hRBPome: a central repository of all known human RNA-binding proteins

Ghosh, Pritha; Murugavel, Pavalam; Sowdhamini, Ramanathan

doi:10.1101/269043

Cited by 7 publications

(5 citation statements)

References 13 publications

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“…Chromatin remodeler proteins were obtained from UniProt IDs associated with “GO:0006338” (“chromatin remodeling”) 84 and CORUM protein complex components associated with the five primary chromatin remodelers 32 : NuRD, SWI, ISWI, INO80, SWR1. High-confidence RNA binding proteins were obtained from hRBPome 85 , and transcription factors were obtained from Lambert et al 3 .…”

Section: Methodsmentioning

confidence: 99%

Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

et al. 2021

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The architecture of chromatin regulates eukaryotic cell states by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase/peroxidase approach, i ntegrative D NA A nd P rotein T agging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors, and regulation of chromatin accessibility. We applied iDAPT to profile the epigenomic consequences of granulocytic differentiation of acute promyelocytic leukemia, yielding previously undescribed mechanistic insights. Our findings demonstrate the power of iDAPT as a platform for studying the dynamic epigenomic landscapes and their transcription factor components associated with biological phenomena and disease.

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Section: Methodsmentioning

confidence: 99%

Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

et al. 2021

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“…The RNA is subsequently converted to cDNA and the RBP bound regions isolated by high-throughput sequencing [ 47 , 48 ]. Moreover, numerous databases such as RBPDB [ 49 ], RBPmap [ 50 ], ATtRACT [ 51 ], hRBPome [ 52 ], oRNAment [ 53 ] have subsequently emerged to collect and store information about RBPs including their features and attributes which have further helped develop our understanding of RBP functions across various species.…”

Section: Rbps Are Fundamental Regulators Of Rna Fatementioning

confidence: 99%

RNA-Binding Proteins: Emerging Therapeutics for Vascular Dysfunction

Cornelius

Naderi‐Meshkin

Kelaini

et al. 2022

Cells

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Vascular diseases account for a significant number of deaths worldwide, with cardiovascular diseases remaining the leading cause of mortality. This ongoing, ever-increasing burden has made the need for an effective treatment strategy a global priority. Recent advances in regenerative medicine, largely the derivation and use of induced pluripotent stem cell (iPSC) technologies as disease models, have provided powerful tools to study the different cell types that comprise the vascular system, allowing for a greater understanding of the molecular mechanisms behind vascular health. iPSC disease models consequently offer an exciting strategy to deepen our understanding of disease as well as develop new therapeutic avenues with clinical translation. Both transcriptional and post-transcriptional mechanisms are widely accepted to have fundamental roles in orchestrating responses to vascular damage. Recently, iPSC technologies have increased our understanding of RNA-binding proteins (RBPs) in controlling gene expression and cellular functions, providing an insight into the onset and progression of vascular dysfunction. Revelations of such roles within vascular disease states have therefore allowed for a greater clarification of disease mechanisms, aiding the development of novel therapeutic interventions. Here, we discuss newly discovered roles of RBPs within the cardio-vasculature aided by iPSC technologies, as well as examine their therapeutic potential, with a particular focus on the Quaking family of isoforms.

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“…RNA binding proteins (RBPs) were first defined based on a consensus list of 837 high-confidence human RBPs from the hRBPome database 56 . A total of 470 RBPs were detected in FANS-derive cell populations and subjected to further analysis.…”

Section: Rna Binding Protein and Eclip Enrichment Analysismentioning

confidence: 99%

Cellular and genetic drivers of RNA editing variation in the human brain

Cuddleston

Fan

et al. 2021

Preprint

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Posttranscriptional adenosine-to-inosine modifications amplify the functionality of RNA molecules in the brain, yet the cellular and genetic regulation of RNA editing is poorly described. We quantified base-specific RNA editing across three major cell populations from the human prefrontal cortex: glutamatergic neurons, medial ganglionic eminence GABAergic neurons, and oligodendrocytes. We found more selective editing and RNA hyper-editing in neurons relative to oligodendrocytes. The pattern of RNA editing was highly cell type-specific, with 189,229 cell type-associated sites. The cellular specificity for thousands of sites was confirmed by single nucleus RNA-sequencing. Importantly, cell type-associated sites were enriched in GTEx RNA-sequencing data, edited ~twentyfold higher than all other sites, and variation in RNA editing was predominantly explained by neuronal proportions in bulk brain tissue. Finally, we discovered 661,791 cis-editing quantitative trait loci across thirteen brain regions, including hundreds with cell type-associated features. These data reveal an expansive repertoire of highly regulated RNA editing sites across human brain cell types and provide a resolved atlas linking cell types to editing variation and genetic regulatory effects.

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hRBPome: a central repository of all known human RNA-binding proteins

Cited by 7 publications

References 13 publications

Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

RNA-Binding Proteins: Emerging Therapeutics for Vascular Dysfunction

Cellular and genetic drivers of RNA editing variation in the human brain

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