Direct determination of RNA structures and interactions in living cells is critical for understanding their functions in normal physiology and disease states. Here, we present PARIS2, a dramatically improved method for RNA duplex determination in vivo with >4000-fold higher efficiency than previous methods. PARIS2 captures ribosome binding sites on mRNAs, reporting translation status on a transcriptome scale. Applying PARIS2 to the U8 snoRNA mutated in the neurological disorder LCC, we discover a network of dynamic RNA structures and interactions which are destabilized by patient mutations. We report the first whole genome structure of enterovirus D68, an RNA virus that causes polio-like symptoms, revealing highly dynamic conformations altered by antiviral drugs and different pathogenic strains. We also discover a replication-associated asymmetry on the (+) and (−) strands of the viral genome. This study establishes a powerful technology for efficient interrogation of the RNA structurome and interactome in human diseases.

Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety of biological processes. However, direct determination of RNA 3D structures in vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present a method, Spatial 2′-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation, and high throughput sequencing, SHARC enables transcriptome-wide tertiary structure contact maps at high accuracy and precision, revealing heterogeneous RNA structures and interactions. SHARC data provide constraints that improves Rosetta-based RNA 3D structure modeling at near-nanometer resolution. Integrating SHARC-exo with other crosslinking-based methods, we discover compact folding of the 7SK RNA, a critical regulator of transcriptional elongation. These results establish a strategy for measuring RNA 3D distances and alternative conformations in their native cellular context.

The recent development and application of methods based on the general principle of “crosslinking and proximity ligation” (crosslink-ligation) are revolutionizing RNA structure studies in living cells. However, extracting structure information from such data presents unique challenges. Here, we introduce a set of computational tools for the systematic analysis of data from a wide variety of crosslink-ligation methods, specifically focusing on read mapping, alignment classification, and clustering. We design a new strategy to map short reads with irregular gaps at high sensitivity and specificity. Analysis of previously published data reveals distinct properties and bias caused by the crosslinking reactions. We perform rigorous and exhaustive classification of alignments and discover eight types of arrangements that provide distinct information on RNA structures and interactions. To deconvolve the dense and intertwined gapped alignments, we develop a network/graph-based tool Crosslinked RNA Secondary Structure Analysis using Network Techniques (CRSSANT), which enables clustering of gapped alignments and discovery of new alternative and dynamic conformations. We discover that multiple crosslinking and ligation events can occur on the same RNA, generating multisegment alignments to report complex high-level RNA structures and multi-RNA interactions. We find that alignments with overlapped segments are produced from potential homodimers and develop a new method for their de novo identification. Analysis of overlapping alignments revealed potential new homodimers in cellular noncoding RNAs and RNA virus genomes in the Picornaviridae family. Together, this suite of computational tools enables rapid and efficient analysis of RNA structure and interaction data in living cells.

Molecular crystals with the ability to transform light energy into macroscopic mechanical motions are a promising class of materials with potential applications in actuating and photonic devices. In regard to such materials, coordination polymers that exhibit dynamic photomechanical motion, associated with a phase transition, are unknown. Herein, we report an intriguing photoactive, one‐dimensional ZnII coordination polymer, 1, derived from 1,3,5‐tri‐4‐pyridyl‐1,2‐ethenylbenzene and 3,5‐difluorobenzoate. Single crystals of 1 under UV light irradiation exhibit rapid shrinking and bending, violent bursting‐jumping, splitting, and cracking behavior. Single‐crystal X‐ray diffraction analysis and 1H NMR spectroscopy reveal an unusual photoinduced phase transition involving a single‐crystal‐to‐single‐crystal [2+2] cycloaddition reaction that results in photomechanical responses. Interestingly, crystals of 1, which are triclinic with space group , are transformed into a higher symmetry, monoclinic cell with space group C2/c. This process represents a rare example of symmetry enhancement upon photoirradiation. The photomechanical activity is likely due to the sudden release of stress associated with strained molecular geometries and significant solid‐state molecular movement arising from cleavage and formation of chemical bonds. A composite membrane fabricated from 1 and polyvinyl alcohol (PVA) also displays interesting photomechanical behavior under UV light illumination, indicating the material's potential as a photoactuator.

Induced pluripotent stem cells (iPSCs) resemble embryonic stem cells (ESCs) in morphology, gene expression and in vitro differentiation, raising new hope for personalized clinical therapy. While many efforts have been made to improve reprogramming efficiency, significant problems such as genomic instability of iPSCs need to be addressed before clinical therapy. In this study, we try to figure out the real genomic state of iPSCs and their DNA damage response to ionizing radiation (IR). We found that iPSC line 3FB4-1 had lower DNA damage repair ability than mouse embryonic fibroblast (MEF) cells, from which 3FB4-1line was derived. After the introduction of DNA damage by IR, the number of γ-H2AX foci in 3FB4-1 increased modestly compared to a large increase seen in MEF, albeit both significantly (P < 0.01). In addition, whole-genome sequencing analysis showed that after IR, 3FB4-1 possessed more point mutations than MEF and the point mutations spread all over chromosomes. These observations provide evidence that iPSCs are more sensitive to ionizing radiation and their relatively low DNA damage repair capacity may account for their high radiosensitivity. The compromised DNA damage repair capacity of iPSCs should be considered when used in clinical therapy.