Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering

Functional innovation through new genes as a general evolutionary process

In the past decade, our understanding of how new genes originate in diverse organisms has advanced substantially, and more than a dozen molecular mechanisms for generating initial gene structures were identified, in addition to gene duplication. These new genes have been found to integrate into and modify pre-existing gene networks primarily through mutation and selection, revealing new patterns and rules with stable origination rates across various organisms. This progress has challenged the prevailing belief that new proteins evolve from pre-existing genes, as new genes may arise de novo from noncoding DNA sequences in many organisms, with high rates observed in flowering plants. New genes have important roles in phenotypic and functional evolution across diverse biological processes and structures, with detectable fitness effects of sexual conflict genes that can shape species divergence. Such knowledge of new genes can be of translational value in agriculture and medicine.

Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease

Genome organization is intricately tied to regulating genes and associated cell fate decisions. Here, we examine the positioning and functional significance of human genes, grouped by their lineage restriction level, within the 3D organization of the genome. We reveal that genes of different lineage restriction levels have distinct positioning relationships with both domains and loop anchors, and remarkably consistent relationships with boundaries across cell types. While the functional associations of each group of genes are primarily cell type-specific, associations of conserved genes maintain greater stability across 3D genomic features and disease than recently evolved genes. Furthermore, the expression of these genes across various tissues follows an evolutionary progression, such that RNA levels increase from young lineage restricted genes to ancient genes present in most species. Thus, the distinct relationships of gene evolutionary age, function, and positioning within 3D genomic features contribute to tissue-specific gene regulation in development and disease.

A new computational methodology for the characterization of complex molecular environments using IR spectroscopy: bridging the gap between experiments and computations

The molecular interactions and dynamics of complex liquid solutions are now routinely measured using IR and 2DIR spectroscopy. In particular, the use of the latter allows the determination of the frequency fluctuation correlation function (FFCF), while the former provides us with the average frequency. In turn, the FFCF can be used to quantify the vibrational dynamics of a molecule in a solution, and the center frequency provides details about the chemical environment, solvatochromism, of the vibrational mode. In simple solutions, the IR methodology can be used to unambiguously assign the interactions and dynamics observed by a molecule in solution. However, in complex environments with molecular heterogeneities, this assignment is not simple. Therefore, a method that allows for such an assignment is essential. Here, a parametrization free method, called Instantaneous Frequencies of Molecules or IFM, is presented. The IFM method, when coupled to classical molecular simulations, can predict the FFCF of a molecule in solutions. Here, N-methylacetamide (NMA) in seven different chemical environments, both simple and complex, is used to test this new method. The results show good agreement with experiments for the NMA solvatochromism and FFCF dynamics, including characteristic times and amplitudes of fluctuations. In addition, the new method shows equivalent or improved results when compared to conventional frequency maps. Overall, the use of the new method in conjunction with molecular dynamics simulations allows unlocking the full potential of IR spectroscopy to generate molecular maps from vibrational observables, capable of describing the interaction landscape of complex molecular systems.

Aptamer Screening: Current Methods and Future Trend towards Non-SELEX Approach

Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide non-SELEX methods into an immobilized format and non-immobilized format and discuss how high-resolution partitioning methods could facilitate the further improvement of selection efficiency and accuracy.

1H, 13C and 15N backbone and side-chain resonance assignments of the human oncogenic protein NCYM

NCYM is a cis-antisense gene of MYCN oncogene and encodes an oncogenic protein that stabilizes MYCN via inhibition of GSK3b. High NCYM expression levels are associated with poor clinical outcomes in human neuroblastomas, and NCYM overexpression promotes distant metastasis in animal models of neuroblastoma. Using vacuum-ultraviolet circular dichroism and small-angle X-ray scattering, we previously showed that NCYM has high flexibility with partially folded structures; however, further structural characterization is required for the design of anti-cancer agents targeting NCYM. Here we report the 1H, 15N and 13C nuclear magnetic resonance assignments of NCYM. Secondary structure prediction using Secondary Chemical Shifts and TALOS-N analysis demonstrates that the structure of NCYM is essentially disordered, even though residues in the central region of the peptide clearly present a propensity to adopt a dynamic helical structure. This preliminary study provides foundations for further analysis of interaction between NCYM and potential partners.