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1.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38605641

ABSTRACT

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.


Subject(s)
Genome , RNA , RNA-Seq , Sequence Analysis, RNA , Computer Simulation , RNA/genetics , High-Throughput Nucleotide Sequencing
2.
Sci Transl Med ; 15(696): eabo2022, 2023 05 17.
Article in English | MEDLINE | ID: mdl-37196066

ABSTRACT

Longitudinal studies associate shiftwork with cardiometabolic disorders but do not establish causation or elucidate mechanisms of disease. We developed a mouse model based on shiftwork schedules to study circadian misalignment in both sexes. Behavioral and transcriptional rhythmicity were preserved in female mice despite exposure to misalignment. Females were protected from the cardiometabolic impact of circadian misalignment on a high-fat diet seen in males. The liver transcriptome and proteome revealed discordant pathway perturbations between the sexes. Tissue-level changes were accompanied by gut microbiome dysbiosis only in male mice, biasing toward increased potential for diabetogenic branched chain amino acid production. Antibiotic ablation of the gut microbiota diminished the impact of misalignment. In the United Kingdom Biobank, females showed stronger circadian rhythmicity in activity and a lower incidence of metabolic syndrome than males among job-matched shiftworkers. Thus, we show that female mice are more resilient than males to chronic circadian misalignment and that these differences are conserved in humans.


Subject(s)
Cardiovascular Diseases , Gastrointestinal Microbiome , Humans , Male , Female , Animals , Mice , Diet, High-Fat , Sex Characteristics , Circadian Rhythm
3.
bioRxiv ; 2023 Apr 24.
Article in English | MEDLINE | ID: mdl-37162982

ABSTRACT

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

4.
BMC Genomics ; 22(1): 692, 2021 Sep 25.
Article in English | MEDLINE | ID: mdl-34563123

ABSTRACT

BACKGROUND: The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accurately assess the performance of RNA-Seq analysis methods. However, existing RNA-Seq simulators focus on modeling the technical biases and artifacts of sequencing, rather than on simulating the original RNA samples. A first step in simulating RNA-Seq is to simulate RNA. RESULTS: To fill this need, we developed the Configurable And Modular Program Allowing RNA Expression Emulation (CAMPAREE), a simulator using empirical data to simulate diploid RNA samples at the level of individual molecules. We demonstrated CAMPAREE's use for generating idealized coverage plots from real data, and for adding the ability to generate allele-specific data to existing RNA-Seq simulators that do not natively support this feature. CONCLUSIONS: Separating input sample modeling from library preparation/sequencing offers added flexibility for both users and developers to mix-and-match different sample and sequencing simulators to suit their specific needs. Furthermore, the ability to maintain sample and sequencing simulators independently provides greater agility to incorporate new biological findings about transcriptomics and new developments in sequencing technologies. Additionally, by simulating at the level of individual molecules, CAMPAREE has the potential to model molecules transcribed from the same genes as a heterogeneous population of transcripts with different states of degradation and processing (splicing, editing, etc.). CAMPAREE was developed in Python, is open source, and freely available at https://github.com/itmat/CAMPAREE .


Subject(s)
High-Throughput Nucleotide Sequencing , Software , Algorithms , Gene Expression Profiling , RNA/genetics , Sequence Analysis, RNA
5.
BMC Bioinformatics ; 22(1): 266, 2021 May 25.
Article in English | MEDLINE | ID: mdl-34034652

ABSTRACT

BACKGROUND: Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short. RESULTS: Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control. CONCLUSIONS: Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively.


Subject(s)
Gene Expression Profiling , Transcriptome , Protein Isoforms/genetics , RNA-Seq , Sequence Analysis, RNA
6.
Nat Commun ; 10(1): 4107, 2019 09 11.
Article in English | MEDLINE | ID: mdl-31511530

ABSTRACT

Influenza is a leading cause of respiratory mortality and morbidity. While inflammation is essential for fighting infection, a balance of anti-viral defense and host tolerance is necessary for recovery. Circadian rhythms have been shown to modulate inflammation. However, the importance of diurnal variability in the timing of influenza infection is not well understood. Here we demonstrate that endogenous rhythms affect survival in influenza infection. Circadian control of influenza infection is mediated by enhanced inflammation as proven by increased cellularity in bronchoalveolar lavage (BAL), pulmonary transcriptomic profile and histology and is not attributable to viral burden. Better survival is associated with a time dependent preponderance of NK and NKT cells and lower proportion of inflammatory monocytes in the lung. Further, using a series of genetic mouse mutants, we elucidate cellular mechanisms underlying circadian gating of influenza infection.


