PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave.

Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression. We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames in mRNA leader sequences. We also find that 60% of PAMP response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors (TFs) whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct mitogen-activated protein kinase control, support the notion that the rapidly induced TFs could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.

Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis.

Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that inactivation of the exosome subunit RRP45B and SKI2 results in similar patterns of miRNA-induced siRNA production. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that in exosome mutants, miRNA targets can be sorted into producers and non-producers of illicit secondary siRNAs based on trigger miRNA levels and miRNA:target affinity rather than on presence of 5'-cleavage fragments. We propose that stalled RNA-Induced Silencing Complex (RISC) and ribosomes, but not mRNA cleavage fragments released from RISC, trigger siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.

Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways.

In animals, RNA polymerase II initiates transcription bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are degraded by the nuclear exosome. Previous studies based on nascent RNA approaches concluded that Arabidopsis (Arabidopsis thaliana) does not produce PROMPTs. Here, we used steady-state RNA sequencing in mutants defective in nuclear RNA decay including the exosome to reassess the existence of Arabidopsis PROMPTs. While they are rare, we identified ∼100 cases of exosome-sensitive PROMPTs in Arabidopsis. Such PROMPTs are sources of small interfering RNAs in exosome-deficient mutants, perhaps explaining why plants have evolved mechanisms to suppress PROMPTs. In addition, we found ∼200 long, unspliced and exosome-sensitive antisense RNAs that arise from transcription start sites within parts of the genome encoding 3'-untranslated regions on the sense strand. The previously characterized noncoding RNA that regulates expression of the key seed dormancy regulator, DELAY OF GERMINATION1, is a typical representative of this class of RNAs. Transcription factor genes are overrepresented among loci with exosome-sensitive antisense RNAs, suggesting a potential for widespread control of gene expression via this class of noncoding RNAs. Lastly, we assess the use of alternative promoters in Arabidopsis and compare the accuracy of existing TSS annotations.

Organismal benefits of transcription speed control at gene boundaries.

RNA polymerase II (RNAPII) transcription is crucial for gene expression. RNAPII density peaks at gene boundaries, associating these key regions for gene expression control with limited RNAPII movement. The connections between RNAPII transcription speed and gene regulation in multicellular organisms are poorly understood. Here, we directly modulate RNAPII transcription speed by point mutations in the second largest subunit of RNAPII in Arabidopsis thaliana. A RNAPII mutation predicted to decelerate transcription is inviable, while accelerating RNAPII transcription confers phenotypes resembling auto-immunity. Nascent transcription profiling revealed that RNAPII complexes with accelerated transcription clear stalling sites at both gene ends, resulting in read-through transcription. The accelerated transcription mutant NRPB2-Y732F exhibits increased association with 5' splice site (5'SS) intermediates and enhanced splicing efficiency. Our findings highlight potential advantages of RNAPII stalling through local reduction in transcription speed to optimize gene expression for the development of multicellular organisms.

Emotional and Physical Health Impact in Children and Adolescents and Their Caregivers Using Open-source Automated Insulin Delivery: Qualitative Analysis of Lived Experiences.

BACKGROUND: Given the limitations in the access and license status of commercially developed automated insulin delivery (AID) systems, open-source AID systems are becoming increasingly popular among people with diabetes, including children and adolescents. OBJECTIVE: This study aimed to investigate the lived experiences and physical and emotional health implications of children and their caregivers following the initiation of open-source AID, their perceived challenges, and sources of support, which have not been explored in the existing literature. METHODS: Data were collected through 2 sets of open-ended questions from a web-based multinational survey of 60 families from 16 countries. The narratives were thematically analyzed, and a coding framework was identified through iterative alignment. RESULTS: A range of emotions and improvements in quality of life and physical health were reported, as open-source AID enabled families to shift their focus away from diabetes therapy. Caregivers were less worried about hypoglycemia at night and outside their family homes, leading to increased autonomy for the child. Simultaneously, the glycemic outcomes and sleep quality of both the children and caregivers improved. Nonetheless, the acquisition of suitable hardware and technical setup could be challenging. The #WeAreNotWaiting community was the primary source of practical and emotional support. CONCLUSIONS: Our findings show the benefits and transformative impact of open-source AID and peer support on children with diabetes and their caregivers and families, where commercial AID systems are not available or suitable. Further efforts are required to improve the effectiveness and usability and facilitate access for children with diabetes, worldwide, to benefit from this innovative treatment. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/15368.

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.

