Regulation of nuclear transcription by mitochondrial RNA in endothelial cells.

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, thus termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.

A genome-wide single-cell 3D genome atlas of lung cancer progression.

Alterations in three-dimensional (3D) genome structures are associated with cancer1-5. However, how genome folding evolves and diversifies during subclonal cancer progression in the native tissue environment remains unknown. Here, we leveraged a genome-wide chromatin tracing technology to directly visualize 3D genome folding in situ in a faithful Kras-driven mouse model of lung adenocarcinoma (LUAD)6, generating the first single-cell 3D genome atlas of any cancer. We discovered stereotypical 3D genome alterations during cancer development, including a striking structural bottleneck in preinvasive adenomas prior to progression to LUAD, indicating a stringent selection on the 3D genome early in cancer progression. We further showed that the 3D genome precisely encodes cancer states in single cells, despite considerable cell-to-cell heterogeneity. Finally, evolutionary changes in 3D genome compartmentalization - partially regulated by polycomb group protein Rnf2 through its ubiquitin ligase-independent activity - reveal novel genetic drivers and suppressors of LUAD progression. Our results demonstrate the importance of mapping the single-cell cancer 3D genome and the potential to identify new diagnostic and therapeutic biomarkers from 3D genomic architectures.

Perturb-tracing enables high-content screening of multiscale 3D genome regulators.

Three-dimensional (3D) genome organization becomes altered during development, aging, and disease1-23, but the factors regulating chromatin topology are incompletely understood and currently no technology can efficiently screen for new regulators of multiscale chromatin organization. Here, we developed an image-based high-content screening platform (Perturb-tracing) that combines pooled CRISPR screen, a new cellular barcode readout method (BARC-FISH), and chromatin tracing. We performed a loss-of-function screen in human cells, and visualized alterations to their genome organization from 13,000 imaging target-perturbation combinations, alongside perturbation-paired barcode readout in the same single cells. Using 1.4 million 3D positions along chromosome traces, we discovered tens of new regulators of chromatin folding at different length scales, ranging from chromatin domains and compartments to chromosome territory. A subset of the regulators exhibited 3D genome effects associated with loop-extrusion and A-B compartmentalization mechanisms, while others were largely unrelated to these known 3D genome mechanisms. We found that the ATP-dependent helicase CHD7, the loss of which causes the congenital neural crest syndrome CHARGE24 and a chromatin remodeler previously shown to promote local chromatin openness25-27, counter-intuitively compacts chromatin over long range in different genomic contexts and cell backgrounds including neural crest cells, and globally represses gene expression. The DNA compaction effect of CHD7 is independent of its chromatin remodeling activity and does not require other protein partners. Finally, we identified new regulators of nuclear architectures and found a functional link between chromatin compaction and nuclear shape. Altogether, our method enables scalable, high-content identification of chromatin and nuclear topology regulators that will stimulate new insights into the 3D genome functions, such as global gene and nuclear regulation, in health and disease.

Combined effects of high relative humidity and ultraviolet irradiation: Enhancing the production of gaseous NO2 from the photolysis of NH4NO3.

Free radicals and nitrogen-containing species produced by nitrate photolysis can affect various atmospheric chemical processes, and thereby the photochemical behavior of atmospheric nitrate aerosols has been attracting much attention. However, the photolysis mechanism of NH4NO3 and its products under different atmospheric conditions remain unclear. In this study, the effects of relative humidity (RH), pH, NH3, ultraviolet (UV) light intensity and halogen ions (Cl-, Br- and I-) on the photolysis of particulate NH4NO3 have been investigated through a flow tube reactor. The results show that RH can significantly enhance the production of gaseous NO2 from the photolysis of NH4NO3 when RH is higher than its deliquescence RH, but almost no NO2 is generated under dry conditions. Under high RH and UV light, the main product of NH4NO3 photolysis is NO2, rather than NO and HONO, and another main species HNO3 which mainly comes from the hydrolysis of product NO2 in the gas path was detected. Almost no NO2 and HNO3 are produced under high RH without UV light or low RH with UV light, showing the combined effect of high RH and UV irradiation on the photolysis of NH4NO3. In addition, under high RH, the lower the pH and the stronger the light intensity, the higher the NO2 production. Furthermore, surprising yields of NO and HONO are detected in the presence of halogen ions, especially in the presence of I-, indicating the important role of halogen ion in the nitrate photolysis. These results provide new insights into the photolysis of atmospheric nitrate aerosols, and may contribute to elucidating the formation and migration of atmospheric nitrate aerosols and the potential mechanisms of the occurrence and evolution of atmospheric pollution and ozone pollution.

