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ABSTRACT Heart failure with preserved ejection fraction (HFpEF) is a lethal, heterogeneous, geriatric syndrome. Long noncoding RNAs (lncRNAs) constitute the majority of the functional mammalian transcriptome and are key regulators in complex pathophysiological processes. However, the roles of lncRNAs in aging HFpEF associated with thyroid hormone (TH) dysfunction are unclear. We used the well-established ZSF1 rat model to investigate early and severe age-related HFpEF in 5-, 13- or 20-months-old (mo) animals. Both serum THs significantly decreased in HFpEF in a temporal manner. Echocardiograms showed preserved cardiac function. Gravimetric and histologic analyses showed significant cardiac hypertrophy in HFpEF. Microarrays and RT-qPCR revealed that three lncRNAs were significantly increased predominantly in 13-mo HFpEF. Knockdown of lncRNA showed improvement in cell viability, which was further enhanced with T3 (active TH). Microarray analyses showed that two mRNAs were significantly altered in early HFpEF. We also identified previously unreported tissue and serum inflammatory cytokine markers in early and late HFpEF. Taken together, we have shown novel noncoding and coding markers in early- and/or late-aging-related hypothyroid HFpEF. Further studies may develop translatable diagnostic and therapeutic targets for HFpEF. 

SEquence Evaluation throughk-mer Representation (SEEKR) is a method of sequence comparison that uses sequence substrings calledk-mers to quantify the nonlinear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimateP-values that ascribe statistical significance to SEEKR-derived similarities, as well as visualize different aspects ofk-mer similarity. We apply the new functions to identify chromatin-enriched lncRNAs that containXIST-like sequence features, and we demonstrate the utility of applying SEEKR on lncRNA fragments to identify potential RNA-protein interaction domains. We also highlight ways in which SEEKR can be applied to augment studies of lncRNA conservation, and we outline the best practice of visualizing RNA-seq read density to evaluate support for lncRNA annotations before their in-depth study in cell types of interest. 

Stanniocalcin 1 (Stc1) is well known for its role in regulating calcium uptake in fish by acting on ionocytes or NaR cells. A hallmark of NaR cells is the expression of Trpv6, a constitutively open calcium channel. Recent studies in zebrafish suggest that genetical deletion of Stc1a and Trpv6 individually both increases IGF signaling and NaR cell proliferation. Whiletrpv6^-/-fish suffered from calcium deficiency and died prematurely,stc1a^-/-fish had elevated body calcium levels but also died prematurely. The relationship between Stc1a, Trpv6, and IGF signaling in regulating calcium homeostasis and organismal survival is unclear. Here we report that loss of Stc1a increases Trpv6 expression in NaR cells in an IGF signaling-dependent manner. Treatment with CdCl₂, a Trpv6 inhibitor, reduced NaR cell number instc1a^-/-fish to the sibling levels. Genetic and biochemical analysis results suggest that Stc1a and Trpv6 regulate NaR cell proliferation via the same IGF pathway. Alizarin red staining detected abnormal calcium deposits in the yolk sac region and kidney stone-like structures instc1a^-/-fish. Double knockout or pharmacological inhibition of Trpv6 alleviated these phenotypes, suggesting that Stc1a inhibit epithelial Ca²⁺uptake by regulating Trpv6 expression and activity.stc1a^-/-mutant fish developed cardiac edema, body swelling, and died prematurely. Treatment ofstc1a^-/-fish with CdCl₂or double knockout of Trpv6 alleviated these phenotypes. These results provide evidence that Stc1a regulates calcium homeostasis and organismal survival by suppressing Trpv6 expression and inhibiting IGF signaling in ionocytes. 

The lncRNAs Airn and Kcnq1ot1 recruit Polycomb Repressive Complexes (PRCs) and repress genes over multi-megabase genomic intervals, but how they interact with proteins to direct repression remains poorly understood. We conducted formaldehyde-linked RNA- immunoprecipitations of 27 proteins from trophoblast stem cells, using a protocol exhibiting similar signal-to-noise and post-lysis reassociation ratios as CLIP and CLAP. Patterns of protein associations across Airn and Kcnq1ot1 were more similar to each other than to nearly all other transcripts and partitioned to extents that mirrored degree of repression each lncRNA induced, implying connections to mechanism. Indeed, HNRNPU, an essential protein that helps Xist localize to chromatin, was enriched within and required to direct PRC-catalyzed modifications by Airn and Kcnq1ot1, without being required for their localization. Our study provides insights into the role of HNRNPU in lncRNA-mediated gene regulation and reports architectures of protein association across Airn and Kcnq1ot1 relative to the transcriptome at large.