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RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF

ABSTRACT: RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF

PROVIDER: PRJNA420499 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6334320_1.fastq.gz	Fastqsanger.gz
	SRR6334320_2.fastq.gz	Fastqsanger.gz
	SRR6334317_1.fastq.gz	Fastqsanger.gz
	SRR6334317_2.fastq.gz	Fastqsanger.gz
	SRR6334318_1.fastq.gz	Fastqsanger.gz

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RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF

Project description:It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex forming capacity promote exon inclusion. Destroying G-quadruplex forming capacity while keeping G-tracts intact abrogates exon inclusion. Analysis of RNA binding protein footprints revealed that G-quadruplexes are enriched in hnRNPF-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome. Moreover, hnRNPF regulates an EMT-associated CD44 isoform switch in a G-quadruplex-dependent manner, which results in inhibition of EMT. Mining breast cancer TCGA datasets, we demonstrate that hnRNPF negatively correlates with an EMT gene signature and positively correlates with patient survival. These data suggest a critical role for RNA G-quadruplexes in regulating alternative splicing. Modulation of G-quadruplex structural integrity may control cellular processes important for tumor progression.

2018-01-22 | GSE107542 | GEO

RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF.

Project description:It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex-forming capacity promote exon inclusion. Destroying G-quadruplex-forming capacity while keeping G tracts intact abrogates exon inclusion. Analysis of RNA-binding protein footprints revealed that G quadruplexes are enriched in heterogeneous nuclear ribonucleoprotein F (hnRNPF)-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome. Moreover, hnRNPF regulates an epithelial-mesenchymal transition (EMT)-associated CD44 isoform switch in a G-quadruplex-dependent manner, which results in inhibition of EMT. Mining breast cancer TCGA (The Cancer Genome Atlas) data sets, we demonstrate that hnRNPF negatively correlates with an EMT gene signature and positively correlates with patient survival. These data suggest a critical role for RNA G quadruplexes in regulating alternative splicing. Modulation of G-quadruplex structural integrity may control cellular processes important for tumor progression.

| S-EPMC5769772 | biostudies-literature

RNA profiling of wild-type and hnRNPF-knockout splenic B cells

Project description:Alternative splicing (AS) plays an important role in the development and activation of B cells. RNA-binding proteins (RBPs) have emerged as critical players in AS regulation. RNA-binding protein hnRNPF regulates AS of several important genes, such as c-Src, Bcl-xl, Mcl-1 and Tcf3 in tumor cells, but its function in B cell biology is not known.Here we constructed CD19-Cre mediated hnRNPF conditional knockou mice and performed RNA-sequencing to profile mRNA expression and AS regulated by hnRNPF in splenic B cells.

2022-05-11 | GSE188538 | GEO

RIP-Seq of HnRNPF/H in Trypanosoma brucei bloodstream forms

Project description:mRNAs associates with HnRNPF/H in Trypanosoma brucei bloodstream forms

2021-08-31 | E-MTAB-10708 | biostudies-arrayexpress

The impact of HnRNPF knockdown on gene expression in MDA-MB-231 cell line

Project description:We discovered that HnRNPF is significantly upregulated in breast cancer tissues and is closely associated with the cell proliferation signaling pathway. Overexpression of HnRNPF notably inhibits cell proliferation in MDA-MB-231 breast cancer cells. HnRNPF promotes the expression of the cell cycle inhibitor p21.

2024-08-31 | GSE273248 | GEO

G4-RNA binding proteins from K562

Project description:G-quadruplex RNA pulldown followed by mass spectrometry. G4A4 oligoribonucleotide (5’-AAAAAAGGGGAAAAGGGGAAAAGGGGAAAAGGGGAAAAAA-3’) was biotinylated and folded in either K+ or Li+ containing buffers, causing folding of G-quadruplex (K+) or destabilization of the secondary structure (Li+). G4A4 pulldown was used to identify G4-RNA binding proteins from K562 human cell line nuclear extracts, interacting in structure-dependent manner.

2024-02-20 | PXD041154 | Pride

Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5’ UTR of tumor-associated mRNAs

Project description:G-quadruplex structures in the 5’ UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). The identified ribosomal proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. In addition, several proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the set of candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions may be relevant to the regulation of mRNA maturation and may play an important role in tumor biology.

2017-11-14 | PXD005761 | Pride

Non-canonical RNA-binding of the histone lysine demethylase KDM5 through interactions with G-quadruplex sequences

Project description:RNA-binding proteins are important regulators of RNA biogenesis and function, and recent work shows that chromatin- and RNA-binding proteins can have regulatory roles in transcription. Several approaches have been developed to predict RNA-binding proteins and to identify them experimentally at large scale, including binding to structural elements as G-quadruplexes. Here, we show that the histone lysine demethylase protein KDM5 can bind to RNA through interaction with G-quadruplexes with high affinity despite neither being categorized as an RNA-binding protein nor identified as a G-quadruplex binding protein across numerous experimental large-scale and computational studies. In addition to characterizing the KDM5 G-quadruplex interaction we show that RNA is directly involved in the formation of KDM5-containing protein complexes. Computational predictions and comparison to other ARID domain containing proteins suggest that the ARID domain is directly interacting with both DNA and RNA across several proteins. Our work highlights that non-canonical aspects of RNA-binding proteins are present, and that G-quadruplex RNA-binding could provide a regulatory mechanism for chromatin-binding proteins with impact on transcription through linking protein complexes within the cell.

2024-04-11 | PXD050767 | Pride

Temperature dependent RNA secondary structure in Trypanosoma brucei

Project description:Temperature dependent RNA secondary structure in Trypanosoma brucei

| PRJEB14403 | ENA

Temperature dependent RNA secondary structure in Trypanosoma brucei

Project description:Temperature dependent RNA secondary structure in Trypanosoma brucei

| PRJEB14404 | ENA