽  
Asifa Akhtar
Keyword(s):  
High Resolution ◽  
Differential Expression ◽  
Transcription Start Site ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Start Site ◽  
Transcription Start ◽  
Transcription Start Sites

Abstract Below we present a simple and quick TSS quantification protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) that enables users to combine high-resolution detection of transcription start-sites and differential expression analysis. MAPCap can be used to profile TSS from dozens of samples in a multiplexed way, in 16-18 hours. MAPCap data can be analyzed using our easy-to-use software icetea (https://bioconductor.org/packages/icetea), which allows users to detect robust TSS using replicates, and perform differential TSS analysis.

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