G4 motifs correlate with promoter-proximal transcriptional pausing in human genes

Abstract

The RNA Pol II transcription complex pauses just downstream of the promoter in a significant fraction of human genes. The local features of genomic structure that contribute to pausing have not been defined. Here, we show that genes that pause are more G-rich within the region flanking the transcription start site (TSS) than RefSeq genes or non-paused genes. We show that enrichment of binding motifs for common transcription factors, such as SP1, may account for G-richness upstream but not downstream of the TSS. We further show that pausing correlates with the presence of a GrIn1 element, an element bearing one or more G4 motifs at the 5′-end of the first intron, on the non-template DNA strand. These results suggest potential roles for dynamic G4 DNA and G4 RNA structures in cis-regulation of pausing, and thus genome-wide regulation of gene expression, in human cells.

Using CellMiner 1.6 for Systems Pharmacology and Genomic Analysis of the NCI-60

“…CellMiner previously has enabled us to: i) identify promoter-proximal transcriptional pausing in human genes (37, 38), ii) discover the helicase SLFN11 as a causal determinant of response to DNA-damaging agents (18), iii) recognize the regulation of MYC expression by miR-375 (39), iv) recognize the importance of MYC as a driver of mitochondrial genes (40), v) reveal genetic inactivation or endogenous activation of CHEK2 across the NCI-60 (40); vi) link USP7 and Daxx to taxane resistance (41), vi) link TP53 wild type status, Mdm2 transcript level, and miR-34a transcript level with nutlin activity (10), viii) reveal the interrelationship between RAS (H, K, and NRAS)-BRAF-PTEN mutational status, EGFR expression, and ERBB2 expression with erlotinib activity (10), ix) demonstrate the strong correlation between ABCB1 expression and doxorubicin activity (2), x) recognize both known and novel genes expression levels, microRNA expression levels, and drug activities with a colon-specific pattern input to “Pattern comparison” (2), xi) identify predominant co-regulation among cell migration genes (42), xii) identify co-regulation among kinetochore genes, their prospective regulatory elements, and their association with genomic instability (43), xiii) show the connection between accumulation of mass homozygotes in the cancer cell lines as compared to non-cancerous HapMap trios (44), xiv) identify the drug Ro5-3335 as a candidate treatment for core binding factor leukemias (45), xv) associate CDKN2A DNA copy number and expression to mitoxantrone activity (8), xvi) define an epithelial gene expression signature (46), and xvii) recognize the composite relationship between the mutational status of multiple genes from the EGFR-ERBB2 pathway and drug response, including the directionality of that influence as a function of molecular pathway considerations (14). The diversity among these observations gives an indication of the boundless scope and range of the types of possible discoveries that can be made using the NCI-60 database and CellMiner set of tools.…”

Genomic c-Myc Quadruplex DNA Selectively Kills Leukemia

“…This DNA duplex element can slowly equilibrate between transcriptionally active forms (duplex and single-stranded) to a silenced form (14). Single G to A mutations within PU27 destabilize quadruplex formation and induce a 3-fold increase in transcriptional activity suggesting a role for quadruplexes in gene regulation and that their formation may be critical for transcriptional silencing (15–17). …”

Variation and constraints in species-specific promoter sequences

“…Despite this mathematical definition, such sequences are expected to be associated with structural properties and functional processes of high biological importance and complexity. For instance, it has been proved that they are endowed with functional properties by controlling gene expression (Eddy et al, 2011;Vinces et al, 2009;Chen et al, 2011), by enhancing non-specific TF-DNA binding affinity (Gemayel et al, 2010;Sela and Lukatsky, 2011) and by influencing chromatin organization (Segal and Widom, 2009). On the basis of these remarks, we have decided to investigate the role played by such regular components in determining the bias described by h n ðlÞ.…”

“…In a more general perspective, one should also consider that promoter regions typically undergo non-neutral evolutionary dynamics due to their role in encoding regulatory information (Calistri et al, 2011;Bernardi, 2007;Taher et al, 2011). Thus, the presence of low-complexity sequences in promoters suggests a functional involvement of these over-represented structures (Eddy et al, 2011;Gemayel et al, 2010;Sela and Lukatsky, 2011;Ganapathi et al, 2005).…”

“…In particular, functional properties are expected to be related to the presence of specific motifs, i.e. over-/under-expressed nucleotide substrings which interact with regulatory proteins (Carey et al, 2012;Neph et al, 2012) or to peculiar structural and mechanical features of DNA (Eddy et al, 2011;Gemayel et al, 2010;Sela and Lukatsky, 2011). Then, we introduce a specific spatial entropy indicator, the Normalized Positional Shannon Entropy (NPSE), that is measured in the binary code based on the distinction between Weak (A and T) and Strong (C and G) bases.…”