Lighting Up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification

TET-mediated 5hmC in breast cancer: mechanism and clinical potential

Breast cancer is the most common cancer among women, with differences in clinical features due to its distinct molecular subtypes. Current studies have demonstrated that epigenetic modifications play a crucial role in regulating the progression of breast cancer. Among these mechanisms, DNA demethylation and its reverse process have been studied extensively for their roles in activating or silencing cancer related gene expression. Specifically, Ten-Eleven Translocation (TET) enzymes are involved in the conversion process from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which results in a significant difference in the global level of 5hmC in breast cancer compared with normal tissues. In this review, we summarize the functions of TET proteins and the regulated 5hmC levels in the pathogenesis of breast cancer. Discussions on the clinical values of 5hmC in early diagnosis and the prediction of prognosis are also mentioned.

Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments below Spatial Resolution

Cellular biomolecules may exhibit dense distribution and organization at the nanoscale to govern vital biological processes. However, it remains a common challenge to digitize the spatially dense biomolecules under the spatial resolution of microscopies. Here, a proof-of-principle method, molecule differentiation encoding microscopy by orthogonal tandem repeat DNA identifiers is reported, to resolve the copy numbers of dense biomolecules in cellular nanoenvironments. The method encodes each copy of the same biomolecules into different types of DNA barcodes based on stochastic multiplexed reactions. It can transform the overlap of the same spectrum into the overlap of different spectra. Furthermore, an algorithm is developed to automatically quantitate overlapping spots and individual spots. Using this method, RNAs in the cytoplasm, DNA epigenetic modifications in the cell nucleus, and glycans and glycoRNAs on the cell surface are dissected, respectively. It is found that all these biomolecules present dense distribution with diverse degrees in crowded cellular nanoenvironments. Especially, an average 17% copies of U1 glycoRNA of single cells are gathered in various nano environments on the cell surface. The strategy provides a powerful tool for digitally quantitative visualization of dense biomolecules below the spatial resolution of microscopies and can provide insights into underlying functions and mechanisms of the dense distribution information.

Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING

Epigenetic modifications and spatial proximities of nucleic acids and proteins play important roles in regulating physiological processes and disease progression. Currently available cell imaging methods, such as fluorescence in situ hybridization (FISH) and immunofluorescence, struggle to detect low-abundance modifications and their spatial proximities. Here we describe a step-by-step protocol for three DNA-encoded amplifying FISH-based imaging strategies to overcome these challenges for varying applications: base-encoded amplifying FISH (BEA-FISH), pairwise proximity-differentiated amplifying FISH (PPDA-FISH) and cellular macromolecules-tethered DNA walking indexing (Cell-TALKING). They all use the similar core principle of DNA-encoded amplification, which transforms different nonsequence molecular features into unique DNA barcodes for in situ rolling circle amplification and FISH analysis. This involves three key reactions in fixed cell samples: target labeling, DNA encoding and rolling circle amplification imaging. Using this protocol, these three imaging strategies achieve in situ counting of low-abundance modifications alone, the pairwise proximity-differentiated visualization of two modifications and the exploration of multiple modifications around one protein (one-to-many proximity), respectively. Low-abundance modifications, including 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil and 5-formyluracil, are clearly visualized in single cells. Various combinatorial patterns of nucleic acid modifications and/or histone modifications are found. The whole protocol takes ~2-4 d to complete, depending on different imaging applications.

Space-Confined Amplification for In Situ Imaging of Single Nucleic Acid and Single Pathogen on Biological Samples

