scholarly journals Features of the RAP1A and RAP1B core promoters: recombinant approaches to testing regulatory element function in expression control (946.10)

2014 ◽  
Vol 28 (S1) ◽  
Author(s):  
Ryan Augustin ◽  
Mark Painter ◽  
Amy Niemela ◽  
Jennifer Cruise
Keyword(s):  
Regulatory Element ◽  
Core Promoters ◽  
Expression Control ◽  
Element Function

scholarly journals Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

2017 ◽  
Author(s):  
Sarah Rennie ◽  
Maria Dalby ◽  
Marta Lloret-Llinares ◽  
Stylianos Bakoulis ◽  
Christian Dalager Vaagensø ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Core Promoter ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Chromatin Interaction ◽  
Promoter Strength ◽  
Gene Promoters ◽  
Core Promoters ◽  
Promoter Architecture ◽  
Regulatory Functions

ABSTRACTMammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in D. melanogaster. Surprisingly, we find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The different layers of regulation mediated by gene-distal enhancers and gene promoters are also reflected in chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements.

Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing

2018 ◽  
pp. 447-480 ◽  
Author(s):  
Tyler S. Klann ◽  
Gregory E. Crawford ◽  
Timothy E. Reddy ◽  
Charles A. Gersbach
Keyword(s):  
Regulatory Element ◽  
Epigenome Editing ◽  
Element Function

scholarly journals The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Hamish W King ◽  
Robert J Klose
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Embryonic Stem Cells ◽  
Regulatory Element ◽  
Embryonic Stem ◽  
Cellular Reprogramming ◽  
Factor Binding ◽  
Pioneer Factor ◽  
Pioneer Factors ◽  
Element Function

Pioneer transcription factors recognise and bind their target sequences in inaccessible chromatin to establish new transcriptional networks throughout development and cellular reprogramming. During this process, pioneer factors establish an accessible chromatin state to facilitate additional transcription factor binding, yet it remains unclear how different pioneer factors achieve this. Here, we discover that the pluripotency-associated pioneer factor OCT4 binds chromatin to shape accessibility, transcription factor co-binding, and regulatory element function in mouse embryonic stem cells. Chromatin accessibility at OCT4-bound sites requires the chromatin remodeller BRG1, which is recruited to these sites by OCT4 to support additional transcription factor binding and expression of the pluripotency-associated transcriptome. Furthermore, the requirement for BRG1 in shaping OCT4 binding reflects how these target sites are used during cellular reprogramming and early mouse development. Together this reveals a distinct requirement for a chromatin remodeller in promoting the activity of the pioneer factor OCT4 and regulating the pluripotency network.

scholarly journals Genome-wide quantification of the effects of DNA methylation on human gene regulation

2017 ◽  
Author(s):  
Amanda J. Lea ◽  
Christopher M. Vockley ◽  
Rachel A. Johnston ◽  
Christina A. Del Carpio ◽  
Luis B. Barreiro ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factors ◽  
Human Genome ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Trait Variation ◽  
Methylated Dna ◽  
Genome Wide ◽  
The Many ◽  
Element Function

AbstractChanges in DNA methylation are important in development and disease, but not all regulatory elements act in a methylation-dependent (MD) manner. Here, we developed mSTARR-seq, a high-throughput approach to quantify the effects of DNA methylation on regulatory element function. We assay MD activity in 14% of the euchromatic human genome, identify 2,143 MD regulatory elements, and predict MD activity using sequence and chromatin state information. We identify transcription factors associated with higher activity in unmethylated or methylated states, including an association between pioneer transcription factors and methylated DNA. Finally, we use mSTARR-seq to predict DNA methylation-gene expression correlations in primary cells. Our findings provide a map of MD regulatory activity across the human genome, facilitating interpretation of the many emerging associations between methylation and trait variation.

scholarly journals Functional Analysis of Ground Squirrel Hepatitis Virus Enhancer II

1998 ◽  
Vol 72 (2) ◽  
pp. 1616-1622
Author(s):  
Geneviève Fourel ◽  
François Ringeisen ◽  
Marc Flajolet ◽  
Pierre Tiollais ◽  
Marie Annick Buendia
Keyword(s):  
Ground Squirrel ◽  
Hepatitis Virus ◽  
Core Promoter ◽  
Regulatory Element ◽  
Human Hepatoma Cells ◽  
Independent Manner ◽  
Distinctive Features ◽  
Core Promoters ◽  
Level Of Activity ◽  
Enhancer Ii

ABSTRACT We have characterized a major regulatory element of ground squirrel hepatitis virus (GSHV) located within a 90-nucleotide fragment of the core promoter upstream sequences and have compared its organization to that of woodchuck hepatitis virus (WHV) enhancer II (We2). The GSHV element (Ge2) stimulates transcription from the viral core promoter and heterologous promoters in an orientation-independent manner but displays a lower level of activity than We2 in transient transfection assays in human hepatoma cells. The general organization of Ge2 into binding sites for the liver-enriched HNF-1 and HNF-4 proteins and for ubiquitous factors of the NF1 and Oct families was found to be mostly conserved with respect to the homologous We2 region. Accordingly, transactivation by HNF-1 and HNF-4 plays an essential role in the liver-specific transcriptional activity of both the GSHV and WHV core promoters. Distinctive features of the GSHV enhancer consist of its ability to bind C/EBP family factors in a central motif that overlaps with one of the two HNF-4 sites and its differential binding affinities for HNF-4.

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