A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome

PROTEOMICS, Год журнала: 2023, Номер 23(13-14)

Опубликована: Апрель 6, 2023

Enhancers are non-coding DNA elements that play a crucial role in enhancing the transcription rate of specific gene genome. Experiments for identifying enhancers can be restricted by their conditions and involve complicated, time-consuming, laborious, costly steps. To overcome these challenges, computational platforms have been developed to complement experimental methods enable high-throughput identification enhancers. Over last few years, development various enhancer tools has resulted significant progress predicting putative Thus, researchers now able use variety strategies enhance advance study. In this review, an overview machine learning (ML)-based prediction related databases provided. The existing enhancer-prediction also reviewed regarding algorithms, feature selection processes, validation techniques, software utility. addition, advantages drawbacks ML approaches guidelines developing bioinformatic highlighted more efficient prediction. This review will serve as useful resource experimentalists selecting appropriate tool study, bioinformaticians accurate advanced ML-based predictors.

Язык: Английский

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Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in Drosophila

International Journal of Molecular Sciences, Год журнала: 2021, Номер 22(6), С. 2856 - 2856

Опубликована: Март 11, 2021

The chromatin remodeler SWI/SNF is an important participant in gene activation, functioning predominantly by opening the structure on promoters and enhancers. Here, we describe its novel mode of action which factors mediate targeted enhancer. We studied functions two signature subunits PBAP subfamily, BAP170 SAYP, Drosophila. These were stably tethered to a transgene reporter carrying hsp70 core promoter. transcription pattern that generated enhancers close insertion site multiple loci throughout genome. Both SAYP recruit whole complex However, found BAP170-dependent more resistant depletion other subunits, suggesting may play critical role establishing enhancer-dependent transcription.

Язык: Английский

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BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(3), С. 1903 - 1903

Опубликована: Фев. 5, 2024

The concept of cis-regulatory modules located in gene promoters represents today's vision the organization transcriptional regulation. Such are a combination two or more single, short DNA motifs. bioinformatic identification such belongs to so-called NP-hard problems with extreme computational complexity, and therefore, simplifications, assumptions, heuristics usually deployed tackle problem. In practice, this requires, first, many parameters be set before search, second, it leads locally optimal results. Here, novel method is presented, aimed at identifying elements based on an exhaustive search all feasible modules' configurations. All required automatically estimated using positive negative datasets. To computationally efficient, accelerated multidimensional hash function, allowing complete few hours regular laptop (for example, CPU Intel i7, 3.2 GH, 32 Gb RAM). Tests established benchmark real data show better performance BestCRM compared available methods according several metrics like specificity, sensitivity, AUC, etc. A great practical advantage its minimum number input parameters-apart from promoters, only desired level module presence required.

Язык: Английский

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Identifying inflammation-related targets of natural lactones using network pharmacology, molecular modeling and in vitro approaches

Journal of Biomolecular Structure and Dynamics, Год журнала: 2024, Номер unknown, С. 1 - 16

Опубликована: Фев. 9, 2024

Natural lactones have been used in traditional and folklore medicine for centuries owing to their anti-inflammatory properties. The study uses a multifaceted approach identify lead from the SISTEMATX natural products database. analyzed lactone database, revealing 18 linked inflammation targets. primary targets were PTGES, PTGS1, COX-2, ALOX5 IL1B. STX 12273 was best hit, with lowest binding energy potential inhibiting COX-2 enzyme. suggested lactone, 12273, database postulated its use treatment or prevention.

Язык: Английский

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New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity

Nucleic Acids Research, Год журнала: 2024, Номер 52(12), С. 6886 - 6905

Опубликована: Май 20, 2024

Abstract In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to chromatin, an interaction that is essential for functional activity promoters and insulators. this study, we describe new C2H2 called Madf Zinc-Finger Protein 1 (Mzfp1) interacts with CP190. Mzfp1 has unusual structure includes six domains organized in C-terminal cluster two tandem MADF domains. predominantly binds housekeeping gene located both euchromatin heterochromatin genome regions. vivo mutagenesis studies showed protein, region are required its activity. The sufficient specific binding regulatory elements, while second domain recruitment heterochromatin. proximal part Fub boundary separates Ubx abd-A genes Bithorax complex. participates functions cooperation Pita Su(Hw). Thus, involved organization active insulators Drosophila.

Язык: Английский

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