The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method mapping accessibility due to its time and input material efficiency. However, it can be difficult evaluate data quality identify sources of technical bias across samples. Here, we present ataqv, a computational toolkit efficiently measuring, visualizing, comparing control (QC) results samples experiments. We use ataqv analyze 2,009 public ATAC-seq datasets; their QC metrics display...

Abstract STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the complexity depth is that coverage in experiments non-uniform, overdispersed, often confounded by biases, such as GC content. Furthermore, readout RNA secondary structure thermodynamic stability. To address these potential confounders, we developed a negative binomial regression framework for uniformly processing data, called STARRPeaker. Moreover, to aid...

Cooperative, synergistic gene regulation by nuclear hormone receptors can increase sensitivity and amplify cellular responses to hormones. We investigated thyroid (TH) glucocorticoid (GC) synergy on the Krüppel-like factor 9 (Klf9) gene, which codes for a zinc finger transcription involved in development homeostasis of diverse tissues. identified regions Xenopus mouse Klf9 genes 5-6 kb upstream start sites that supported transactivation TH plus GC. Within these regions, we found an...

A central feature of models associative memory formation is the reliance on information convergence from pathways responsive to conditioned stimulus (CS) and unconditioned (US). In particular, cells receiving coincident input are held be critical for subsequent plasticity. Yet identification neurons in mammalian brain that respond such inputs during a learning event remains elusive. Here we use Arc cellular compartmental analysis temporal gene transcription by fluorescence situ hybridization...

Abstract Interactions between transcription factors and chromatin are fundamental to genome organization regulation and, ultimately, cell state. Here, we use information theory measure signatures of organized resulting from factor-chromatin interactions encoded in the patterns accessible genome, which term enrichment (CIE). We calculate CIE for hundreds factor motifs across human samples identify two classes: low high CIE. The 10–20% common tissue-specific motifs, associate with higher...

Thyroid hormone (T3) is essential for proper neurological development. The hormone, bound to its receptors, regulates gene transcription in part by modulating posttranslational modifications of histones. Methylation DNA, which established the de novo DNA methyltransferase (DNMT)3a and DNMT3b, maintained DNMT1 another epigenetic modification influencing transcription. expression Dnmt3a, but not other Dnmt genes, increases mouse brain parallel with postnatal rise plasma [T3]. We found that...

Atypical antipsychotic (AAP) medication is a critical tool for treating symptoms of psychiatric disorders. While AAPs primarily target dopamine (D2) and serotonin (5HT2A 5HT1A) receptors, they also exhibit intrinsic antimicrobial activity as an off-target effect. Because are often prescribed to patients many years, potential risk associated with long-term AAP use the unintended emergence bacteria resistance (AMR). Here, we show that exposure quetiapine at estimated gut concentrations...

Thyroid hormone is essential for normal development in vertebrates. In amphibians, T3 controls metamorphosis by inducing tissue-specific gene regulation programs. A hallmark of action the modification chromatin structure, which underlies changes transcription. We found that mRNA de novo DNA methyltransferase (DNMT) dnmt3a, but not dnmt1, increased brain Xenopus tadpoles during parallel with plasma [T3]. Addition to rearing water caused a time-dependent increase dnmt3a tadpole brain, tail,...

Thyroid hormone (T3) plays pivotal roles in vertebrate development, acting via nuclear T3 receptors (TRs) that regulate gene transcription by promoting post-translational modifications to histones. Methylation of cytosine residues deoxyribonucleic acid (DNA) also modulates transcription, and our recent finding predominant DNA demethylation the brain Xenopus tadpoles at metamorphosis, a T3-dependent developmental process, caused us hypothesize induces these changes vivo. Treatment...

In vertebrates, multiple transcription factors (TFs) bind to gene regulatory elements (promoters, enhancers, and silencers) execute developmental expression changes. ChIP experiments are often used identify where TFs in the genome, but requirement of TF-specific antibodies hampers analyses tens at loci. Here we tested whether TF binding predictions using ATAC-seq can be infer identity that functionally validated enhancers Cd4, Cd8, Gata3 genes thymocytes. We performed four distinct stages...

Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene mechanisms. Here, we identify transcription start sites (TSS) using cap analysis expression (CAGE) across 57 human pancreatic islet samples. We 9,954 reproducible CAGE tag clusters (TCs), ∼20% which are specific and occur mostly distal known TSS. integrated data with histone modification chromatin accessibility profiles epigenomic initiation. Using a massively parallel reporter...

Abstract Background High-throughput reporter assays, such as self-transcribing active regulatory region sequencing (STARR-seq), allow for unbiased and quantitative assessment of enhancers at a genome-wide scale. Recent advances in STARR-seq technology have employed progressively more complex genomic libraries increased depths, to assay larger sized regions, up the entire human genome. These necessitate reliable processing pipeline peak-calling algorithm. Results Most studies relied on...

The combination of carbapenem resistance and hypervirulence in Klebsiella pneumoniae is an emerging urgent threat due to its potential resist common antibiotics cause life-threatening infections healthy hosts. This study aimed evaluate the activity clinically relevant antibiotic regimens against carbapenem-resistant K. with plasmids identify pathways associated tolerance using transcriptomics. We studied two isolates, CDI694 CDI231, both harboring plasmids. Time-kill dynamic one-compartment...

Amphibian metamorphosis is controlled by thyroid hormone (TH), which binds TH receptors (TRs) to regulate gene expression programs that underlie morphogenesis. Gene screens using tissues from premetamorphic tadpoles treated with identified some target genes, but few studies have analyzed genome-wide changes in regulation during spontaneous metamorphosis. We RNA sequencing data at four developmental stages the beginning end of metamorphosis, conducted on neuroendocrine centers Xenopus...

Abstract Transposon directed insertion-site sequencing (TraDIS), a variant of transposon insertion commonly known as Tn-Seq, is high-throughput assay that defines essential bacterial genes across diverse growth conditions. However, the variability between laboratory environments often requires laborious, time-consuming modifications to its protocol. In this technical study, we aimed refine protocol by identifying key parameters can impact complexity mutant libraries. Firstly, discovered...

Introduction & Objective: Massively parallel reporter assays (MPRAs) are an increasingly popular method of assessing the sequence-dependent activity variants associated with complex diseases such as type 2 diabetes (T2D). Many MPRA libraries use a single plasmid configuration, minimal promoter, and strand orientation, which may fail to capture context-dependent expression T2D-associated cis-regulatory elements. Here, we interrogate potential differences introduced by variable...

Abstract Recent genome-wide association studies have established that most complex disease-associated loci are found in noncoding regions where defining their function is nontrivial. In this study, we leverage a modular massively parallel reporter assay (MPRA) to uncover sequence features linked context-specific regulatory activity. We screened enhancer activity across panel of 198-bp fragments spanning over 10k type 2 diabetes- and metabolic trait-associated variants the 832/13 rat...

Abstract Interactions between transcription factors (TFs) and chromatin are fundamental to genome organization regulation and, ultimately, cell state. Here, we use information theory measure signatures of TF-chromatin interactions encoded in the patterns accessible genome, which call enrichment (CIE). We calculate CIE for hundreds TF motifs across human tissues identify two classes: low high CIE. The 10-20% with associate higher protein-DNA residence time, including different binding sites...

Abstract Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene mechanisms. Here, we identify transcription start sites (TSS) using cap analysis expression (CAGE) across 57 human pancreatic islet samples. We 9,954 reproducible CAGE tag clusters (TCs), ~20% which are islet-specific and occur mostly distal known TSSs. integrated data with histone modification chromatin accessibility profiles epigenomic initiation. Using a massively...