EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model
نویسندگان
چکیده
منابع مشابه
Exploiting sequence-based features for predicting enhancer–promoter interactions
Motivation A large number of distal enhancers and proximal promoters form enhancer-promoter interactions to regulate target genes in the human genome. Although recent high-throughput genome-wide mapping approaches have allowed us to more comprehensively recognize potential enhancer-promoter interactions, it is still largely unknown whether sequence-based features alone are sufficient to predict...
متن کاملPredicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks
In the human genome, distal enhancers are involved in regulating target genes through proximal promoters by forming enhancer-promoter interactions. Although recently developed highthroughput experimental approaches have allowed us to recognize potential enhancer-promoter interactions genome-wide, it is still largely unclear to what extent the sequence-level information encoded in our genome hel...
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Using Brownian dynamics simulations, we investigate here one of possible roles of supercoiling within topological domains constituting interphase chromosomes of higher eukaryotes. We analysed how supercoiling affects the interaction between enhancers and promoters that are located in the same or in neighbouring topological domains. We show here that enhancer-promoter affinity and supercoiling a...
متن کاملDynamic enhancer-gene body contacts during transcription elongation.
Enhancers govern transcription through multiple mechanisms, including the regulation of elongation by RNA polymerase II (RNAPII). We characterized the dynamics of looped enhancer contacts during synchronous transcription elongation. We found that many distal enhancers form stable contacts with their target promoters during the entire interval of elongation. Notably, we detected additional dynam...
متن کاملPredicting protein residue-residue contacts using deep networks and boosting
MOTIVATION Protein residue-residue contacts continue to play a larger and larger role in protein tertiary structure modeling and evaluation. Yet, while the importance of contact information increases, the performance of sequence-based contact predictors has improved slowly. New approaches and methods are needed to spur further development and progress in the field. RESULTS Here we present DNC...
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ژورنال
عنوان ژورنال: PeerJ
سال: 2019
ISSN: 2167-8359
DOI: 10.7717/peerj.7657