Aqueous phase oxidation of bisulfite influenced by nitrate and its photolysis.

Nitrate aerosol is ubiquitous in the atmosphere. Nitrate in the particulate and aqueous phase can affect various atmospheric chemical processes through its hygroscopicity and photolysis. The impacts of nitrate photolysis on the heterogeneous oxidation of SO2 have been attracting attention. However, the influence of nitrate on heterogeneous aqueous phase formation of atmospheric sulfate aerosol is still not very clear. In this study, the effects of nitrate on aqueous phase oxidation of bisulfite under different conditions were investigated. Results show that nitrate photolysis can promote the oxidation of bisulfite to sulfate, especially in the presence of O2. It is found that pH plays a significant role in the reaction, and ammonium sulfate has significant impacts on the enhancement of aqueous phase sulfate production through regulating the pH of solution. An apparent synergism is found among halogen chemistry, nitrate and its photochemistry and S (IV) aqueous oxidation, especially the oxidation of halide ions by nitrate and its photolysis and by the intermediate products produced by the free radical chain oxidation of S (IV) in acidic solution, leading to the coupling of the redox cycle of halogen with the oxidation of bisulfite, which promotes the continuous aqueous oxidation of bisulfite and the formation of sulfate. In addition, the role of nitrate itself in the aqueous phase oxidation of bisulfite is revealed. These results provide a new insight into the heterogeneous aqueous phase oxidation pathways and mechanisms of SO2 in cloud and fog droplets and haze particles.

Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue.

The genome is hierarchically organized into several 3D architectures, including chromatin loops, domains, compartments and regions associated with nuclear lamina and nucleoli. Changes in these architectures have been associated with normal development, aging and a wide range of diseases. Despite its critical importance, understanding how the genome is spatially organized in single cells, how organization varies in different cell types in mammalian tissue and how organization affects gene expression remains a major challenge. Previous approaches have been limited by a lack of capacity to directly trace chromatin folding in 3D and to simultaneously measure genomic organization in relation to other nuclear components and gene expression in the same single cells. We have developed an image-based 3D genomics technique termed 'chromatin tracing', which enables direct 3D tracing of chromatin folding along individual chromosomes in single cells. More recently, we also developed multiplexed imaging of nucleome architectures (MINA), which enables simultaneous measurements of multiscale chromatin folding, associations of genomic regions with nuclear lamina and nucleoli and copy numbers of numerous RNA species in the same single cells in mammalian tissue. Here, we provide detailed protocols for chromatin tracing in cell lines and MINA in mammalian tissue, which take 3-4 d for experimental work and 2-3 d for data analysis. We expect these developments to be broadly applicable and to affect many lines of research on 3D genomics by depicting multiscale genomic architectures associated with gene expression, in different types of cells and tissue undergoing different biological processes.

Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead.

Covalent inhibitors of wild-type HIV-1 reverse transcriptase (CRTIs) are reported. Three compounds derived from catechol diether non-nucleoside inhibitors (NNRTIs) with addition of a fluorosulfate warhead are demonstrated to covalently modify Tyr181 of HIV-RT. X-ray crystal structures for complexes of the CRTIs with the enzyme are provided, which fully demonstrate the covalent attachment, and confirmation is provided by appropriate mass shifts in ESI-TOF mass spectra. The three CRTIs and six noncovalent analogues are found to be potent inhibitors with both IC50 values for in vitro inhibition of WT RT and EC50 values for cytopathic protection of HIV-1-infected human T-cells in the 5-320 nM range.