Subject(s)
Circadian Rhythm/physiology , Orthomyxoviridae Infections/complications , Orthomyxoviridae Infections/physiopathology , Pneumonia/complications , Pneumonia/physiopathology , ARNTL Transcription Factors/deficiency , ARNTL Transcription Factors/metabolism , Animals , Antigens, Ly , Female , Influenza A virus/physiology , Male , Mice, Inbred C57BL , Mice, Knockout , Monocytes/metabolism , Myeloid Cells/metabolism , Natural Killer T-Cells/immunology , Orthomyxoviridae Infections/genetics , Orthomyxoviridae Infections/virology , Phenotype , Pneumonia/virology , Time Factors , Transcriptome/genetics , Virus Replication
7.
Elife ; 72018 12 05.
Article in English | MEDLINE | ID: mdl-30516472

ABSTRACT

Transcription-translation feedback loops that comprise eukaryotic circadian clocks rely upon temporal delays that separate the phase of active transcription of clock genes, such as Drosophila period (per) and timeless (tim), from negative feedback by the two proteins. However, our understanding of the mechanisms involved is incomplete. Through an RNA interference screen, we found that pre-mRNA processing 4 (PRP4) kinase, a component of the U4/U5.U6 triple small nuclear ribonucleoprotein (tri-snRNP) spliceosome, and other tri-snRNP components regulate cycling of the molecular clock as well as rest:activity rhythms. Unbiased RNA-Sequencing uncovered an alternatively spliced intron in tim whose increased retention upon prp4 downregulation leads to decreased TIM levels. We demonstrate that the splicing of tim is rhythmic with a phase that parallels delayed accumulation of the protein in a 24 hr cycle. We propose that alternative splicing constitutes an important clock mechanism for delaying the daily accumulation of clock proteins, and thereby negative feedback by them. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).


Subject(s)
CLOCK Proteins/genetics , Drosophila Proteins/genetics , Drosophila melanogaster/genetics , Feedback, Physiological , RNA Splicing , Spliceosomes/genetics , Animals , CLOCK Proteins/metabolism , Circadian Clocks/genetics , Circadian Rhythm/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/metabolism , Exons , Introns , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Period Circadian Proteins/genetics , Period Circadian Proteins/metabolism , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism , Sequence Analysis, RNA , Signal Transduction , Spliceosomes/metabolism
8.
PLoS One ; 13(7): e0200477, 2018.
Article in English | MEDLINE | ID: mdl-29995933

ABSTRACT

Synapse associated protein of 97KDa (SAP97) belongs to a family of scaffolding proteins, the membrane-associated guanylate kinases (MAGUKs), that are highly enriched in the postsynaptic density of synapses and play an important role in organizing protein complexes necessary for synaptic development and plasticity. The Dlg-MAGUK family of proteins are structurally very similar, and an effort has been made to parse apart the unique function of each Dlg-MAGUK protein by characterization of knockout mice. Knockout mice have been generated and characterized for PSD-95, PSD-93, and SAP102, however SAP97 knockout mice have been impossible to study because the SAP97 null mice die soon after birth due to a craniofacial defect. We studied the transcriptomic and behavioral consequences of a brain-specific conditional knockout of SAP97 (SAP97-cKO). RNA sequencing from hippocampi from control and SAP97-cKO male animals identified 67 SAP97 regulated transcripts. As large-scale genetic studies have implicated MAGUKs in neuropsychiatric disorders such as intellectual disability, autism spectrum disorders, and schizophrenia (SCZ), we analyzed our differentially expressed gene (DEG) set for enrichment of disease risk-associated genes, and found our DEG set to be specifically enriched for SCZ-related genes. Subjecting SAP97-cKO mice to a battery of behavioral tests revealed a subtle male-specific cognitive deficit and female-specific motor deficit, while other behaviors were largely unaffected. These data suggest that loss of SAP97 may have a modest contribution to organismal behavior. The SAP97-cKO mouse serves as a stepping stone for understanding the unique role of SAP97 in biology.


Subject(s)
Behavior, Animal , Discs Large Homolog 1 Protein/metabolism , Gene Expression Regulation , Hippocampus/metabolism , Schizophrenia/metabolism , Animals , Discs Large Homolog 1 Protein/genetics , Female , Hippocampus/pathology , Mice , Mice, Knockout , Schizophrenia/genetics , Schizophrenia/physiopathology
9.
Int J Biochem Cell Biol ; 93: 129-135, 2017 12.
Article in English | MEDLINE | ID: mdl-28860003

ABSTRACT

Sleep curtailment is ubiquitous in modern day society. Sleep debt is associated with maladaptive physiological changes that can lead to cardiometabolic and neuropsychiatric pathologies. Recent literature has shown the effects of sleep restriction (SR) on systemic metabolic profiles in biofluids, implying that tissue-specific metabolomes are impacted by SR. To test this hypothesis, we assessed hepatic metabolic profiles of rats after 5days of SR using UPLC-MS based metabolomics analysis and gene expression analysis. Our data suggests distinctive effects of SR on the liver metabolic profile of rats compared to forced-activity control animals. We observed specific impacts of SR on NAD metabolism through NAD accumulation and upregulation of Nampt, the rate determining step of NAD salvage. Additional multi-omic changes were observed in methionine metabolism, with an elevated SAM:SAH ratio under SR. This effect on one carbon metabolism is indicative of increased methylation potential. Changes in TCA cycle intermediates and ATP-citrate lyase (Acly) gene expression were observed that may be related to altered circulatory lipid profiles previously reported documenting the chrono-metabolic connection. Taken together with previous investigations, these observations are consistent with a model of decreased TCA activity with concomitant increase in lipogenesis induced by SR. These tissue-specific mechanistic insights into metabolic effects of SR provide a springboard to future metabolic intervention studies.


Subject(s)
Energy Metabolism , Lipogenesis , Liver/metabolism , Sleep Deprivation/metabolism , Animals , Gene Expression Profiling , Liver/pathology , Male , Metabolomics , Methylation , Rats , Rats, Sprague-Dawley , Sleep Deprivation/pathology
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