Structural and functional analyses of the spliceosome requires a multi-disciplinary approach

Ohi, Melanie D.

doi:10.1016/j.ymeth.2017.07.022

Cited by 4 publications

(4 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the KEGG analysis, the target genes of IGF2BP1 were found to be involved in protein processing in the endoplasmic reticulum, RNA transport, and spliceosome pathways. The spliceosome can be involved in pre-mRNA splicing, whereby introns are excised from pre-mRNA to generate mature mRNA [ 36 ]. These results suggest that IGF2BP1 can be involved in the modification and translation of various RNAs in stem cells.…”

Section: Resultsmentioning

confidence: 99%

Profiling the role of m6A effectors in the regulation of pluripotent reprogramming

Wang,

Zhou,

et al. 2024

Hum Genomics

View full text Add to dashboard Cite

The N6-methyladenosine (m6A) RNA modification plays essential roles in multiple biological processes, including stem cell fate determination. To explore the role of the m6A modification in pluripotent reprogramming, we used RNA-seq to map m6A effectors in human iPSCs, fibroblasts, and H9 ESCs, as well as in mouse ESCs and fibroblasts. By integrating the human and mouse RNA-seq data, we found that 19 m6A effectors were significantly upregulated in reprogramming. Notably, IGF2BPs, particularly IGF2BP1, were among the most upregulated genes in pluripotent cells, while YTHDF3 had high levels of expression in fibroblasts. Using quantitative PCR and Western blot, we validated the pluripotency-associated elevation of IGF2BPs. Knockdown of IGF2BP1 induced the downregulation of stemness genes and exit from pluripotency. Proteome analysis of cells collected at both the beginning and terminal states of the reprogramming process revealed that the IGF2BP1 protein was positively correlated with stemness markers SOX2 and OCT4. The eCLIP-seq target analysis showed that IGF2BP1 interacted with the coding sequence (CDS) and 3’UTR regions of the SOX2 transcripts, in agreement with the location of m6A modifications. This study identifies IGF2BP1 as a vital pluripotency-associated m6A effector, providing new insight into the interplay between m6A epigenetic modifications and pluripotent reprogramming.

show abstract

Section: Resultsmentioning

confidence: 99%

Profiling the role of m6A effectors in the regulation of pluripotent reprogramming

Wang,

Zhou,

et al. 2024

Hum Genomics

View full text Add to dashboard Cite

show abstract

“…Surprisingly, the majority of KDM3 interacting proteins belonged to the RNA processing machinery (Figure 1C and D) along with the FACT and PAF complexes that associate with actively elongating RNAPII. The RNA processing proteins included members of the spliceosomal machinery, which removes introns from pre-mRNA (63), and RNA helicases, which are important for general RNA metabolism and rearrangement of ribonucleoprotein complexes (64). We also found components of the exon junction complex, which control post-transcriptional export and stability of mRNAs (65) (Figure 1D and E).…”

Section: Resultsmentioning

confidence: 99%

KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing

Dillingham

Cormaty

Morgan

et al. 2023

Preprint

View full text Add to dashboard Cite

Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cells (ESCs) identity is characterized by lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 histone demethylase family removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find through immunoaffinity purification of the KDM3A or KDM3B interactome and proximity ligation assays that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. By generating double degron ESCs to degrade KDM3A and KDM3B in the rapid timescale of splicing, we find altered splicing, independent of H3K9me2 status. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone modifying enzymes in splicing to regulate cell identity.

show abstract

“…The spliceosome is a large protein-rich complex responsible for removing introns from the pre-mRNA generated in the cell to produce mature messenger RNA (mRNA). The spliceosome process is essential for cell function and dysregulation or mutation of components of the spliceosome complex has been identified as a driver of many forms of cancers [ 47 ]. Modification in the expression levels of components of the spliceosome complex results in alternative splicing.…”

Section: Discussionmentioning

confidence: 99%

Multiple Myeloma Derived Extracellular Vesicle Uptake by Monocyte Cells Stimulates IL-6 and MMP-9 Secretion and Promotes Cancer Cell Migration and Proliferation

Sheridan,

Brennan,

Bazou

et al. 2024

Cancers

View full text Add to dashboard Cite

Multiple Myeloma (MM) is an incurable haematological malignancy caused by uncontrolled growth of plasma cells. MM pathogenesis is attributed to crosstalk between plasma cells and the bone marrow microenvironment, where extracellular vesicles (EVs) play a role. In this study, EVs secreted from a panel of MM cell lines were isolated from conditioned media by ultracentrifugation and fluorescently stained EVs were co-cultured with THP-1 monocyte cells. MM EVs from three cell lines displayed a differential yet dose-dependent uptake by THP-1 cells, with H929 EVs displaying the greatest EV uptake compared to MM.1s and U266 EVs suggesting that uptake efficiency is dependent on the cell line of origin. Furthermore, MM EVs increased the secretion of MMP-9 and IL-6 from monocytes, with H929 EVs inducing the greatest effect, consistent with the greatest uptake efficiency. Moreover, monocyte-conditioned media collected following H929 EV uptake significantly increased the migration and proliferation of MM cells. Finally, EV proteome analysis revealed differential cargo enrichment that correlates with disease progression including a significant enrichment of spliceosome-related proteins in H929 EVs compared to the U266 and MM.1s EVs. Overall, this study demonstrates that MM-derived EVs modulate monocyte function to promote tumour growth and metastasis and reveals possible molecular mechanisms involved.

show abstract

Structural and functional analyses of the spliceosome requires a multi-disciplinary approach

Cited by 4 publications

References 47 publications

Profiling the role of m6A effectors in the regulation of pluripotent reprogramming

Profiling the role of m6A effectors in the regulation of pluripotent reprogramming

KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing

Multiple Myeloma Derived Extracellular Vesicle Uptake by Monocyte Cells Stimulates IL-6 and MMP-9 Secretion and Promotes Cancer Cell Migration and Proliferation

Contact Info

Product

Resources

About