Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods

SUMMARY

Experimental methods using microRNA/target ligation have recently provided significant insights into microRNA functioning through generation of chimeric (hybrid) RNA sequences. Here, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence data in the "hyb" file format to enable customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes a suite of python objects for developing custom analyses of hybrid data as well as miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA/target interactions in Vienna format.

AVAILABILITY AND IMPLEMENTATION

Hybkit is provided free and open source under the GNU GPL license at github.com/RenneLab/hybkit and archived on Zenodo (doi.org/10.5281/zenodo.7834299). Hybkit distributions are also provided via PyPI (pypi.org/project/hybkit), Conda (bioconda.github.io/recipes/hybkit/README.html), and Docker (quay.io/repository/biocontainers/hybkit).

DExD/H Box Helicases DDX24 and DDX49 Inhibit Reactivation of Kaposi’s Sarcoma Associated Herpesvirus by Interacting with Viral mRNAs

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus that is the causative agent of primary effusion lymphoma and Kaposi’s sarcoma. In healthy carriers, KSHV remains latent, but a compromised immune system can lead to lytic viral replication that increases the probability of tumorigenesis. RIG-I-like receptors (RLRs) are members of the DExD/H box helicase family of RNA binding proteins that recognize KSHV to stimulate the immune system and prevent reactivation from latency. To determine if other DExD/H box helicases can affect KSHV lytic reactivation, we performed a knock-down screen that revealed DHX29-dependent activities appear to support viral replication but, in contrast, DDX24 and DDX49 have antiviral activity. When DDX24 or DDX49 are overexpressed in BCBL-1 cells, transcription of all lytic viral genes and genome replication were significantly reduced. RNA immunoprecipitation of tagged DDX24 and DDX49 followed by next-generation sequencing revealed that the helicases bind to mostly immediate-early and early KSHV mRNAs. Transfection of expression plasmids of candidate KSHV transcripts, identified from RNA pull-down, demonstrated that KSHV mRNAs stimulate type I interferon (alpha/beta) production and affect the expression of multiple interferon-stimulated genes. Our findings reveal that host DExD/H box helicases DDX24 and DDX49 recognize gammaherpesvirus transcripts and convey an antiviral effect in the context of lytic reactivation.

Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) to Identify MicroRNA Targets

This protocol was designed to identify microRNA (miRNA) targetomes from smaller‐input samples by performing a simplified workflow of the Cross‐Linking and Sequencing of Hybrids (CLASH) technique developed in the Tollervey group. In this ribonomics‐based technique, Cross‐Linking and Immunoprecipitation (CLIP) of Argonaute (Ago) is combined with an RNA ligase reaction that yields covalently bound “hybrids” between miRNAs and their target RNAs. While this iteration of CLIP identifies “high‐confidence” or “unambiguous” miRNA targets, the added ligation step is highly inefficient and therefore requires large numbers of cultured cells. To make this powerful approach applicable to smaller cell numbers, we created qCLASH, incorporating a workflow that performs all enzymatic reactions on bead‐bound complexes and omits gel purification of immunoprecipitated Ago complexes associated with major loss of RNA. At a sequencing depth of 100 million reads per library, which is highly feasible with rapidly decreasing sequencing costs, qCLASH, when used with three biological replicates, results in thousands of high‐confidence miRNA targets. qCLASH was first developed to identify viral miRNA targetomes of endothelial cells infected with Kaposi's sarcoma−associated herpesvirus. Since then, qCLASH has been applied to Epstein‐Barr virus− and MHV68‐infected cells, and more recently to metastatic melanoma and breast cancer cells. Currently, protocols are under development to apply qCLASH to human solid tumor specimens. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol: Quick Cross‐Linking and Sequencing of Hybrids (qCLASH)

Support Protocol: Optimization of Ago immunoprecipitation

Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells

MicroRNAs are key post-transcriptional gene regulators often displaying aberrant expression patterns in cancer. As microRNAs are promising disease-associated biomarkers and modulators of responsiveness to anti-cancer therapies, a solid understanding of their targetome is crucial. Despite enormous research efforts, the success rates of available tools to reliably predict microRNAs (miRNA)-target interactions remains limited. To investigate the disease-associated miRNA targetome, we have applied modified cross-linking ligation and sequencing of hybrids (qCLASH) to BRAF-mutant melanoma cells. The resulting RNA-RNA hybrid molecules provide a comprehensive and unbiased snapshot of direct miRNA-target interactions. The regulatory effects on selected miRNA target genes in predicted vs. non-predicted binding regions was validated by miRNA mimic experiments. Most miRNA-target interactions deviate from the central dogma of miRNA targeting up to 60% interactions occur via non-canonical seed pairing with a strong contribution of the 3' miRNA sequence, and over 50% display a clear bias towards the coding sequence of mRNAs. miRNAs targeting the coding sequence can directly reduce gene expression (miR-34a/CD68), while the majority of non-canonical miRNA interactions appear to have roles beyond target gene suppression (miR-100/AXL). Additionally, non-mRNA targets of miRNAs (lncRNAs) whose interactions mainly occur via non-canonical binding were identified in melanoma. This first application of CLASH sequencing to cancer cells identified over 8 K distinct miRNA-target interactions in melanoma cells. Our data highlight the importance non-canonical interactions, revealing further layers of complexity of post-transcriptional gene regulation in melanoma, thus expanding the pool of miRNA-target interactions, which have so far been omitted in the cancer field.

