2022
DOI: 10.1093/bfgp/elac009
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A survey on protein–DNA-binding sites in computational biology

Abstract: Transcription factors are important cellular components of the process of gene expression control. Transcription factor binding sites are locations where transcription factors specifically recognize DNA sequences, targeting gene-specific regions and recruiting transcription factors or chromatin regulators to fine-tune spatiotemporal gene regulation. As the common proteins, transcription factors play a meaningful role in life-related activities. In the face of the increase in the protein sequence, it is urgent … Show more

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Cited by 16 publications
(11 citation statements)
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“…To overcome these limitations of tsCUT&Tag, we tested the combination of tsCUT&Tag with state‐of‐the‐art machine‐learning methods. Several machine‐learning neural networks, such as the long short‐term memory (LSTM) and temporal convolutional network (TCN), can powerfully predict TFBSs from DNA sequences (Koo and Ploenzke, 2020; Chen et al, 2021; Zhang et al, 2022). As genome accessibility plays an important role in TF binding (Buenrostro et al, 2013), we obtained open chromatin information of maize yellow and green leaves with an assay for transposase accessible chromatin using sequencing (ATAC‐seq) (Ricci et al, 2019; Sun et al, 2020).…”
Section: Resultsmentioning
confidence: 99%
“…To overcome these limitations of tsCUT&Tag, we tested the combination of tsCUT&Tag with state‐of‐the‐art machine‐learning methods. Several machine‐learning neural networks, such as the long short‐term memory (LSTM) and temporal convolutional network (TCN), can powerfully predict TFBSs from DNA sequences (Koo and Ploenzke, 2020; Chen et al, 2021; Zhang et al, 2022). As genome accessibility plays an important role in TF binding (Buenrostro et al, 2013), we obtained open chromatin information of maize yellow and green leaves with an assay for transposase accessible chromatin using sequencing (ATAC‐seq) (Ricci et al, 2019; Sun et al, 2020).…”
Section: Resultsmentioning
confidence: 99%
“…The interactions between DNA and proteins form the basis of numerous cellular processes crucial for biological functions (Zhang et al, 2022). Approximately 6-7% of eukaryotic proteins are known to interact with DNA.…”
Section: Introductionmentioning
confidence: 99%
“…These proteins guide strand separation, maintain DNA integrity, regulate gene expression, compact genetic material, and reorganize chromatin structure. Understanding the characteristics and functions of DNA-binding proteins has become essential across various scientific disciplines (Zhang et al, 2022). Identifying these proteins enhances its comprehension of structural regulations and facilitates understanding of relations between gene mutations and genetic diseases (Kabir et al, 2024; Alendar and Berns, 2021a).…”
Section: Introductionmentioning
confidence: 99%
“…Molecular-level details are learned using X-ray crystallography, electron microscopy, and nuclear magnetic resonance, with around 7000 structures of protein-DNA complexes in PDB ( 6 ). However, these techniques do not keep up with a rapid accumulation of the protein and DNA sequence data ( 7 , 8 ), motivating the development and use of fast computational predictors of protein-DNA interactions from protein sequences ( 9–14 ) and DNA sequences ( 15 , 16 ). These methods are developed using a limited amount of the experimental data and can be applied to predict interactions in a high-throughput manner for the uncharacterized sequences.…”
Section: Introductionmentioning
confidence: 99%