RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins

RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation and disease. Their binding sites cover more of the genome than coding exons; nevertheless, most noncoding variant prioritization methods only focus on transcriptional regulation. Here, we integrate the portfolio of ENCODE-RBP experiments to develop RADAR, a variant-scoring framework. RADAR uses conservation, RNA structure, network centrality, and motifs to provide an overall impact score. Then, it further incorporates tissue-specific inputs to highlight disease-specific variants. Our results demonstrate RADAR can successfully pinpoint variants, both somatic and germline, associated with RBP-function dysregulation, which cannot be found by most current prioritization methods, for example, variants affecting splicing.

Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair

Mature adipocytes store fatty acids and are a common component of tissue stroma. Adipocyte function in regulating bone marrow, skin, muscle, and mammary gland biology is emerging, but the role of adipocyte-derived lipids in tissue homeostasis and repair is poorly understood. Here, we identify an essential role for adipocyte lipolysis in regulating inflammation and repair after injury in skin. Genetic mouse studies revealed that dermal adipocytes are necessary to initiate inflammation after injury and promote subsequent repair. We find through histological, ultrastructural, lipidomic, and genetic experiments in mice that adipocytes adjacent to skin injury initiate lipid release necessary for macrophage inflammation. Tamoxifen-inducible genetic lineage tracing of mature adipocytes and single-cell RNA sequencing revealed that dermal adipocytes alter their fate and generate ECM-producing myofibroblasts within wounds. Thus, adipocytes regulate multiple aspects of repair and may be therapeutic for inflammatory diseases and defective wound healing associated with aging and diabetes.

Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA

Chemical probing has the power to provide insight into RNA conformation in vivo and in vitro, but interpreting the results depends on methods to detect the chemically modified nucleotides. Traditionally, the presence of modified bases was inferred from their ability to halt reverse transcriptase during primer extension and the locations of termination sites observed by electrophoresis or sequencing. More recently, modification-induced mutations have been used as a readout for chemical probing data. Given the variable propensity for mismatch incorporation and read-through with different reverse transcriptases, we examined how termination and mutation events compare to each other in the same chemical probing experiments. We found that mutations and terminations induced by dimethyl sulfate probing are both specific for methylated bases, but these two measures have surprisingly little correlation and represent largely nonoverlapping indicators of chemical modification data. We also show that specific biases for modified bases depend partly on local sequence context and that different reverse transcriptases show different biases toward reading a modification as a stop or a mutation. These results support approaches that incorporate analysis of both termination and mutation events into RNA probing experiments.

The Properties of Long Noncoding RNAs That Regulate Chromatin

Beyond coding for proteins, RNA molecules have well-established functions in the posttranscriptional regulation of gene expression. Less clear are the upstream roles of RNA in regulating transcription and chromatin-based processes in the nucleus. RNA is transcribed in the nucleus, so it is logical that RNA could play diverse and broad roles that would impact human physiology. Indeed, this idea is supported by well-established examples of noncoding RNAs that affect chromatin structure and function. There has been dramatic growth in studies focused on the nuclear roles of long noncoding RNAs (lncRNAs). Although little is known about the biochemical mechanisms of these lncRNAs, there is a developing consensus regarding the challenges of defining lncRNA function and mechanism. In this review, we examine the definition, discovery, functions, and mechanisms of lncRNAs. We emphasize areas where challenges remain and where consensus among laboratories has underscored the exciting ways in which human lncRNAs may affect chromatin biology.

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.

To do their jobs, many RNAs need to fold into structures (through base-paring). We were interested in the conformation of a specific mammalian RNA, Xist, when it is inside a cell. Xist is a very large non-coding RNA (lncRNA), that is >17,000 nt long. Xist is particularly important because it is one of the first lncRNAs to be discovered, and turns genes off across an entire chromosome. To figure out how Xist RNA is folded in mouse cells, we developed a new approach, Targeted Structure-Seq, to examine the conformation of large RNAs like Xist. Using computer modeling, we identified parts of Xist that are base paired into RNA duplexes. We also determined which parts of the Xist RNA are likely to be structured. This work provides a new tool for studying the secondary structure of any large RNA, and helps us understand what the important pieces of Xist look like while Xist does its work in the cell.

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

We describe a chemical method to label and purify 4-thiouridine (s(4)U)-containing RNA. We demonstrate that methanethiosulfonate (MTS) reagents form disulfide bonds with s(4)U more efficiently than the commonly used HPDP-biotin, leading to higher yields and less biased enrichment. This increase in efficiency allowed us to use s(4)U labeling to study global microRNA (miRNA) turnover in proliferating cultured human cells without perturbing global miRNA levels or the miRNA processing machinery. This improved chemistry will enhance methods that depend on tracking different populations of RNA, such as 4-thiouridine tagging to study tissue-specific transcription and dynamic transcriptome analysis (DTA) to study RNA turnover.