Deciphering the multi-scale, quantitative cis-regulatory code

Molecular Cell, Год журнала: 2023, Номер 83(3), С. 373 - 392

Опубликована: Янв. 23, 2023

Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome cellular state remains central goal of biology. Here, we discuss major layers regulation influence transcriptional outputs are encoded by DNA sequence context. We first transcription factors bind specific sequences dosage-dependent cooperative manner then proceed to cofactors facilitate factor function mediate activity modular elements such as enhancers, silencers, promoters. consider complex poorly understood interplay these diverse within regulatory landscapes its relationships with chromatin states nuclear organization. propose mechanistically informed, quantitative model integrates multiple will be key ultimately cracking code.

Язык: Английский

---

DNA-guided transcription factor cooperativity shapes face and limb mesenchyme

Cell, Год журнала: 2024, Номер 187(3), С. 692 - 711.e26

Опубликована: Янв. 22, 2024

Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regions embryonic face limb mesenchyme. Coordinator guides cooperative selective binding between bHLH family mesenchymal regulator TWIST1 collective HD associated with regional limb. required open chromatin at sites, whereas stabilize occupancy titrate away from HD-independent sites. This results shared regulation genes involved cell-type positional ultimately shapes facial morphology evolution.

Язык: Английский

---

Non-linear transcriptional responses to gradual modulation of transcription factor dosage

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

Опубликована: Март 4, 2024

Genomic loci associated with common traits and diseases are typically non-coding likely impact gene expression, sometimes coinciding rare loss-of-function variants in the target gene. However, our understanding of how gradual changes dosage affect molecular, cellular, organismal is currently limited. To address this gap, we induced expression four genes using CRISPR activation inactivation. Downstream transcriptional consequences modulation three master trans-regulators blood cell (GFI1B, NFE2, MYB) were examined targeted single-cell multimodal sequencing. We showed that guide tiling around TSS most effective way to modulate

Язык: Английский

---

The evolution of developmental biology through conceptual and technological revolutions

Cell, Год журнала: 2024, Номер 187(14), С. 3461 - 3495

Опубликована: Июнь 20, 2024

Developmental biology-the study of the processes by which cells, tissues, and organisms develop change over time-has entered a new golden age. After molecular genetics revolution in 80s 90s diversification field early 21st century, we have phase when powerful technologies provide approaches open unexplored avenues. Progress has been accelerated advances genomics, imaging, engineering, computational biology emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary led remarkable progress understanding animal development. describe classic questions gene regulation, pattern formation, morphogenesis, organogenesis, stem cell are being revisited. discuss connections development with evolution, self-organization, metabolism, time, ecology. speculate developmental might evolve an era synthetic biology, artificial intelligence, human engineering.

Язык: Английский

---

Decoding heterogeneous single-cell perturbation responses

Nature Cell Biology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 26, 2025

Understanding how cells respond differently to perturbation is crucial in cell biology, but existing methods often fail accurately quantify and interpret heterogeneous single-cell responses. Here we introduce the perturbation-response score (PS), a method diverse responses at level. Applied datasets such as Perturb-seq, PS outperforms quantifying partial gene perturbations. further enables dosage analysis without needing titrate perturbations, identifies 'buffered' 'sensitive' response patterns of essential genes, depending on whether their moderate perturbations lead strong downstream effects. reveals differential cellular perturbing key genes contexts T stimulation, latent HIV-1 expression pancreatic differentiation. Notably, identified previously unknown role for coiled-coil domain containing 6 (CCDC6) regulating liver fate decisions. provides powerful dose-to-function analysis, offering deeper insights from data. In two independent studies, Song et al. Jiang, Dalgarno present computational frameworks, Mixscale, respectively, determine individual variation perturbation.

Язык: Английский

---

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

Cell Genomics, Год журнала: 2025, Номер unknown, С. 100780 - 100780

Опубликована: Фев. 1, 2025

Язык: Английский

---

Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database

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

Опубликована: Июнь 13, 2024

ABSTRACT Incomplete penetrance, or absence of disease phenotype in an individual with a disease-associated variant, is major challenge variant interpretation. Studying individuals apparent incomplete penetrance can shed light on underlying drivers altered penetrance. Here, we investigate clinically relevant variants from ClinVar 807,162 the Genome Aggregation Database (gnomAD), demonstrating improved representation gnomAD version 4. We then conduct comprehensive case-by-case assessment 734 predicted loss function (pLoF) 77 genes associated severe, early-onset, highly penetrant haploinsufficient disease. identified explanations for presumed lack manifestation 701 (95%). Individuals unexplained this set disorders rarely occur, underscoring need and power deep presented here to minimize false assignments risk, particularly unaffected higher rates secondary properties that result rescue.

Язык: Английский

---

Large-scale analysis of the integration of enhancer-enhancer signals by promoters

eLife, Год журнала: 2023, Номер 12

Опубликована: Ноя. 3, 2023

Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it not clear which of these modes more frequent in mammalian genomes. Here, we systematically tested pairs activate promoters using a three-way combinatorial reporter assay mouse embryonic stem cells. By assaying about 69,000 enhancer-enhancer-promoter combinations found generally near-additively. This behaviour was conserved across seven developmental tested. Surprisingly, scale signals non-linear manner depends on strength. A housekeeping showed an overall different response pairs, and smaller dynamic range. Thus, our data indicate mostly act but transform their collective effect non-linearly.

Язык: Английский

---

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

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

Опубликована: Янв. 1, 2024

Abstract Understanding the role of transcription and factors in cellular identity disease, such as cancer autoimmunity, is essential. However, comprehensive data resources for cell line-specific factor-to-target gene annotations are currently limited. To address this, we developed a straightforward method to define regulons that capture cell-specific aspects TF binding transcript expression levels. By integrating transcriptome factor data, generated four 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 single-cell datasets showcase utility these cell-type-specific exploring transcriptional dysregulation. In summary, this study provides valuable tool resource systematically regulations, emphasizing network analysis deciphering disease mechanisms.

Язык: Английский

---

Dissecting reprogramming heterogeneity at single-cell resolution using scTF-seq

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

Опубликована: Фев. 2, 2024

Abstract Reprogramming approaches often produce heterogeneous cell fates and the mechanisms behind this heterogeneity are not well-understood. To address gap, we developed scTF-seq, a technique inducing single-cell barcoded doxycycline-inducible TF overexpression while quantifying dose-dependent transcriptomic changes. Applied to mouse embryonic multipotent stromal cells (MSCs), scTF-seq produced gain-of-function atlas for 384 murine TFs. This offers valuable resource gene regulation reprogramming research, identifying key TFs governing MSC lineage differentiation, cycle control, their interplay. Leveraging resolution, dissected along dose pseudotime. We thereby revealed stochastic fate branching, unveiling expression signatures that enhance our understanding prediction of efficiency. also allowed us classify into four sensitivity classes based on response determining features. Finally, in combinatorial observed same can exhibit both synergistic antagonistic effects another depending its dose. In summary, provides powerful tool gaining mechanistic insights how determine states, offering novel perspectives cellular engineering strategies.

Язык: Английский

---