Structural switch from a multistranded G-quadruplex to single strands as a consequence of point mutation in the promoter of the human GRIN1 gene

Abstract

A huge number of G-rich sequences forming quadruplexes are found in the human genome, especially in telomeric regions, UTRs, and the promoter regions of a number of genes. One such gene is GRIN1 encoding the NR1 subunit of the N-methyl-d-aspartate receptor (NMDA). Several lines of reports have implicated that attenuated function of NMDA results in schizophrenia, a genetic disorder characterized by hallucinations, delusions, and psychosis. Involvement of the GRIN1 gene in the pathogenesis of schizophrenia has been extensively analysed. Recent reports have demonstrated that polymorphism in the promoter region of GRIN1 at position -855 (G/C) has a possible association with schizophrenia. The binding site for the NF-κB transcription factor gets altered due to this mutation, resulting in reduced gene expression as well as NMDA activity. By combining gel electrophoresis (PAGE), circular dichroism (CD) and CD melting techniques, the G → C single nucleotide polymorphism (SNP) at the G-rich sequence (d-CTTAGCCCGAGGAG[combining low line]GGGGGTCCCAAGT; GRIN1) was investigated. We report that the GRIN1 sequence can form an octameric/multistranded quadruplex structure with parallel conformation in the presence of K as well as Na. CD and gel studies are in good correlation in order to detect molecularity and strand conformation. The parallel G-quadruplex species was hypothesized to be octameric in K/Na salts. The mutated sequence (d-CTTAGCCCGAGGAC[combining low line]GGGGGTCCCAAGT; GRIN1M) remained single stranded under physiological conditions. CD melting studies support the formation of an interstranded G-quadruplex structure by the GRIN1 sequence. Two structural models are propounded for a multistranded parallel G-quadruplex conformation which might be responsible for regulating the gene expression normally underlying memory and learning.

An experimental study of the effects of SNPs in the TATA boxes of the <i>GRIN1, ASCL3</i> and <i>NOS1</i> genes on interactions with the TATA-binding protein

“…Overall, these changes somewhat shortened the complex's half-life (from 25 to 20 min), that is, made it less stable. Judging from the sequence of the ODN in question, which is identical to the region of the GRIN1 promoter, this promoter does not contain the TATA box consensus sequence but contains a G-rich box, which can bind to transcription Experimental in vitro verification of our predictions of the effect of rs1402667001, rs1049743008, and rs1195040887 (from genes GRIN1, ASCL3, and NOS1, respectively) on affinity and kinetic characteristics of TBP-TATA complexes factor SP3, which activates transcription of genes in chicken embryonic cortical neurons and represses it in undifferentiated cells (Chaudhary et al, 2017), as demonstrated in a study on the chicken GRIN1 gene.…”

Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants

“…Properties of G4s’ structure indicate that it can be easily compromised by a single point mutation (Chaudhary et al, 2017; Zeraati et al, 2017). Therefore, a mutation rate assessment of pG4s sequences may be a good indicator of their biological relevance, especially since G4s themselves are thought to be factors contributing to genomic instability (Lemmens et al, 2015).…”

Formation of G‐wires, bimolecular and tetramolecular quadruplex: Cation‐induced structural polymorphs of G‐rich DNA sequence of human SYTX gene

“…The guanine‐rich sequences have shown their existence in several regions of the human genome, such as at telomeric ends, immunoglobulin switch regions and regions of gene promoters of many proto‐oncogenes like c‐MYB, c‐MYC, c‐KRAS, c‐KIT . In a report by Chaudhary et al a G‐rich sequence of GRIN1 gene is propounded to form G‐quadruplex, which governs the expression of the gene responsible for down‐regulation of onset of a genetic disorder called schizophrenia . During DNA replication, a normal cell loses 50 to 200 bases in the whole process .…”