Direct in situ imaging of nucleic acids on biological samples is advantageous for rapid analysis without DNA extraction. However, traditional nucleic acid amplification in aqueous solutions tends to lose spatial information because of the high mobility of molecules. Similar to a cellular matrix, hydrogels with biomimetic 3D nanoconfined spaces can limit the free diffusion of nucleic acids, thereby allowing for ultrafast in situ enzymatic reactions. In this study, hydrogel-based in situ space-confined interfacial amplification (iSCIA) is developed for direct imaging of single nucleic acid and single pathogen on biological samples without formaldehyde fixation. With a polyethylene glycol hydrogel coating, nucleic acids on the sample are nanoconfined with restricted movement, while in situ amplification can be successfully performed. As a result, the nucleic acids are lighted-up on the large-scale surface in 20 min, with a detection limit as low as 1 copy/10 cm2. Multiplex imaging with a deep learning model is also established to automatically analyze multiple targets. Furthermore, the iSCIA imaging of pathogens on plant leaves and food is successfully used to monitor plant health and food safety. The proposed technique, a rapid and flexible system for in situ imaging, has great potential for food, environmental, and clinical applications.

In Situ Self-Assembly of Fluorogenic RNA Nanozipper Enables Real-Time Imaging of Single Viral mRNA Translation

Real-time visualization of individual viral mRNA translation activities in live cells is essential to obtain critical details of viral mRNA dynamics and to detect its transient responses to environmental stress. Fluorogenic RNA aptamers are powerful tools for real-time imaging of mRNA in live cells, but monitoring the translation activity of individual mRNAs remains a challenge due to their intrinsic photophysical properties. Here, we develop a genetically encoded turn-on 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI)-binding RNA nanozipper with superior brightness and high photostability by in situ self-assembly of multiple nanozippers along single mRNAs. The nanozipper enables real-time imaging of the mobility and dynamic translation of individual viral mRNAs in live cells, providing information on the spatial dynamics and translational elongation rate of viral mRNAs.

Enzymatic Cleavage-Mediated Extension Stalling Enables Accurate Recognition and Quantification of Locus-Specific Uracil Modification in DNA

Chemical modifications in DNA have profound influences on the structures and functions of DNA. Uracil, a naturally occurring DNA modification, can originate from the deamination of cytosine or arise from misincorporation of dUTP into DNA during DNA replication. Uracil in DNA will imperil genomic stability due to their potential in producing detrimental mutations. An in-depth understanding of the functions of uracil modification requires the accurate determination of its site as well as content in genomes. Herein, we characterized that a new member of the uracil-DNA glycosylase (UDG) family enzyme (UdgX-H109S) could selectively cleave both uracil-containing single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Based on this unique property of UdgX-H109S, we developed an enzymatic cleavage-mediated extension stalling (ECES) method for the locus-specific detection and quantification of uracil in genomic DNA. In the ECES method, UdgX-H109S specifically recognizes and cleaves the N-glycosidic bond of uracil from dsDNA and generates an apurinic/apyrimidinic (AP) site, which could be broken by APE1 to form a one-nucleotide gap. The specific cleavage by UdgX-H109S is then evaluated and quantified by qPCR. With the developed ECES approach, we demonstrated that the level of uracil at position Chr4:50566961 in genomic DNA of breast cancer tissues was significantly decreased. Collectively, the ECES method has been proved to be accurate and reproducible in the locus-specific quantification of uracil in genomic DNA from biological and clinical samples.

Enzymatic Synthesis of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase

Development of unnatural base pairs (UBPs) has significantly expanded the genetic alphabet both in vitro and in vivo and led to numerous potential applications in the biotechnology and biopharmaceutical industry. Efficient synthesis of oligonucleotides containing unnatural nucleobases is undoubtedly an essential prerequisite for making full use of the UBPs, and de novo synthesis of oligonucleotides with terminal deoxynucleotidyl transferases (TdTs) has emerged as a method of great potential to overcome limitations of traditional solid-phase synthesis. Herein, we report the efficient template-independent incorporation of nucleotides of unnatural nucleobases dTPT3 and dNaM, which have been designed to make one of the most successful UBPs to date, dTPT3-dNaM, into DNA oligonucleotides with a TdT enzyme under optimized conditions. We also demonstrate the efficient TdT incorporation of dTPT3 derivatives with different functional linkers into oligonucleotides for orthogonal labeling of nucleic acids and applications thereof. The development of a method for the daily laboratory preparation of DNAs with UBPs at arbitrary sites with the assistance of TdT is also described.