Nov 5, 2024 · MYC directly binds to the TSS of GSPT1 in multiple leukemia and lymphoma cells in the IGV dataset. We observed that MYC knockdown reduced transcription of GSPT1 in HL-60 cells.

Jan 14, 2022 · To demonstrate the power and utility of IGV-ScanFold, we analyzed the pre-mRNA of a previously studied mature mRNA, MYC, in which we had shown the presence of functional secondary structure in the 3′ UTR.

Jan 11, 2021 · IGV analysis showed that the level of m 6 A modification of CDKN1A mRNA was also increased when MYC was low (Fig EV2G), suggesting the possibility that MYC regulates the gene expression of CDKN1A via m 6 A modification.

The MYC oncogene, particularly, contains a G4-forming region in its proximal promoter NHE III 1, which controls 75 to 85% of transcription. ... IGV tracks) for the MYC (left) and KRAS genes (right). The promoter G4-forming sites are labeled at …

Oct 29, 2024 · The igvR package provides easy programmatic access in R to the web-based javascript library igv.js to create and display genome tracks in its richly interactive web browser visual interface. In this vignette we present a few very simple uses of igvR: Your display will look like this at the conclusion of this demo:

Feb 28, 2024 · We identified a previously unknown MYCN enhancer, active in multiple AML subtypes, essential for MYCN mRNA levels and survival in inv (16) AML cells. We also identified eukaryotic translation initiation factor 4 gamma 1 (eIF4G1) as a key N-MYC target that sustains leukemic survival in inv (16) AML cells.

Supplemental File S5 contains all of the tracks used to analyze MYC. These tracks include all ScanFold metrics, various annotations, and probing data. Supplemental Video S6 is an informational video on how to generate and annotate 2D models of RNA secondary structure found with IGV-ScanFold using the VARNA applet.

Jul 1, 2019 · Balanced translocations have diagnostic and prognostic value in B-cell lymphoproliferative disorders (LPDs). Most of these translocations involve the juxtaposition of a strong immunoglobulin (Ig) enhancer to proto-oncogenes, such as BCL2, BCL6, and MYC, leading to their overexpression.

All data have been uploaded to the RNAStructuromeDB, allowing for easy searching of transcripts, visualization of data tracks (via the Integrative Genomics Viewer or IGV), and download of...

Expression levels were 1–3 mg of IgV/liter of bacterial culture, determined by anti-c-myc immunoblotting. Soluble IgVs were purified from periplasmic extracts of HB2151 cells by metal affinity chromatography.