DNA Secondary Structures and Their Regulatory Roles in Gene Transcription
Kangkang Niu1, Xiaojuan Zhang1, Huimin Deng1, Feng Wu1, Hui Xiang1, Qisheng Song2, Qili Feng1,*
1Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China,
2Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
Guanine- and cytosine-rich DNA regions can form four-stranded DNA secondary structures called G-quadruplex (G4) and i-motif, respectively. These structures widely exist in genomes and play important roles in transcription, replication, translation and protection of telomeres. G4 and i-motif structures were identified in the promoter of the transcription factor gene BmPOUM2, which regulates the expression of the wing disc cuticle protein gene (BmWCP4) during metamorphosis in Bombyx mori. Disruption of the i-motif structure by base mutation, anti-sense oligonucleotides (ASOs) or inhibitory ligands resulted in significant decrease in the activity of the BmPOUM2 promoter. A novel i-motif binding protein (BmILF) was identified by pull-down experiment and EMSA demonstrated that BmILF specifically bound to the i-motif and activated the transcription of BmPOUM2. The promoter activity of BmPOUM2 was enhanced when BmILF was over-expressed or decreased when BmILF was knocked-down by RNA interference. A nuclear protein was also identified to bind to the G4 structure in the promoter of BmPOUM2 and regulated the gene transcription. Totally, 38 representative species in evolution were selected for genomic analysis of the DNA secondary structure, distribution and evolution. The data indicate that the average density of the motif in the genome gradually increased with evolution. The number of the G4 motif in the upstream regulatory region of the genes increased from lower to higher organisms. The results of this study provide new insights into the molecular mechanism of the secondary structures in epigenetic regulation of gene transcription.
Acknowledgements: This study is supported by the grants from the Chinese National Natural Science Foundation (31330071, 31672494,31720103916).
Key words: DNA secondary structure, G-quadruplex, Promoter, Transcription factor, Gene transcription, Epigenetic regulation, Silkworm
Kangkang Niu1, Xiaojuan Zhang1, Huimin Deng1, Feng Wu1, Hui Xiang1, Qisheng Song2, Qili Feng1,*
1Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China,
2Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
Guanine- and cytosine-rich DNA regions can form four-stranded DNA secondary structures called G-quadruplex (G4) and i-motif, respectively. These structures widely exist in genomes and play important roles in transcription, replication, translation and protection of telomeres. G4 and i-motif structures were identified in the promoter of the transcription factor gene BmPOUM2, which regulates the expression of the wing disc cuticle protein gene (BmWCP4) during metamorphosis in Bombyx mori. Disruption of the i-motif structure by base mutation, anti-sense oligonucleotides (ASOs) or inhibitory ligands resulted in significant decrease in the activity of the BmPOUM2 promoter. A novel i-motif binding protein (BmILF) was identified by pull-down experiment and EMSA demonstrated that BmILF specifically bound to the i-motif and activated the transcription of BmPOUM2. The promoter activity of BmPOUM2 was enhanced when BmILF was over-expressed or decreased when BmILF was knocked-down by RNA interference. A nuclear protein was also identified to bind to the G4 structure in the promoter of BmPOUM2 and regulated the gene transcription. Totally, 38 representative species in evolution were selected for genomic analysis of the DNA secondary structure, distribution and evolution. The data indicate that the average density of the motif in the genome gradually increased with evolution. The number of the G4 motif in the upstream regulatory region of the genes increased from lower to higher organisms. The results of this study provide new insights into the molecular mechanism of the secondary structures in epigenetic regulation of gene transcription.
Acknowledgements: This study is supported by the grants from the Chinese National Natural Science Foundation (31330071, 31672494,31720103916).
Key words: DNA secondary structure, G-quadruplex, Promoter, Transcription factor, Gene transcription, Epigenetic regulation, Silkworm