An RNA Aptamer That Selectively Recognizes Symmetric Dimethylation of Arginine 8 in the Histone H3 N-Terminal Peptide

Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo

Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.

Phosphoserine inhibits neighboring arginine methylation in the RKS motif of histone H3

The effects of phosphorylation of histone H3 at serine 10 have been studied in the context of other posttranslational modifications such as lysine methylation. We set out to investigate the impact of phosphoserine-10 on arginine-8 methylation. We performed methylation reactions using peptides based on histone H3 that contain a phosphorylated serine and compared the extent of arginine methylation with unmodified peptides. Results obtained via fluorography indicate that peptides containing a phosphorylated serine-10 inhibit deposition of methyl groups to arginine-8 residues. To further explore the effects of phosphoserine on neighboring arginine residues, we physically characterized the non-covalent interactions between histone H3 phosphoserine-10 and arginine-8 using 31P NMR spectroscopy. A salt bridge was detected between the negatively charged phosphoserine-10 and the positively charged unmodified arginine-8 residue. This salt bridge was not detected when arginine-8 was symmetrically dimethylated. Finally, molecular simulations not only confirm the presence of a salt bridge but also identify a subset of electrostatic interactions present when arginine is replaced with alanine. Taken together, our work suggests that the negatively charged phosphoserine maximizes its interactions. By limiting its exposure and creating new contacts with neighboring residues, it will inhibit deposition of neighboring methyl groups, not through steric hindrance, but by forming intrapeptide interactions that may mask substrate recognition. Our work provides a mechanistic framework for understanding the role of phosphoserine on nearby amino acid residues and arginine methylation.

Nucleic Acid Aptamers Targeting Epigenetic Regulators: An Innovative Therapeutic Option

Epigenetic mechanisms include DNA methylation, posttranslational modifications of histones, chromatin remodeling factors, and post transcriptional gene regulation by noncoding RNAs. All together, these processes regulate gene expression by changing chromatin organization and DNA accessibility. Targeting enzymatic regulators responsible for DNA and chromatin modifications hold promise for modulating the transcriptional regulation of genes that are involved in cancer, as well as in chronic noncommunicable metabolic diseases like obesity, diabetes, and cardiovascular diseases. Increasingly studies are emerging, leading to the identification of specific and effective molecules targeting epigenetic pathways involved in disease onset. In this regard, RNA interference, which uses small RNAs to reduce gene expression and nucleic acid aptamers are arising as very promising candidates in therapeutic approach. Common to all these strategies is the imperative challenge of specificity. In this regard, nucleic acid aptamers have emerged as an attractive class of carrier molecules due to their ability to bind with high affinity to specific ligands, their high chemical flexibility as well as tissue penetration capability. In this review, we will focus on the recent progress in the field of aptamers used as targeting moieties able to recognize and revert epigenetics marks involved in diseases onset.

Vasorin is a potential serum biomarker and drug target of hepatocarcinoma screened by subtractive-EMSA-SELEX to clinic patient serum

We report a new biomarker of hepatocarcinoma, vasorin (VASN), screened by a subtractive EMSA-SELEX strategy from AFP negative serum of hepatocellular carcinoma (HCC) patients with extrahepatic metastases. VASN was verified to be highly expressed in sera of 100 cases of HCC patients compared with 97 cases of normal persons and 129 cases of hepatitis patients. Further validation by Q-PCR, IFA and Western blot showed higher expression of VASN at mRNA and protein levels in HCC cell lines and HCC tissues than in normal controls. RNA interference and forced overexpression assays verified that VASN promotes cell proliferation and migration and inhibits apoptosis. Down-regulation of microRNA miR145 and miR146a is an important mechanism leading to high expression of VASN. Conclusion: As a membrane protein and/or as free protein, VASN may be an effective target for biological treatment of liver cancer and is a potential biomarker for HCC diagnosis. Small molecular nucleotides targeting VASN are promising biological therapies to HCC.

Analysis of Combinatorial Epigenomic States

Hundreds of distinct chemical modifications to DNA and histone amino acids have been described. Regulation exerted by these so-called epigenetic marks is vital to normal development, stability of cell identity through mitosis, and nongenetic transmission of traits between generations through meiosis. Loss of this regulation contributes to many diseases. Evidence indicates epigenetic marks function in combinations, whereby a given modification has distinct effects on local genome control, depending on which additional modifications are locally present. This review summarizes emerging methods for assessing combinatorial epigenomic states, as well as challenges and opportunities for their refinement.

Identification of lysine K18 acetylation on histone H3 peptide using gold nanoparticles' aggregation behaviour

Acetylation of histones, the major protein component of eukaryotic chromosomes, contributes to the epigenetic regulation of gene expression and is also involved in cancer development. A recent study revealed the correlation between tumour formation and acetylation level of lysine K18 on histone H3. In this study, we developed two colorimetric in vitro assays using gold nanoparticles (AuNPs) for identification of lysine K18 acetylation on histone H3 peptide. In assay I, citrate ion-capped AuNP without further modification was employed. Simply mixing the K18 peptide with AuNP solution leads to distinct particle aggregation, relative to that by non-acetylated or lysine K14 acetylated control peptides. In assay II, an AuNP-peptide-antibody composite was synthesized and used as both the sensing probe and the transducing element. By mixing the sample peptides with the composite solution followed by PBS screening, different aggregation behaviours were observed between the K18 acetylated target peptide and the control sequences. Both assays are capable of identifying the acetylated peptides, and also differentiating the distinctive acetylation positions that differ merely by a distance of three amino acids.

Two helices in the third intracellular loop determine anoctamin 1 (TMEM16A) activation by calcium

Anoctamin 1 (ANO1)/TMEM16A is a Cl⁻ channel activated by intracellular Ca²⁺ mediating numerous physiological functions. However, little is known of the ANO1 activation mechanism by Ca²⁺. Here, we demonstrate that two helices, “reference” and “Ca²⁺ sensor” helices in the third intracellular loop face each other with opposite charges. The two helices interact directly in a Ca²⁺-dependent manner. Positively and negatively charged residues in the two helices are essential for Ca²⁺-dependent activation because neutralization of these charges change the Ca²⁺ sensitivity. We now predict that the Ca²⁺ sensor helix attaches to the reference helix in the resting state, and as intracellular Ca²⁺ rises, Ca²⁺ acts on the sensor helix, which repels it from the reference helix. This Ca²⁺-dependent push-pull conformational change would be a key electromechanical movement for gating the ANO1 channel. Because chemical activation of ANO1 is viewed as an alternative means of rescuing cystic fibrosis, understanding its gating mechanism would be useful in developing novel treatments for cystic fibrosis.

Developing epigenetic diagnostics and therapeutics for brain disorders

Perturbations in epigenetic mechanisms have emerged as cardinal features in the molecular pathology of major classes of brain disorders. We therefore highlight evidence which suggests that specific epigenetic signatures measurable in central - and possibly even in peripheral tissues - have significant value as translatable biomarkers for screening, early diagnosis, and prognostication; developing molecularly targeted medicines; and monitoring disease progression and treatment responses. We also draw attention to existing and novel therapeutic approaches directed at epigenetic factors and mechanisms, including strategies for modulating enzymes that write and erase DNA methylation and histone/chromatin marks; protein-protein interactions responsible for reading epigenetic marks; and non-coding RNA pathways.