Transcriptome data are insufficient to control false discoveries in regulatory network inference

Cell Systems, Год журнала: 2024, Номер 15(8), С. 709 - 724.e13

Опубликована: Авг. 1, 2024

Inference of causal transcriptional regulatory networks (TRNs) from transcriptomic data suffers notoriously false positives. Approaches to control the discovery rate (FDR), for example, via permutation, bootstrapping, or multivariate Gaussian distributions, suffer several complications: difficulty in distinguishing direct indirect regulation, nonlinear effects, and structure inference requiring "causal sufficiency," meaning experiments that are free any unmeasured, confounding variables. Here, we use a recently developed statistical framework, model-X knockoffs, FDR while accounting dose-response, user-provided covariates. We adjust procedure estimate correctly even when measured against incomplete gold standards. However, benchmarking chromatin immunoprecipitation (ChIP) other standards reveals higher observed than reported FDR. This indicates unmeasured is major driver TRN inference. A record this paper's transparent peer review process included supplemental information.

Язык: Английский

---

Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs

NAR Genomics and Bioinformatics, Год журнала: 2025, Номер 7(1)

Опубликована: Янв. 7, 2025

Abstract Understanding the role of transcription and factors (TFs) in cellular identity disease, such as cancer, is essential. However, comprehensive data resources for cell line-specific TF-to-target gene annotations are currently limited. To address this, we employed a straightforward method to define regulons that capture cell-specific aspects TF binding transcript expression levels. By integrating transcriptome data, generated 40 common lines comprising both proximal distal regulatory events. Through systematic benchmarking involving knockout experiments, demonstrated performance on par with state-of-the-art methods, our being easily applicable other types interest. We present case studies using three cancer single-cell datasets showcase utility these cell-type-specific exploring transcriptional dysregulation. In summary, this study provides valuable pipeline resource systematically regulations, emphasizing network analysis deciphering disease mechanisms.

Язык: Английский

---

Massively parallel assessment of gene regulatory activity at human cortical structure associated variants

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 8, 2025

Abstract Genetic association studies have identified hundreds of largely non-coding loci associated with inter-individual differences in the structure human cortex, though specific genetic variants that impact regulatory activity are unknown. We implemented a Massively Parallel Reporter Assay (MPRA) to measure 9,092 cortical DNA neural progenitor cells during Wnt stimulation and at baseline. 918 potential from 150 (76% studied), which >50% showed allelic effects. modified subset functioned as condition-dependent enhancers. Regulatory MPRA was induced by Alu elements were hypothesized contribute expansion. The regionally disrupt motifs is likely mediated through levels transcription factor expression development, further clarifying molecular mechanisms altering structure.

Язык: Английский

---

Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma

Molecular Cell, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

---

Programmable promoter editing for precise control of transgene expression

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 20, 2024

Subtle changes in gene expression direct cells to distinct cellular states. Identifying and controlling dose-dependent transgenes require tools for precisely titrating expression. To this end, we developed a highly modular, extensible framework called DIAL building editable promoters that allow fine-scale, heritable transgene Using DIAL, increase by recombinase-mediated excision of spacers between the binding sites synthetic zinc finger transcription factor core promoter. By nesting varying numbers lengths spacers, generates tunable range unimodal setpoints from single Through small-molecule control factors recombinases, supports temporally defined, user-guided is additional factors. Lentiviral delivery multiple primary iPSCs. As promoter editing stable states, are heritable, facilitating mapping levels phenotypes. The opens new opportunities tailoring improving predictability performance circuits across diverse applications.

Язык: Английский

---

Transcriptome-wide characterization of genetic perturbations

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 3, 2024

Abstract Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these are often noisy due to cost and technical constraints, limiting power detect true effects with conventional differential expression analyses. Here, we introduce TRanscriptome-wide Analysis Differential Expression (TRADE), a statistical framework which estimates transcriptome-wide distribution from gene-level measurements. Within TRADE, derive multiple novel, interpretable metrics, including “transcriptome-wide impact”, an estimator overall transcriptional effect perturbation is stable across sampling depths. We analyze new published large-scale datasets show that many not statistically significant, but detectable in aggregate TRADE. In genome-scale screen, find typical gene affects estimated 45 genes, whereas essential over 500 genes. An advantage our approach its ability compare contexts dosages despite differences power. use this identify cell-type dependent examples where responses only larger magnitude, also qualitatively different, function dosage. Lastly, expand analysis case/control comparison for neuropsychiatric conditions, finding correlations greater than diagnoses. TRADE lays analytic foundation systematic atlases, well experiments more broadly.

Язык: Английский

---

Buffering and non-monotonic behavior of gene dosage response curves for human complex traits

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 11, 2024

A bstract The genome-wide burdens of deletions, loss-of-function mutations, and duplications correlate with many traits. Curiously, for most these traits, variants that decrease expression have the same average direction effect as increase expression. This seemingly contradicts intuition that, at individual genes, reducing should opposite on a phenotype increasing To understand this paradox, we introduce concept called gene dosage response curve (GDRC) relates changes in to expected phenotype. We show GDRCs are systematically biased one trait relative other and, surprisingly, 40% non-monotone, large increases decreases affecting direction. develop simple theoretical model explains bias Our results broad implications complex drug discovery, statistical genetics.

Язык: Английский

---

Convergent impact of schizophrenia risk genes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Март 30, 2022

ABSTRACT Genetic studies of schizophrenia reveal a complex polygenic risk architecture comprised hundreds variants; most are common in the population at-large, non-coding, and act by genetically regulating expression one or more gene targets (“eGenes”). It remains unclear how genetic variants predicted to confer individually small effects combine yield substantial clinical impacts aggregate. Here, we demonstrate that eGenes have shared downstream transcriptomic (“convergence”) may underlie unexpected interactions (“non-additive effects”) observed when manipulated combination. We apply pooled CRISPR approach perturb human induced pluripotent stem cell-derived glutamatergic neurons. The strength specificity convergence increased between functionally similar eGenes. Predicting might impact additive relationships loci inherited together, use an arrayed explore bidirectional combinatorial perturbations partially overlapping set fifteen When specifically considering groups synaptic epigenetic eGenes, eGene changes smaller than summing individual (“sub-additive effects”). Moreover, convergent non-additive overlap, suggesting functional redundancy be major mechanism underlying non-additivity. Combinatorial result outcomes not yet well-predicted single alone, indicating cannot necessarily extrapolated from experiments testing at time.

Язык: Английский

---

Large-scale discovery of chromatin dysregulation induced by oncofusions and other protein-coding variants

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Июль 24, 2024

Язык: Английский

---

Synthetic enhancers reveal design principles of cell state specific regulatory elements in hematopoiesis

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 26, 2024

Abstract During cellular differentiation, enhancers transform overlapping gradients of transcription factors (TFs) to highly specific gene expression patterns. However, the vast complexity regulatory DNA impedes identification underlying cis-regulatory rules. Here, we have characterized 62,126 fully synthetic sequences bottom-up dissect design principles cell-state in context differentiation blood stem cells seven myeloid lineages. Focusing on binding sites for 38 TFs and their pairwise interactions, found that identical displayed both repressive activating function, as a consequence context, site combinatorics, or simply predicted occupancy TF an enhancer. Surprisingly, combinations frequently neutralized each other even gained function. These negative synergies convert quantitative imbalances factor into binary downstream activity patterns, principle can be exploited build differentiation-state from scratch.

Язык: Английский

---