Fission yeast, Schizosaccharomyces pombe, is an attractive model organism for transcriptional and chromatin biology research. Such research is contingent on accurate annotation of transcription start sites (TSSs). However, comprehensive genome-wide maps of TSSs and their usage across commonly applied laboratory conditions and treatments for S. pombe are lacking. To this end, we profiled TSS activity genome-wide in S. pombe cultures exposed to heat shock, nitrogen starvation, hydrogen peroxide and two commonly applied media, YES and EMM2, using Cap Analysis of Gene Expression (CAGE). CAGE-based annotation of TSSs is substantially more accurate than existing PomBase annotation; on average, CAGE TSSs fall 50-75 bp downstream of PomBase TSSs and co-localize with nucleosome boundaries. In contrast to higher eukaryotes, dispersed TSS distributions are not common in S. pombe. Our data recapitulate known S. pombe stress expression response patterns and identify stress- and media-responsive alternative TSSs. Notably, alteration of growth medium induces changes of similar magnitude as some stressors. We show a link between nucleosome occupancy and genetic variation, and that the proximal promoter region is genetically diverse between S. pombe strains. Our detailed TSS map constitutes a central resource for S. pombe gene regulation research.

Why #WeAreNotWaiting-Motivations and Self-Reported Outcomes Among Users of Open-source Automated Insulin Delivery Systems: Multinational Survey.

BACKGROUND: Automated insulin delivery (AID) systems have been shown to be safe and effective in reducing hyperglycemia and hypoglycemia but are not universally available, accessible, or affordable. Therefore, user-driven open-source AID systems are becoming increasingly popular. OBJECTIVE: This study aims to investigate the motivations for which people with diabetes (types 1, 2, and other) or their caregivers decide to build and use a personalized open-source AID. METHODS: A cross-sectional web-based survey was conducted to assess personal motivations and associated self-reported clinical outcomes. RESULTS: Of 897 participants from 35 countries, 80.5% (722) were adults with diabetes and 19.5% (175) were caregivers of children with diabetes. Primary motivations to commence open-source AID included improving glycemic outcomes (476/509 adults, 93.5%, and 95/100 caregivers, 95%), reducing acute (443/508 adults, 87.2%, and 96/100 caregivers, 96%) and long-term (421/505 adults, 83.3%, and 91/100 caregivers, 91%) complication risk, interacting less frequently with diabetes technology (413/509 adults, 81.1%; 86/100 caregivers, 86%), improving their or child's sleep quality (364/508 adults, 71.6%, and 80/100 caregivers, 80%), increasing their or child's life expectancy (381/507 adults, 75.1%, and 84/100 caregivers, 84%), lack of commercially available AID systems (359/507 adults, 70.8%, and 79/99 caregivers, 80%), and unachieved therapy goals with available therapy options (348/509 adults, 68.4%, and 69/100 caregivers, 69%). Improving their own sleep quality was an almost universal motivator for caregivers (94/100, 94%). Significant improvements, independent of age and gender, were observed in self-reported glycated hemoglobin (HbA1c), 7.14% (SD 1.13%; 54.5 mmol/mol, SD 12.4) to 6.24% (SD 0.64%; 44.7 mmol/mol, SD 7.0; P<.001), and time in range (62.96%, SD 16.18%, to 80.34%, SD 9.41%; P<.001). CONCLUSIONS: These results highlight the unmet needs of people with diabetes, provide new insights into the evolving phenomenon of open-source AID technology, and indicate improved clinical outcomes. This study may inform health care professionals and policy makers about the opportunities provided by open-source AID systems. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/15368.

CAGEfightR: analysis of 5'-end data using R/Bioconductor.

BACKGROUND: 5'-end sequencing assays, and Cap Analysis of Gene Expression (CAGE) in particular, have been instrumental in studying transcriptional regulation. 5'-end methods provide genome-wide maps of transcription start sites (TSSs) with base pair resolution. Because active enhancers often feature bidirectional TSSs, such data can also be used to predict enhancer candidates. The current availability of mature and comprehensive computational tools for the analysis of 5'-end data is limited, preventing efficient analysis of new and existing 5'-end data. RESULTS: We present CAGEfightR, a framework for analysis of CAGE and other 5'-end data implemented as an R/Bioconductor-package. CAGEfightR can import data from BigWig files and allows for fast and memory efficient prediction and analysis of TSSs and enhancers. Downstream analyses include quantification, normalization, annotation with transcript and gene models, TSS shape statistics, linking TSSs to enhancers via co-expression, identification of enhancer clusters, and genome-browser style visualization. While built to analyze CAGE data, we demonstrate the utility of CAGEfightR in analyzing nascent RNA 5'-data (PRO-Cap). CAGEfightR is implemented using standard Bioconductor classes, making it easy to learn, use and combine with other Bioconductor packages, for example popular differential expression tools such as limma, DESeq2 and edgeR. CONCLUSIONS: CAGEfightR provides a single, scalable and easy-to-use framework for comprehensive downstream analysis of 5'-end data. CAGEfightR is designed to be interoperable with other Bioconductor packages, thereby unlocking hundreds of mature transcriptomic analysis tools for 5'-end data. CAGEfightR is freely available via Bioconductor: bioconductor.org/packages/CAGEfightR .

Out-of-pocket expenses and rationing of insulin and diabetes supplies: findings from the 2022 T1International cross-sectional web-based survey.

