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IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.

ABSTRACT: The human genome is regulated in a multi-dimensional way. While biophysical factors like Non-specific Transcription factor Binding Affinity (nTBA) act at DNA sequence level, other factors act above sequence levels such as histone modifications and 3-D chromosomal interactions. This multidimensionality of regulation requires many of these factors for a proper understanding of the regulatory landscape of the human genome. Here, we propose a new biophysical model for estimating nTBA. Integration of nTBA with chromatin modifications and chromosomal interactions, using a new Integrative Genome Analysis Pipeline (IGAP), reveals additive effects of nTBA to regulatory DNA sequences and identifies three types of genomic zones in the human genome (Inactive Genomic Zones, Poised Genomic Zones, and Active Genomic Zones). It also unveils a novel long distance gene regulatory model: chromosomal interactions reduce the physical distance between the high occupancy target (HOT) regions that results in high nTBA to DNA in the area, which in turn attract TFs to such regions with higher binding potential. These findings will help to elucidate the three-dimensional diffusion process that TFs use during their search for the right targets.

SUBMITTER: Sahaf Naeini A

PROVIDER: S-EPMC7303559 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.

Sahaf Naeini Alireza A Farooq Amna A Bjørås Magnar M Wang Junbai J

Computational and structural biotechnology journal 20200602

The human genome is regulated in a multi-dimensional way. While biophysical factors like Non-specific Transcription factor Binding Affinity (nTBA) act at DNA sequence level, other factors act above sequence levels such as histone modifications and 3-D chromosomal interactions. This multidimensionality of regulation requires many of these factors for a proper understanding of the regulatory landscape of the human genome. Here, we propose a new biophysical model for estimating nTBA. Integration of ...[more]

PMID: 32612751

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Project description:The high-resolution crystal structure of HIV-1 reverse transcriptase (RT) bound to a 38-mer DNA hairpin aptamer with low pM affinity was previously described. The high-affinity binding aptamer contained 2'-O-methyl modifications and a seven base-pair GC-rich tract and the structure of the RT-aptamer complex revealed specific contacts between RT and the template strand of the aptamer. Similar to all crystal structures of RT bound to nucleic acid template-primers, the aptamer bound RT with a bend in the duplex DNA. To understand the structural basis for the ultra-high-affinity aptamer binding, an integrative structural biology approach was used. Hydrogen-deuterium exchange coupled to liquid chromatography-mass spectrometry (HDX-MS) was used to examine the structural dynamics of RT alone and in the presence of the DNA aptamer. RT was selectively labeled with 15N to unambiguously identify peptides from each subunit. HDX of unliganded RT shows a mostly stable core. The p66 fingers and thumb subdomains, and the RNase H domain are relatively dynamic. HDX indicates that both the aptamer and a scrambled version significantly stabilize regions of RT that are dynamic in the absence of DNA. No substantial differences in RT dynamics are observed between aptamer and scrambled aptamer binding, despite a large difference in binding affinity. Small-angle X-ray scattering and circular dichroism spectroscopy were used to investigate the aptamer conformation in solution and revealed a pre-bent DNA that possesses both A- and B-form helical character. Both the 2'-O-methyl modifications and the GC tract appear to contribute to an energetically favorable conformation for binding to RT that contributes to the aptamer's ultra-high affinity for RT. The X-ray structure of RT with an RNA/DNA version of the aptamer at 2.8 Å resolution revealed a potential role of the hairpin positioning in affinity. Together, the data suggest that both the 2'-O-methyl modifications and the GC tract contribute to an energetically favorable conformation for high-affinity binding to RT.

Dataset Information

IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.

Publications

IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.

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