Age-Related Changes in miRNA Expression Influence GSTZ1 and Other Drug Metabolizing Enzymes

Previous work has shown that hepatic levels of human glutathione transferase zeta 1 (GSTZ1) protein, involved in tyrosine catabolism and responsible for metabolism of the investigational drug dichloroacetate, increase in cytosol after birth before reaching a plateau around age 7. However, the mechanism regulating this change of expression is still unknown, and previous studies showed that GSTZ1 mRNA levels did not correlate with GSTZ1 protein expression. In this study, we addressed the hypothesis that microRNAs (miRNAs) could regulate expression of GSTZ1. We obtained liver samples from donors aged less than 1 year or older than 13 years and isolated total RNA for use in a microarray to identify miRNAs that were downregulated in the livers of adults compared with children. From a total of 2578 human miRNAs tested, 63 miRNAs were more than 2-fold down-regulated in adults, of which miR-376c-3p was predicted to bind to the 3' untranslated region of GSTZ1 mRNA. There was an inverse correlation of miR-376c-3p and GSTZ1 protein expression in the liver samples. Using cell culture, we confirmed that miR-376c-3p could downregulate GSTZ1 protein expression. Our findings suggest that miR-376c-3p prevents production of GSTZ1 through inhibition of translation. These experiments further our understanding of GSTZ1 regulation. Furthermore, our array results provide a database resource for future studies on mechanisms regulating human hepatic developmental expression. SIGNIFICANCE STATEMENT: Hepatic glutathione transferase zeta 1 (GSTZ1) is responsible for metabolism of the tyrosine catabolite maleylacetoacetate as well as the investigational drug dichloroacetate. Through examination of microRNA (miRNA) expression in liver from infants and adults and studies in cells, we showed that expression of GSTZ1 is controlled by miRNA. This finding has application to the dosing regimen of the drug dichloroacetate. The miRNA expression profiles are provided and will prove useful for future studies of drug-metabolizing enzymes in infants and adults.

Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs

Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi’s Sarcoma-associated herpes virus (KSHV) and Epstein–Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA–miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA–lncRNA interactions broadly contribute to the regulation of gene expression.

Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery

Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong latent infection in B cells and are associated with a variety of tumors. In addition to protein coding genes, these viruses encode numerous microRNAs (miRNAs) within their genomes. While putative host targets of EBV and KSHV miRNAs have been previously identified, the specific functions of these miRNAs during in vivo infection are largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV genetic elements such as miRNAs in the context of infection and disease. However, the specific targets of MHV68 miRNAs remain completely unknown. Using a technique known as qCLASH (quick crosslinking, ligation, and sequencing of hybrids), we have now identified thousands of Ago-associated, direct miRNA-mRNA interactions during lytic infection, latent infection and reactivation from latency. Validating this approach, detailed molecular analyses of specific interactions demonstrated repression of numerous host mRNA targets of MHV68 miRNAs, including Arid1a, Ctsl, Ifitm3 and Phc3. Notably, of the 1,505 MHV68 miRNA-host mRNA targets identified in B cells, 86% were shared with either EBV or KSHV, and 64% were shared among all three viruses, demonstrating significant conservation of gammaherpesvirus miRNA targeting. Pathway analysis of MHV68 miRNA targets further revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including eIF2 Signaling, mTOR signaling and protein ubiquitination, pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs.

Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong infections and are associated with a variety of tumors. These viruses encode numerous molecules called microRNAs (miRNAs) within their genomes, which target and suppress the products of specific genes within infected host cells. However, the function of these miRNAs during in vivo infection is largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV. Here, we describe the identification and validation of thousands of new MHV68 miRNA targets. Notably, 86% of the MHV68 miRNA targets identified were shared with either EBV or KSHV, and 64% were shared among all three viruses. Further analyses revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs.

Does usefulness of potassium supplementation depend on speed?

