ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins

Leung, Ricky Wai Tak; Jiang, Xiaoying; Chu, Ka Hou; Qin, Jing

doi:10.1093/nar/gky1112

Cited by 10 publications

(9 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genetic regulations are vital processes in all organisms, which allow an organism to respond to its environment and promote its complexity. This can be achieved with the help of nucleic acid-binding proteins (Tak Leung et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

“…In corn kernels, approximately 70% of the seed is made up of storage compounds (Ali and Elozeiri, 2017); therefore, the classification of proteins must show a breakdown of the processes that have to be carried out during the germination process after inhibition, the activation of metabolic processes, such as the synthesis of hydrolytic enzymes for the degradation of starches (Ali and Elozeiri, 2017) by hydrolases or oxidoreductases, but also in the genetic regulation of the vital processes of its environment (Tak Leung et al ., 2019) such as transcription, translation, gene silencing (Hudson and Ortlud, 2014) in the case of the classification of genes that encode nucleic acid-binding proteins.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Comparative proteomic analysis of hybrid maize MR2008 and its parental lines

et al. 2021

View full text Add to dashboard Cite

Maize is one of the three staple foods in the world. The white variety represents 60% of the maize importation with a world consumption of 1125 million tons in 2019/2020. Currently, new technologies could contribute to the analysis of this seed, supporting quality control and improvement. This study aims to carry out the morphological and proteomic comparison between the hybrid MR2008 and its parental lines LUG03 and CML491 through mass spectrometry and bioinformatics analysis. Herein, we identified that 34.8% of the hybrid proteome differs from the parental proteome. Also, ontological and morphological analyses determined that the hybrid exhibits more characteristics related to CML491 than LUG03, for example, metabolic pathways and enzymes, such as anthocyanidin 3-O-glucosyltransferase (UniProt P16166). This analysis allowed the identification of dominant characters, metabolic pathways and confirms the utility of this methodology in agricultural practices, mainly in processes of selection and quality control of a crop.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Comparative proteomic analysis of hybrid maize MR2008 and its parental lines

et al. 2021

View full text Add to dashboard Cite

show abstract

“…To generate a meaningful list of DRBPs involved in cancer, we performed searches in four databases—UniProt [ 55 ], Gene Ontology (GO) [ 56 ], the Eukaryotic Nucleic Acid Binding Protein Database (ENPD) [ 57 ], and the RNA-Binding Protein Database (RBPDB) [ 58 ]—containing records of DNA and/or RNA binding properties and with overlapping or distinct annotations. Data were compared using Venn diagrams based on the names and synonyms of the proteins.…”

Section: Cancer-associated Dna/rna Binding Proteinsmentioning

confidence: 99%

DNA and RNA Binding Proteins: From Motifs to Roles in Cancer

Bonczek

Wang

Gnanasundram

et al. 2022

IJMS

View full text Add to dashboard Cite

DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.

show abstract

“…However, this is an outdated concept as there is an increasing number of evidence suggesting that there are no well-defined differences between DBPs and RBPs, whereas many proteins are capable of interacting with both nucleic acids. These proteins are called DNA- and RNA-binding proteins (DRBPs) ( Hudson and Ortlund 2014 ; Leung et al, 2019 ). DRBPs typically possess multiple functions and regulate gene expression from more than one level.…”

Section: Introductionmentioning

confidence: 99%

DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia

Wang

Zong

et al. 2022

Front. Mol. Biosci.

Self Cite

View full text Add to dashboard Cite

DNA- and RNA-binding proteins (DRBPs) typically possess multiple functions to bind both DNA and RNA and regulate gene expression from more than one level. They are controllers for post-transcriptional processes, such as splicing, polyadenylation, transportation, translation, and degradation of RNA transcripts in eukaryotic organisms, as well as regulators on the transcriptional level. Although DRBPs are reported to play critical roles in various developmental processes and diseases, it is still unclear how they work with DNAs and RNAs simultaneously and regulate genes at the transcriptional and post-transcriptional levels. To investigate the functional mechanism of DRBPs, we collected data from a variety of databases and literature and identified 118 DRBPs, which function as both transcription factors (TFs) and splicing factors (SFs), thus called DRBP-SF. Extensive investigations were conducted on four DRBP-SFs that were highly expressed in chronic myeloid leukemia (CML), heterogeneous nuclear ribonucleoprotein K (HNRNPK), heterogeneous nuclear ribonucleoprotein L (HNRNPL), non-POU domain–containing octamer–binding protein (NONO), and TAR DNA-binding protein 43 (TARDBP). By integrating and analyzing ChIP-seq, CLIP-seq, RNA-seq, and shRNA-seq data in K562 using binding and expression target analysis and Statistical Utility for RBP Functions, we discovered a two-layer regulatory network system centered on these four DRBP-SFs and proposed three possible regulatory models where DRBP-SFs can connect transcriptional and alternative splicing regulatory networks cooperatively in CML. The exploration of the identified DRBP-SFs provides new ideas for studying DRBP and regulatory networks, holding promise for further mechanistic discoveries of the two-layer gene regulatory system that may play critical roles in the occurrence and development of CML.

show abstract

ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins

Cited by 10 publications

References 46 publications

Comparative proteomic analysis of hybrid maize MR2008 and its parental lines

Comparative proteomic analysis of hybrid maize MR2008 and its parental lines

DNA and RNA Binding Proteins: From Motifs to Roles in Cancer

DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia

Contact Info

Product

Resources

About