Introduction: Continue investigating Out-of-Pocket Expenses (OoPEs) and rationing of insulin and diabetes supplies, including impacts of the COVID-19 pandemic, for people with type 1 diabetes (T1D). Methods: A cross-sectional web-based survey was conducted in English and advertised by T1International's global network of patient advocates from May through September 2022. Participants provided monthly OoPEs and rationing frequency for insulin and supplies, impacts of the COVID-19 pandemic, and open-ended comments. Results: In the seven most represented countries, mean monthly OoPEs were highest in the United States, followed by Panama, Canada, and India, and were much lower in the United Kingdom, Germany, and Sweden. OoPEs were highest for participants with partial healthcare coverage, followed by those with no healthcare coverage. The COVID-19 pandemic negatively impacted access and/or affordability of insulin and/or supplies for over half of participants. Globally, 19.5% reported insulin rationing and 36.6% reported rationing glucose testing supplies. Qualitative analysis of open-ended responses identified themes such as 'mental health impacts' and 'limits to life choices.' Discussion: High OoPEs lead to rationing of insulin and supplies for many people with T1D globally. Healthcare systems improvements and price reductions of insulin and supplies are needed to ensure adequate, equitable access for all.

Costs and underuse of insulin and diabetes supplies: Findings from the 2020 T1International cross-sectional web-based survey.

AIMS: To investigate self-reported out-of-pocket expenses (OoPE) associated with insulin and diabetes supplies for people living with type 1 diabetes (T1D) worldwide. METHODS: A web-based, cross-sectional survey was conducted from August to December 2020. The analysis included comparisons between responses from countries with no, partial, and full healthcare coverage. RESULTS: 1,066 participants from 64 countries took part in the study. ~25% of respondents reported having underused insulin at least once within the last year due to perceived cost. A significant correlation was observed between OoPEs and reported household income for respondents with partial healthcare coverage. 63.2% of participants reported disruption of insulin supplies and 25.3% reported an increase of prices related to the COVID-19 pandemic. CONCLUSIONS: This study confirms previous reports of ~25% of people in the United States with T1D using less insulin and/or fewer supplies at least once in the last year due to cost, a trend associated with the extent of healthcare coverage. Similar trends were observed in some middle/low income countries. Moreover, patients reported an increase in insulin prices and disruption of supplies during the COVID-19 pandemic. This study highlights the importance of self-reported OoPEs and its association with underuse/rationing of insulin.

Shaping Workflows in Digital and Remote Diabetes Care During the COVID-19 Pandemic via Service Design: Prospective, Longitudinal, Open-label Feasibility Trial.

BACKGROUND: The COVID-19 pandemic poses new challenges to health care providers and the delivery of continuous care. Although many diabetes technologies, such as insulin pumps and continuous glucose monitors, have been established, the data from these devices are rarely assessed. Furthermore, telemedicine has not been sufficiently integrated into clinical workflows. OBJECTIVE: We sought to remotely support children with type 1 diabetes and their caregivers, enhance the clinical outcomes and quality of life of children with diabetes, increase multiple stakeholders' engagement with digital care via a participatory approach, evaluate the feasibility of using an interoperable open-source platform in a university hospital setting, and analyze the success factors and barriers of transitioning from conventional care to digital care. METHODS: Service design methods were used to adapt clinical workflows. Remote consultations were performed on a monthly and on-demand basis. Diabetes device data were uploaded from patients' homes to an open-source platform. Clinical and patient-reported outcomes were assessed before, during, and after the COVID-19 lockdown period in Germany. RESULTS: A total of 28 children with type 1 diabetes and their caregivers enrolled in this study and completed 6 months of remote visits. Of these 28 participants, 16 (57%) also opted to attend at least one of their regular visits remotely. After 3 months of remote visits, participants' time in range (P=.001) and time in hyperglycemia (P=.004) significantly improved, and their time in hypoglycemia did not increase. These improvements were maintained during the COVID-19 lockdown period (ie, between months 3 and 6 of this study). Participants' psychosocial health improved after 6 months. CONCLUSIONS: Remote consultations and commonly shared data access can improve the clinical outcomes and quality of life of children with type 1 diabetes, even during challenging circumstances. A service design approach helped with the delivery of comprehensive and holistic solutions that accounted for the needs of multiple stakeholders. Our findings can inform the future integration of digital tools into clinical care during and beyond the pandemic. TRIAL REGISTRATION: German Clinical Trials Register DRKS00016170; https://tinyurl.com/skz4wdk5.

A new class of genic nuclear RNA species in Arabidopsis.

Targeting of ArabidopsisPHABULOSA (PHB) mRNA by miR166 has been implicated in gene body methylation at the PHB locus. We report that the PHB locus produces an array of stable nuclear RNA species that are neither polyadenylated nor capped. Their biogenesis requires neither RNA polymerases IV/V nor miR166-guided cleavage. The PHB RNAs are insensitive to mutation of nuclear RNA decay pathways and are conserved in several Brassicaceae species, suggesting functional relevance. Similar RNA species are also produced by another body-methylated locus encoding the miR414 target eIF2. Our data reveal the existence of a new class of genic nuclear RNA species.