Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements

Abstract

We have elucidated the hnRNP K promoter as a hotspot for tetraplex-based molecular switches receptive to micro-environmental stimuli. We have characterised the structural features of four tetraplex-forming loci and identified them as binding sites of transcription factors. These segments form either G-quadruplex or i-motif structures, the structural dynamicity of which has been studied in depth via several biophysical techniques. The tetraplexes display high dynamicity and are influenced by both pH and KCl concentrations in vitro. The loci complementary to these sequences form additional non-canonical secondary structures. In the cellular context, the most eminent observation of this study is the binding of hnRNP K to the i-motif forming sequences in its own promoter. We are the first to report a probable transcriptional autoregulatory function of hnRNP K in coordination with higher-order DNA structures. Herein, we also report the positive interaction of the endogenous tetraplexes with Sp1, a well-known transcriptional regulator. Treatment with tetraplex-specific small molecule ligands further uncovered G-quadruplexes’ functioning as repressors and i-motifs as activators in this context. Together, our findings strongly indicate the critical regulatory role of the identified tetraplex elements in the hnRNP K promoter.

Communicated by Ramaswamy H. Sarma

Keywords:

• G-quadruplex
• i-motif
• hairpin
• hnRNP K
• DNA polymorphism

Acknowledgment

The authors acknowledge the CIF facility at Bose Institute, the Director of Bose Institute and the Chairman of the Biophysics Department for their support.

Author contributions

Experiments were performed by Debopriya Bose with help of Ananya Roy and Pallabi Sengupta. Manuscript was written and by Debopriya Bose and edited by Ananya Roy. Nilanjan Banerjee helped in the theoretical experiments. Figures were made by Debopriya Bose. Subhrangsu Chatterjee edited the manuscript. All authors have given approval to the final version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

Debopriya Bose and Ananya Roy are thankful to Bose Institute for their fellowship.