Results 1 to 10 of about 72 (67)
STARRPeaker: Uniform Processing and Accurate Identification of STARR-Seq Active Regions
Genome Biology, 2020 STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and often ...
Kevin White +2 more
exaly +2 more sources
Genome Biology, 2020 Background Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers ...
Tianran Peng +2 more
exaly +3 more sources
Global Quantitative Mapping of Enhancers in Rice by STARR-Seq
Genomics, Proteomics and Bioinformatics, 2019 Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of ...
Sun Jialei, Na He, Longjian Niu
exaly +3 more sources
HDI-STARR-Seq: Condition-Specific Enhancer Discovery in Mouse Liver in Vivo
BMC GenomicsBackground STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular
David J. Waxman
exaly +2 more sources
Uncovering the Whole Genome Silencers of Human Cells via Ss-STARR-Seq
Nature CommunicationsSilencers, the yin to enhancers’ yang, play a pivotal role in fine-tuning gene expression throughout the genome. However, despite their recognized importance, comprehensive identification of these regulatory elements in the genome is still in its early ...
Yubo Zhang, Xiusheng Zhu
exaly +2 more sources
Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique
Frontiers in Cellular and Infection Microbiology, 2023 IntroductionVarious sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion.
Ronald J. Nowling +3 more
doaj +1 more source
Cis-regulatory atlas of primary human CD4+ T cells
BMC Genomics, 2023 Cis-regulatory elements (CRE) are critical for coordinating gene expression programs that dictate cell-specific differentiation and homeostasis. Recently developed self-transcribing active regulatory region sequencing (STARR-Seq) has allowed for genome ...
Kurtis Stefan, Artem Barski
doaj +1 more source
Genome-wide identification of functional enhancers and their potential roles in pig breeding
Journal of Animal Science and Biotechnology, 2022 Background The pig is an economically important livestock species and is a widely applied large animal model in medical research. Enhancers are critical regulatory elements that have fundamental functions in evolution, development and disease.
Yinqiao Wu +10 more
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Integration of Count Difference and Curve Similarity in Negative Regulatory Element Detection
Frontiers in Genetics, 2022 Negative regulatory elements (NREs) down-regulate gene expression by inhibiting the activities of promoters or enhancers. The repressing activity of NREs can be measured globally by massively parallel reporter assays (MPRAs).
Na He +7 more
doaj +1 more source
Frontiers in Genetics, 2022 Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters.
Inge Holm +13 more
doaj +1 more source