Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids.

BACKGROUND: N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability is driven by changes in genetic sequences ('cis') or cellular environments ('trans') and via which mechanisms. RESULTS: Here we dissect the determinants governing RNA methylation via interspecies and intraspecies hybrids in yeast and mammalian systems, coupled with massively parallel reporter assays and m6A-QTL reanalysis. We find that m6A evolution and variability is driven primarily in 'cis', via two mechanisms: (1) variations altering m6A consensus motifs, and (2) variation impacting mRNA secondary structure. We establish that mutations impacting RNA structure - even when distant from an m6A consensus motif - causally dictate methylation propensity. Finally, we demonstrate that allele-specific differences in m6A levels lead to allele-specific changes in gene expression. CONCLUSIONS: Our findings define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.

N4-acetylcytidine (ac4C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA1-3. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac4C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac4C at single-nucleotide resolution. In human and yeast mRNAs, ac4C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac4C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac4C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac4C and its potential thermoadaptive role. Our studies quantitatively define the ac4C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease4-6.

Deciphering the "m6A Code" via Antibody-Independent Quantitative Profiling.

N6-methyladenosine (m6A) is the most abundant modification on mRNA and is implicated in critical roles in development, physiology, and disease. A major limitation has been the inability to quantify m6A stoichiometry and the lack of antibody-independent methodologies for interrogating m6A. Here, we develop MAZTER-seq for systematic quantitative profiling of m6A at single-nucleotide resolution at 16%-25% of expressed sites, building on differential cleavage by an RNase. MAZTER-seq permits validation and de novo discovery of m6A sites, calibration of the performance of antibody-based approaches, and quantitative tracking of m6A dynamics in yeast gametogenesis and mammalian differentiation. We discover that m6A stoichiometry is "hard coded" in cis via a simple and predictable code, accounting for 33%-46% of the variability in methylation levels and allowing accurate prediction of m6A loss and acquisition events across evolution. MAZTER-seq allows quantitative investigation of m6A regulation in subcellular fractions, diverse cell types, and disease states.

Use of a Digital Medication Management System for Effective Assessment and Enhancement of Patient Adherence to Therapy (ReX): Feasibility Study.

BACKGROUND: Medication nonadherence is a major problem in health care, imposing poor clinical outcomes and a heavy financial burden on all stakeholders. Current methods of medication adherence assessment are severely limited: they are applied only periodically, do not relate to actual pill intake, and suffer from patient bias due to errors, misunderstanding, or intentional nonadherence. ReX is an innovative medication management system designed to address poor patient adherence and enhance patient engagement with their therapy. ReX controls and tracks pills from the point of packaging right through to the patient's mouth. ReX generates robust, real-time adherence data. The system enables patients to report outcomes, complete surveys, and receive messages and instructions. ReX includes a reusable drug dispensing unit, disposable cassette containing pills, and a cloud-based data portal. OBJECTIVE: We aimed to evaluate ReX feasibility by human factor studies including evaluation of ReX safety; ReX acceptance and usability; and ReX efficacy of providing pills according to a preprogrammed dose regimen, managing reminders and adherence data, and enhancing the adherence rate compared with the standard of care. METHODS: The ReX system was evaluated in 2 human factor, nonclinical feasibility studies. Human subjects used ReX for the administration of pill-shaped Tic Tac sweets. The initial study evaluated ReX use and pill intake administration; second was a self-controlled, 4-day home-use study. All subjects took pills at home, according to a preprogrammed dose regimen, for 4 days each via the device (ReX test) or from standard packaging (control test). The adherence rate (percent of pills taken) was measured by the study subject's report, remaining pills count, and ReX records (in the ReX test). ReX safety and usability were evaluated by a questionnaire filled out by the subject. RESULTS: The initial feasibility study evaluated usability and acceptance of the ReX novel approach to pill dispensing. All subjects successfully managed 2 pill intakes. The ReX device was rated as easy to use by 81% (48/59) of subjects. The 4-day home-use study evaluated the safety, efficacy, and usability of the ReX system. No adverse event occurred; no pill overdose or pill malformation was reported. The overall adherence rate in the ReX test was 97.6% compared with 76.3% in the control test (P<.001). Real-time, personalized reminders provided in the event of a delay in pill intake contributed to 18.0% of doses taken during the ReX test. The ReX system was found easy to use by 87% (35/40) of subjects; 90% (36/40) felt comfortable using it for their medication. CONCLUSIONS: ReX's novel "tracking to the mouth" technology was found usable and accepted by subjects. The assessment of adherence rates was reliable; adherence of subjects to the dose regimen was significantly enhanced when using ReX compared with the standard of care.