Results 11 to 20 of about 122 (91)
Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise.
PLoS Genetics, 2018 The binding of transcription factors to short recognition sequences plays a pivotal role in controlling the expression of genes. The sequence and shape characteristics of binding sites influence DNA binding specificity and have also been implicated in ...
Stefanie Schöne +7 more
doaj +6 more sources
Scientific Reports, 2023 Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors ...
Ya-Chien Chan +13 more
doaj +5 more sources
BIO-PROTOCOL, 2020 Transcriptional enhancers control cell-type specific gene expression in humans and dysfunction can lead to debilitating diseases, including cancer. Identifying bona-fide enhancers is difficult due to a lack of spatial or sequence constraints. In addition, only a small percentage of the genome is accessible in matured cell types; and therefore, most ...
Tyler Hansen, Emily Hodges
+8 more sources
Challenges and considerations for reproducibility of STARR-seq assays
Genome Research, 2022 Abstract High-throughput methods such as RNA-seq, ChIP-seq and ATAC-seq have well-established guidelines, commercial kits, and analysis pipelines that enable consistency and wider adoption for understanding genome function and regulation.
Maitreya Das +4 more
openaire +2 more sources
Identification of plant enhancers and their constituent elements by STARR-seq in tobacco leaves [PDF]
The Plant Cell, 2020 ABSTRACT Genetic engineering of cis -regulatory elements in crop plants is a promising strategy to ensure food security. However, such engineering is currently hindered by our limited knowledge of plant cis -regulatory elements.
Tobias Jores +5 more
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Functional assessment of human enhancer activities using whole-genome STARR-sequencing
Genome Biology, 2017 Background Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification.
Yuwen Liu +5 more
doaj +1 more source
BasicSTARRseq: a Bioconductor R-package for analyzing STARR-seq data
, 2021 Self-transcribing active regulatory region sequencing (STARR-seq) was first described in 2013 by Arnold et al. and allows to identify and quantify enhancer regions in non-coding DNA in large scale. The R-package BasicSTARRseq provides routines for quality controls, analysis and visualization of STARR-seq data.
Bürger, Annika +3 more
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Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity Mapping [PDF]
, 2020 Abstract STARR-seq assesses millions of fragments in parallel measuring enhancer activity quantitatively. Here we show that STARR-seq is critically flawed with a systematic error in the cells of Arabidopsis thaliana (A. thaliana) .
Longjian Niu +6 more
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Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction
eLife, 2020 Genome-wide association studies have implicated common genomic variants in the gene desert upstream of TBX3 in cardiac conduction velocity. Whether these noncoding variants affect expression of TBX3 or neighboring genes and how they affect cardiac ...
Jan Hendrik van Weerd +7 more
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Global Quantitative Mapping of Enhancers in Rice Genome by STARR-seq [PDF]
, 2018 Abstract Identification of enhancers has been a challenge in plants. STARR-seq measures enhancer activity of millions fragments in parallel. Here we present a global map of rice enhancers quantitatively determined using STARR-seq. Most enhancers are mapped within genes, especially at the 5’ untranslated regions (5’ UTR) and the coding ...
Sun, Jialei +7 more
openaire +1 more source