Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.

Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has transformed our understanding of differentiation during development, regeneration, and disease. However, lineage tracing is technically demanding, often restricted in time-resolution, and most scRNA-seq datasets are devoid of lineage information. Here we introduce Gene Expression Memory-based Lineage Inference (GEMLI), a computational tool allowing to robustly identify small to medium-sized cell lineages solely from scRNA-seq datasets. GEMLI allows to study heritable gene expression, to discriminate symmetric and asymmetric cell fate decisions and to reconstruct individual multicellular structures from pooled scRNA-seq datasets. In human breast cancer biopsies, GEMLI reveals previously unknown gene expression changes at the onset of cancer invasiveness. The universal applicability of GEMLI allows studying the role of small cell lineages in a wide range of physiological and pathological contexts, notably in vivo. GEMLI is available as an R package on GitHub ( https://github.com/UPSUTER/GEMLI ).

Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.

Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.

Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast.

The RPB1 mutants in the foot region of RNA polymerase II affect the assembly of the complex by altering the correct association of both the Rpb6 and the Rpb4/7 dimer. Assembly defects alter both transcriptional activity as well as the amount of enzyme associated with genes. Here, we show that the global transcriptional analysis of foot mutants reveals the activation of an environmental stress response (ESR), which occurs at a permissive temperature under optimal growth conditions. Our data indicate that the ESR that occurs in foot mutants depends mostly on a global post-transcriptional regulation mechanism which, in turn, depends on Rpb4-mRNA imprinting. Under optimal growth conditions, we propose that Rpb4 serves as a key to globally modulate mRNA stability as well as to coordinate transcription and decay. Overall, our results imply that post-transcriptional regulation plays a major role in controlling the ESR at both the transcription and mRNA decay levels.

Antacid (A02A) and antiulcer (A02B) drug prescription patterns: predicting factors, dosage and treatment duration.

BACKGROUND: A study is made of the pharmaco-epidemiology of antacid (ATC class A02A) and antiulcer (A02B) drug prescriptions during the year 1992. METHODS: Prescription data were extracted from 1941 case histories of patients over 15 years old from four health care centers in the Valencian Community (Spain). Dosage and treatment duration were evaluated, along with the way in which morbidity, self-evaluated health, the demographic pattern and life-style characteristics influence drug prescription. RESULTS: The proportion of drug prescriptions increased with age in both sexes (p < 0.01). Drug use depended mainly on chronic diseases. In prescribing antacids, the most influential diagnosis was gastritis (ICD 534, OR: 157), followed by duodenal ulcer (ICD 532, OR: 152) and gastric ulcer (ICD 531, OR: 122), other gastrointestinal disorders (ICD 66, OR: 54) and undefined diagnoses (OR: 15). In the prescription of antiulcer drugs, the most influential diagnoses were gastric and duodenal ulcer (OR: 380 and 342, respectively), and a significant relation was observed with the diagnosis of osteomuscular diseases (OR: 6). Lifestyle and demographic pattern were of marginal importance. The estimated duration of treatment was 85 days. No significant differences were observed in either treatment duration or administered doses of almagate, ranitidine and omeprazole with respect to sex, age or diagnosis. CONCLUSIONS: Prolonged treatment is common for acid suppression. The widespread use of peptic ulcer drugs is mostly due to excessive prescription for non-ulcer dyspepsia. At the same time, many patients consume these drugs on a long-term basis in the absence of a clear diagnosis. This observation supports the need for appropriate diagnostic and prescription protocols to secure increased economical savings and management results.