Transcriptional enhancers in animal development and evolution.

By M. Levine. 2010

470 citations recorded by the source corpus.

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Citations in the corpus

Iterative random forests to discover predictive and stable high-order interactions (2017, background): “Enhancers play a critical role in this process by coordinating combinatorial TF binding, whose integrated activity leads to patterned gene expression during embryogenesis (28).”
Genome-scale functional characterization of Drosophila developmental enhancers in vivo (2014, background): “Transcriptional enhancers are crucial regulators of gene expression and animal development 1 and the characterization of their genomic organization, spatiotemporal activities and sequence properties is a keygoalinmodernbiology 2–8 .”
Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “In addition to their central role in developmental gene regulation, enhancers are fertile targets for evolutionary change, as they are both cell-type specific (allowing for modulation of target gene expression in specific tissue context without affecting other pleiotropic gene functions) and commonl”
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence (2011, background): “Promoters and enhancers are the best understood types of CRE”
Functional and mechanistic diversity of distal transcription enhancers (2011, unknown): “, and Levine, M. (2003). Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex.”
Sequential regulatory activity prediction across chromosomes with convolutional neural networks (2017, methodology): “Even with intra-experiment training data to infer the relevant sequence motifs, the complexity of distal regulation where enhancers can interact with promoters across hundreds of thousands of nucleotides challenges the current generation of methods (Long et al. 2016; Levine 2010) .”
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, unknown): “As histone marks often label broad regions, we first determined the intersection of both H3K4me1 and H3K27ac marked regions and then evaluated the STARR-‐seq enrichment either at the center of the in”
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. (2013, unknown): “These results suggest that despite the well established role of particular TF combinations in cell fate determination and development (Levine, 2010; Takahashi and Yamanaka, 2006), most combinations of TFs observed are not the result of an adaptive process (see also Lynch, 2007), but represents…”
PEDLA: predicting enhancers with a deep learning-based algorithmic framework (2016, background): “(6) The H3K27ac peak had to be at least 2 kb away from all rRNA genes.”
Pioneer transcription factors: establishing competence for gene expression. (2011, background): “This passive mode is supported by the observation that the vast majority of promoters and enhancers, particularly those involved in tissue-specific expression, require binding by a combination of transcription factors for activity (Boyer et al. 2005; MacArthur et al. 2009; Levine 2010).”
Enhancer function: new insights into the regulation of tissue-specific gene expression (2011, unknown): “jpg"/> Differentiation of the various cell types present in multicellular organisms requires the establishment of spatiotemporal patterns of gene expression during developmen”