Bdp1 interacts with SNAPc bound to a U6, but not U1, snRNA gene promoter element to establish a stable protein-DNA complex

BDP1 Variants I1264M and V1347M Significantly Associated with Clinical Outcomes of Pediatric Neuroblastoma Patients Imply a New Prognostic Biomarker: A 121-Patient Cancer Genome Study

Background: Neuroblastoma (N.B.) is the most common tumor in children. The gene BDP1 (B Double Prime 1) plays a role in cancers but is less known in N.B. Thus, we conducted this study to investigate the value of BDP1 mutations in N.B. prognosis. Methods: A dataset of 121 NB patients from the Cancer Genome Atlas database was used to analyze BDP1 gene mutations by RNA sequencing. Kaplan-Meier estimates were performed for overall survival (O.S.) analysis on BDP1 variants, and Cox’s proportional hazards regression model was used for multivariate analysis. Results: In 121 NB patients, we identified two variants of BDP1 associated with N.B., located at chr5:71511131 and chr5:71510884. The prevalence of these BDP1 variants, I1264M and V1347M, was 52.9% (64/121) and 45.5% (55/121), respectively. O.S. analysis showed a significant difference between subgroups with or without BDP1 variants (p < 0.05). Multivariate analysis further revealed that BDP1ariants were independent prognostic variables in N.B. (p < 0.05). Conclusion: Our results suggest BDP1 variants are associated with significantly improved clinical outcomes in N.B., thus providing clinicians with a new tool.

BDP1 Variants I1264M and V1347M Significantly Associated with Clinical Outcomes of Pediatric Neuroblastoma Patients Imply a New Prognostic Biomarker: A 121-Patient Cancer Genome Study

Background: Neuroblastoma (N.B.) is the most common tumor in children. The gene BDP1 (B Double Prime 1) plays a role in cancers but is less known in N.B. Thus, we conducted this study to investigate the value of BDP1 mutations in N.B. prognosis. Methods: A dataset of 121 NB patients from the Cancer Genome Atlas database was used to analyze BDP1 gene mutations by RNA sequencing. Kaplan-Meier estimates were performed for overall survival (O.S.) analysis on BDP1 variants, and Cox’s proportional hazards regression model was used for multivariate analysis. Results: In 121 NB patients, we identified two variants of BDP1 associated with N.B., located at chr5:71511131 and chr5:71510884. The prevalence of these BDP1 variants, I1264M and V1347M, was 52.9% (64/121) and 45.5% (55/121), respectively. O.S. analysis showed a significant difference between subgroups with or without BDP1 variants (p < 0.05). Multivariate analysis further revealed that BDP1ariants were independent prognostic variables in N.B. (p < 0.05). Conclusion: Our results suggest BDP1 variants are associated with significantly improved clinical outcomes in N.B., thus providing clinicians with a new tool.

Silencing of BRF2 inhibits the growth and metastasis of lung cancer cells

Transcription factor II B (TFIIB)‑related factor 2 (BRF2) is involved in the development of cancer, but its role in lung cancer is underreported. The present study aimed to explore the role of BRF2 in the regulation of lung cancer cells. Immunofluorescence staining and immunohistochemistry were performed to detect BRF2 protein expression in human lung cancer cells and tissues. Following cell transfection with small interfering RNA for silencing BRF2, the cell proliferation was examined by Cell Counting Kit‑8 and MTT assays. Cell apoptosis, migration and invasion were determined by flow cytometry, wound‑healing and Transwell assay. The expression levels of Akt, phosphorylated (p)‑Akt, Bax, E‑cadherin, Bcl‑2, N‑cadherin, Snail and epidermal growth factor receptor (EGFR) in human lung cancer A549 cells were detected by western blotting. The results demonstrated that BRF2 expression was increased in human lung cancer cells and tissues, and that silencing of BRF2 promoted cell apoptosis but inhibited cell proliferation and migration. The protein expression levels of Akt, E‑cadherin, p‑Akt, Bcl‑2, N‑cadherin, Snail and EGFR in A549 cells were inhibited by silencing of BRF2, while expression levels of Bax and E‑cadherin were increased by silencing BRF2. In conclusion, BRF2 demonstrates high expression in lung cancer and silencing of BRF2 inhibits the growth and metastasis of lung cancer cells. The current findings provide a novel approach for the treatment of lung cancer.

DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability

The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilise TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.

Assembly of SNAPc, Bdp1, and TBP on the U6 snRNA Gene Promoter in Drosophila melanogaster

U6 snRNA is transcribed by RNA polymerase III (Pol III) and has an external upstream promoter that consists of a TATA sequence recognized by the TBP subunit of the Pol III basal transcription factor IIIB and a proximal sequence element (PSE) recognized by the small nuclear RNA activating protein complex (SNAPc). Previously, we found that Drosophila melanogaster SNAPc (DmSNAPc) bound to the U6 PSE can recruit the Pol III general transcription factor Bdp1 to form a stable complex with the DNA. Here, we show that DmSNAPc-Bdp1 can recruit TBP to the U6 promoter, and we identify a region of Bdp1 that is sufficient for TBP recruitment. Moreover, we find that this same region of Bdp1 cross-links to nucleotides within the U6 PSE at positions that also cross-link to DmSNAPc. Finally, cross-linking mass spectrometry reveals likely interactions of specific DmSNAPc subunits with Bdp1 and TBP. These data, together with previous findings, have allowed us to build a more comprehensive model of the DmSNAPc-Bdp1-TBP complex on the U6 promoter that includes nearly all of DmSNAPc, a portion of Bdp1, and the conserved region of TBP.

How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes

Nuclear eukaryotic genomes are transcribed by three related RNA polymerases (Pol), which transcribe distinct gene sets. Specific Pol recruitment is achieved through selective core promoter recognition by basal transcription factors (TFs). Transcription by an inappropriate Pol appears to be rare and to generate mostly unstable products. A collection of short noncoding RNA genes [for example, small nuclear RNA (snRNA) or 7SK RNA genes], which play essential roles in processes such as maturation of RNA molecules or control of Pol II transcription elongation, possess highly similar core promoters, and yet are transcribed for some by Pol II and for others by Pol III as a result of small promoter differences. Here we discuss the mechanisms of selective Pol recruitment to such promoters.

Transcription initiation factor TBP: old friend new questions

In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. The most conserved initiation factor is the TATA-binding protein (TBP), which is of crucial importance for all archaeal-eukaryotic transcription initiation complexes and the only factor required to achieve full rates of initiation in all three eukaryotic and the archaeal transcription systems. Recent structural, biochemical and genome-wide mapping data that focused on the archaeal and specialized RNAP I and III transcription system showed that the involvement and functional importance of TBP is divergent from the canonical role TBP plays in RNAP II transcription. Here, we review the role of TBP in the different transcription systems including a TBP-centric discussion of archaeal and eukaryotic initiation complexes. We furthermore highlight questions concerning the function of TBP that arise from these findings.