Results 71 to 80 of about 122 (91)
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STARR-Seq for High-Throughput Identification of Plant Enhancers
Trends in Plant Science, 2022Wai-Shing Yung, Mingkun Huang
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Functional Definition of Thyroid Hormone Response Elements Based on a Synthetic STARR-Seq Screen. [PDF]
Endocrinology, 2022 Abstract When bound to thyroid hormone, the nuclear receptor TRα1 activates the transcription of a number of genes in many cell types. It mainly acts by binding DNA as a heterodimer with retinoid X receptors at specific response elements related to the DR4 consensus sequence.
Romain Guyot +2 more
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Correcting Signal Biases and Detecting Regulatory Elements in STARR-Seq Data [PDF]
Genome Research, 2021 High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human genome at once. The resulting data, however, present substantial analytical challenges.
William H Majoros +2 more
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Current Protocols in Molecular Biology, 2019 AbstractThe identification of transcriptional enhancers and the quantitative assessment of enhancer activities is essential to understanding how regulatory information for gene expression is encoded in animal and human genomes. Further, it is key to understanding how sequence variants affect enhancer function.
Alexander Stark +2 more
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Underlying Causes for Prevalent False Positives and False Negatives in STARR-Seq Data.
NAR Genomics and Bioinformatics, 2023 Abstract STARR-seq and its variants have been widely used to characterize enhancers. However, it has been reported that up to 87% of STARR peaks are located in repressive chromatins and are not functional in the tested cells.
Pengyu Ni, Zheng-Chang Su
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Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-Seq
Science, 2013The Regulatory Genome Multicellular organisms contain a variety of cell types that are morphologically and functionally distinct even though they typically contain the same genomic DNA. Differences stem from differential gene expression.
Daniel Gerlach +2 more
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Sequence model evaluation framework for STARR-seq peak calling
Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2021Enhancers are short regions of non-coding DNA that increase transcription rates of genes despite being located distantly from the genes themselves [5]. Enhancers are identified through experimental techniques such as ChIP-Seq or CUT&RUN with H3K4me1 and H3K27ac histone modifications, self-transcribing active regulatory region sequencing (STARR-Seq ...
Christopher R. Beal +2 more
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Filtering STARR-Seq Peaks for Enhancers with Sequence Models
Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, 2020STARR-Seq is a high-throughput technique for directly identifying genomic regions with enhancer activity [1]. Genomic DNA is sheared, inserted into artificial plasmids designed so that DNA with enhancer activity trigger self-transcription, and transfected into culture cells.
Ronald J. Nowling +2 more
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Assessing Genome-Wide Dynamic Changes in Enhancer Activity During Early mESC Differentiation by FAIRE-STARR-Seq. [PDF]
Nucleic Acids Research, 2021 Abstract Embryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess the dynamics of enhancer activity during the early stages of murine ESC differentiation, we analyzed accessible genomic ...
Alisa Fuchs +2 more
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