decode protein-lncRNA, protein-ncRNA, protein-mRNA interactions from CLIP-Seq data

[yjhua2110]

Revealing protein–lncRNA interaction

A review paper described the protein-lncRNA interaction was published in Brief Bioinform (June 2, 2015, doi: 10.1093/bib/bbv031).

Abstract:
Long non-coding RNAs (lncRNAs) are associated to a plethora of cellular functions, most of which require the interaction with one or more RNA-binding proteins (RBPs); similarly, RBPs are often able to bind a large number of different RNAs. The currently available knowledge is already drawing an intricate network of interactions, whose deregulation is frequently associated to pathological states. Several different techniques were developed in the past years to obtain protein–RNA binding data in a high-throughput fashion. In parallel, in silico inference methods were developed for the accurate computational prediction of the interaction of RBP–lncRNA pairs. The field is growing rapidly, and it is foreseeable that in the near future, the protein–lncRNA interaction network will rise, offering essential clues for a better understanding of lncRNA cellular mechanisms and their disease-associated perturbations.

paper website: http://bib.oxfordjournals.org/conten...ib.bbv031.full

[Caroline336]

High-throughput Protein Production

[rnaNGS]

Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq data

a new paper, by analyzing millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies, we identified 22,735 RBP–lncRNA regulatory relationships.

RBP–lncRNA interactions were available at http://starbase.sysu.edu.cn/rbpLncRNA.php.

an invited paper described these protein–lncRNA interactions has been published in Frontiers journal.

The genomic context distributions of binding sites for 47 human RBPs.

[zhxq09]

Could you tell me what's the difference between miRNA-target interaction and miRNA-mRNA interaction? If I want to obtain miRNA regulations to gene, which one is more reliable? Thanks so much.

[yjhua2110]

I am trying to using starBase to identify miRNA-lncRNA interactions.
Is the lncRNAs list that are available on site is complete?

in starBase, all lncRNAs from GENCODE v17 were included.

[zhxq09]

I am trying to using starBase to identify miRNA-lncRNA interactions.
Is the lncRNAs list that are available on site is complete?

[rnaNGS]

The overview of Pan-Cancer protein-lncRNA, protein-ncRNA and protein-mRNA interactions

[rnaNGS]

RBPome special issue

Genome Biology published RBPome special issue that present a collection of Research, Method, Software, Review, Research Highlight and Editorial articles focusing on the theme of ‘the RBPome’, a term we use to describe RNA-binding proteins (RBPs) and their recognition elements within the transcriptome. The issue provides a number of new insights into the role of RBPs in gene regulation and incorporates studies using a variety of different approaches to assay RNA-protein interactions. Advances in computational analyses for the study of RBPome data are also reported.

http://genomebiology.com/content/15/1

[yjhua2110]

Pan-Cancer protein-lncRNA, protein-ncRNA and protein-mRNA interactions

starBase portal also provided Pan-Cancer Interactions between lncRNAs and RNA-Binding Proteins (RBPs), mRNAs and RBPs.

we explored correlation between RNA-Binding Proteins (RBPs) and targets across 14 cancer types (>6000 tumor and normal samples) using pearson correlation test (p-value<0.05).

For example:
(1)RBP-lncRNA: FMRP:TUG1(lncRNA) interaction with significant correlation across 14 cancer types.
(2)RBP-mRNA: TDP-43:CDK6 interaction with significant correlation across 9 cancer types.

The TDP-43(TARDBP) expression profiles across 14 cancer types:


Cancer types as follows:
Urothelial bladder cancer (BLCA)
Breast cancer (BRCA)
Colon and Rectal adenocarcinoma (CRC)
Glioblastoma multiforme (GBM)
Head and neck squamous cell carcinoma (HNSC)
Chromophobe renal cell carcinoma (KICH)
Clear cell kidney carcinoma (KIRC)
Acute Myeloid Leukemia (LAML)
Lung adenocarcinoma (LUAD)
Lung squamous cell carcinoma (LUSC)
Ovarian serous cystadenocarcinoma (OV)
Cutaneous melanoma (SKCM)
Papillary thyroid carcinoma (THCA)
Uterine corpus endometrial carcinoma (UCEC)

[yjhua2110]

High-throughput sequencing of immunoprecipitated RNAs after cross-linking (CLIP-Seq, HITS-CLIP, PAR-CLIP, CLASH, iCLIP) provide powerful ways to identify biologically relevant miRNA-target and protein–RNA interactions.

starBase platform had integrated 111 CLIP-Seq (HITS-CLIP, PAR-CLIP, CLASH, iCLIP) datasets to decipher interactions between RNA-Binding Proteins (RBPs) and RNAs, such as protein-lncRNA, protein-sncRNA, protein-mRNA and protein-pseudogene interactions.

an invited paper described these protein–lncRNA interactions has been published in Frontiers journal.

includes RNA-Binding Proteins:
related with epigenetics: PRC2(EZH2)
related with brain: TDP-43, FMRP, Nova
related with splicing and transcription: PTB, HnRNPC
others: HuR, PUM2, QKI, IGF2BP1-3, FUS, DGCR8, TNRC6, LIN28, UPF1 etc...