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7.976 Aktuelle Fachpublikationen in Nucleic Acids Research

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DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants

02.04.2018 | Wang M, Tai C, E W, et al., Nucleic Acids Research, 2018

Abstract The complex system of gene expression is regulated by the cell type-specific binding of transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding and lead to human diseases remains a great challenge. To address this, we implement sequence-based deep ...

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LSD1 mediates metabolic reprogramming by glucocorticoids during myogenic differentiation

29.03.2018 | Anan K, Hino S, Shimizu N, et al., Nucleic Acids Research, 2018

Abstract The metabolic properties of cells are formed under the influence of environmental factors such as nutrients and hormones. Although such a metabolic program is likely initiated through epigenetic mechanisms, the direct links between metabolic cues and activities of chromatin modifiers ...

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riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions

28.03.2018 | Waters N, Abram F, Brennan F, et al., Nucleic Acids Research, 2018

Abstract The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are ...

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RNA-splicing factor SART3 regulates translesion DNA synthesis

24.03.2018 | Huang M, Zhou B, Gong J, et al., Nucleic Acids Research, 2018

Abstract Translesion DNA synthesis (TLS) is one mode of DNA damage tolerance that uses specialized DNA polymerases to replicate damaged DNA. DNA polymerase η (Polη) is well known to facilitate TLS across ultraviolet (UV) irradiation and mutations in POLH are implicated in skin carcinogenesis. ...

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Long noncoding RNA OCC-1 suppresses cell growth through destabilizing HuR protein in colorectal cancer

21.03.2018 | Lan Y, Xiao X, He Z, et al., Nucleic Acids Research, 2018

Abstract Overexpressed in colon carcinoma-1 (OCC-1) is one of the earliest annotated long noncoding RNAs (lncRNAs) in colorectal cancer (CRC); however, its function remains largely unknown. Here, we revealed that OCC-1 plays a tumor suppressive role in CRC. OCC-1 knockdown by RNA interference ...

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TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction

20.03.2018 | Gunasekara C, Zhang K, Deng W, et al., Nucleic Acids Research, 2018

Abstract Despite their important roles, the regulators for most metabolic pathways and biological processes remain elusive. Presently, the methods for identifying metabolic pathway and biological process regulators are intensively sought after. We developed a novel algorithm called triple-gene ...

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Protein-mediated loops in supercoiled DNA create large topological domains

10.03.2018 | Yan Y, Ding Y, Leng F, et al., Nucleic Acids Research, 2018

Abstract Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria ...

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Overexpression of the base excision repair NTHL1 glycosylase causes genomic instability and early cellular hallmarks of cancer

07.03.2018 | Limpose K, Trego K, Li Z, et al., Nucleic Acids Research, 2018

Abstract Base excision repair (BER), which is initiated by DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. The NTHL1 glycosylase, which excises DNA base damage caused by reactive oxygen species, is thought to be a tumor suppressor. However, in ...

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Overexpression of the base excision repair NTHL1 glycosylase causes genomic instability and early cellular hallmarks of cancer

07.03.2018 | Limpose K, Trego K, Li Z, et al., Nucleic Acids Research, 2018

Abstract Base excision repair (BER), which is initiated by DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. The NTHL1 glycosylase, which excises DNA base damage caused by reactive oxygen species, is thought to be a tumor suppressor. However, in ...

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Human RTEL1 stabilizes long G-overhangs allowing telomerase-dependent over-extension

07.03.2018 | Porreca R, Glousker G, Awad A, et al., Nucleic Acids Research, 2018

Abstract Telomere maintenance protects the cell against genome instability and senescence. Accelerated telomere attrition is a characteristic of premature aging syndromes including Dyskeratosis congenita (DC). Mutations in hRTEL1 are associated with a severe form of DC called Hoyeraal-Hreidarsson ...

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