RNA-seq analysis v1

Lin, Qiaoshan

doi:10.17504/protocols.io.k7vczn6

Cited by 2 publications

(2 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The RNA-seq data have been submitted to the NCBI Gene Expression Omnibus (accession number GSE227406 ) ( 38 ). All other data are included in the article and supporting information .…”

Section: Data Materials and Software Availabilitymentioning

confidence: 99%

A small-molecule inhibitor of TopBP1 exerts anti-MYC activity and synergy with PARP inhibitors

Lin,

Liu,

Garan

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

We have previously identified TopBP1 (topoisomerase IIβ-binding protein 1) as a promising target for cancer therapy, given its role in the convergence of Rb, PI(3)K/Akt, and p53 pathways. Based on this, we conducted a large-scale molecular docking screening to identify a small-molecule inhibitor that specifically targets the BRCT7/8 domains of TopBP1, which we have named 5D4. Our studies show that 5D4 inhibits TopBP1 interactions with E2F1, mutant p53, and Cancerous Inhibitor of Protein Phosphatase 2A. This leads to the activation of E2F1-mediated apoptosis and the inhibition of mutant p53 gain of function. In addition, 5D4 disrupts the interaction of TopBP1 with MIZ1, which in turn allows MIZ1 to bind to its target gene promoters and repress MYC activity. Moreover, 5D4 inhibits the association of the TopBP1-PLK1 complex and prevents the formation of Rad51 foci. When combined with inhibitors of PARP1/2 or PARP14, 5D4 synergizes to effectively block cancer cell proliferation. Our animal studies have demonstrated the antitumor activity of 5D4 in breast and ovarian cancer xenograft models. Moreover, the effectiveness of 5D4 is further enhanced when combined with a PARP1/2 inhibitor talazoparib. Taken together, our findings strongly support the potential use of TopBP1-BRCT7/8 inhibitors as a targeted cancer therapy.

show abstract

“…The RNA-seq data have been submitted to the NCBI Gene Expression Omnibus (accession number GSE227406 ) ( 38 ). All other data are included in the article and supporting information .…”

Section: Data Materials and Software Availabilitymentioning

confidence: 99%

A small-molecule inhibitor of TopBP1 exerts anti-MYC activity and synergy with PARP inhibitors

Lin,

Liu,

Garan

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…WTC-11 Nanopore lrRNA-seq raw reads are available in Encode portal, identifier ENCFF961HLO [35]. WTC-11 Illumina RNA-seq datasets were downloaded from the NCBI portal, identifiers SRR14637256, SRR14637257, and SRR14637258 [36][37][38]. The human genome, version GRCh38.p13, used here as a reference, is available on the NCBI portal [26].…”

Section: Availability Of Data and Materialsmentioning

confidence: 99%

Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data

Jordan

Tseng

Nelson

et al. 2022

Preprint

View full text Add to dashboard Cite

Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is opportunity to call variants encoded in the transcribed regions of genes directly from lrRNA-seq data. However, most state-of-the-art variant callers have been developed for genomic DNA and thus require modifications to call variants from lrRNA-seq data. Here, we benchmark variant callers GATK, DeepVariant, Clair3, and NanoCaller on PacBio lrRNA-seq, or Iso-Seq, data. In particular, we found that careful processing of alignment files is critical to achieve better calling performance of indels and SNPs using DeepVariant and indels using Clair3.

show abstract

RNA-seq analysis v1

Cited by 2 publications

References 0 publications

A small-molecule inhibitor of TopBP1 exerts anti-MYC activity and synergy with PARP inhibitors

A small-molecule inhibitor of TopBP1 exerts anti-MYC activity and synergy with PARP inhibitors

Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data

Contact Info

Product

Resources

About