REASONS FOR PERFORMING STUDY

Electrolyte mixtures given to counter sweat loss usually contain abundant potassium. However, increases in plasma [K+] occur with exercise and supplementation may further increase plasma levels, potentially increasing the risk of neuromuscular hyperexcitability and development of adverse clinical sequellae. This proposition requires study.

OBJECTIVES

To compare effects of a K-rich electrolyte supplement (EM+K) to a K-free one (EM-K) on plasma [K+], [Ca++] and acid-base status during an endurance incremental exercise test on the treadmill.

METHODS

The test consisted of 3 bouts (simulating loops in an endurance race) of 12 km performed at 6, then 7, then 8 m/sec with 25 min rest stops (S1, S2) between loops on 13 endurance trained Arabian horses (7 EM-K, 6 EM+K). Electrolytes were supplied orally 60 mins before exercise (Pre) and at each stop. Blood samples were taken before exercise and during exercise, each S and 120 mins of recovery (R). Blood was analysed for pH, PCO2, packed cell volume (PCV), plasma [Na+], [K+], [Cl-], [Ca++], glucose, and lactate [La-]; plasma [H+] and osmolality (osm) were calculated. The dietary cation anion difference (DCAD) was calculated to be -27 meq/dose EM-K and 109 meq in EM+K, respectively.

RESULTS

Plasma [H+] decreased during the 6 and 7 m/sec loops, increased during the 8 m/sec loop, and returned to Pre at S1, S2 and R. Plasma [K+] was higher at 8 m/sec and plasma [Ca++] was overall lower in the EM+K group compared to EM-K. Other findings included higher overall PCV, overall glucose, and [La-] during the 8 m/sec loop (P<0.040) in EM+K compared to EM-K horses.

CONCLUSIONS

EM+K supplementation leads to higher plasma [K+] increasing the risk of neuromuscular hyperexcitability during exercise. Acute effects of a lower DCAD in EM-K may have led to higher plasma [Ca++]. Potassium-rich electrolytes may have triggered the release of epinephrine, contributing to higher PCV, glucose release and increased lactate production.

POTENTIAL RELEVANCE

Lower plasma [K+] and higher plasma [Ca++] with EM-K supplementation may help reduce the risk of conditions associated with neuromuscular hyperexcitability occurring especially during higher speeds in endurance races.

Seasonal vitamin A depletion in grazing horses is assessed better by the relative dose response test than by serum retinol concentration

Vitamin A influences growth and reproduction in horses. A retinol dose response (RDR) test for retinol has been shown to be better than serum retinol concentration for assessing vitamin A status in other species, so we have compared these two methods in the horse. Forty-five Thoroughbred broodmares were assigned randomly to three groups fed pasture and hay (PH), pasture, hay and vitamin A-free concentrate (PHC), or hay and concentrate (HC) in early summer (May 1991). Mares in pasture groups produced 23 foals (March through June) that had access to their dam's diets and were also studied. In the mares, significant vitamin A depletion developed in 2 mo in the nonpasture group (HC) and in 8 mo in the two pasture groups (PH and PHC) according to the RDR test, and in all three groups at 8 mo as shown by a decrease in serum retinol concentration. In the weanlings (PH and PHC only), no differences between groups were found for serum retinol, but the RDR was significantly higher in the PH group, which had suffered a respiratory infection, than in the PHC group. These findings indicated that vitamin A depletion was detected more readily by the RDR test than by serum retinol concentration, that consumption of pasture delayed depletion in the late fall, and that infection was associated with lower vitamin A status.

The selectivity of the delayed potassium conductance of frog skeletal muscle fibers

A voltage-clamp technique was used to measure reversal potentials of delayed currents in frog skeletal muscle fibres immersed in solutions containing Li2SO4,Na2SO4,K2so4,Rb2SO4, or Cs2SO4. The selectivity sequence found for the underlying permeability mechanism was K greater than or equal to Rb greater than Cs greater than Na greater than or equal to Li.

Cs(+) causes a voltage-dependent block of inward K currents in resting skeletal muscle fibres

When frog skeletal muscle fibres are bathed in solutions containing Cs(+) and K(+) in the ratio 1:4,000, a reduction is observed in the size of inward K currents through the resting membrane. This effect is enhanced by an increase in either hyperpolarisation or external Cs(+) concentration. It can be predicted from these findings that regenerative changes in membrane potential should be obtainable in fibres, in the presence of Cs(+), that are hyperpolarised by means of a current electrode. Such responses are described in the last part of this report. In squid axon and frog node, internal Cs(+) produces a voltage-dependent block of the delayed, outward K currents, though the ratio of Cs(+) to K(+) required for this effect is far greater than that used in the experiments reported here. A closer parallel can be drawn between our findings and those recently reported on the inward K currents in the starfish egg cell.