Epigenome editing technologies for discovery and medicine

Nature Biotechnology, Год журнала: 2024, Номер 42(8), С. 1199 - 1217

Опубликована: Июль 29, 2024

Язык: Английский

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Compendium of human transcription factor effector domains

Molecular Cell, Год журнала: 2021, Номер 82(3), С. 514 - 526

Опубликована: Дек. 3, 2021

Язык: Английский

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Multifunctional Intrinsically Disordered Regions in Transcription Factors

Chemistry - A European Journal, Год журнала: 2023, Номер 29(21)

Опубликована: Янв. 17, 2023

Abstract Eukaryotic transcription factors (TFs) are the final integrators of a complex molecular feedback mechanism that interfaces with genome, consolidating information for transcriptional regulation. TFs consist both structured DNA‐binding domains and long intrinsically disordered regions (IDRs) embedded motifs linked to control. It is now well established dynamic multifunctionality IDRs basis wide spectrum TF functions necessary navigate regulate human genome. This review dissects chemical features endow them structural plasticity central their in nucleus. Sequence analysis set over 1600 through AlphaFold was used identify key IDRs. Recent studies were then highlighted illustrate IDR involvement processes such as protein interactions, DNA binding specificity, chromatin opening, phase separation. To expand our understanding functions, future directions suggested integrating experiments simulations, from vitro living systems.

Язык: Английский

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The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome

Current Opinion in Structural Biology, Год журнала: 2023, Номер 80, С. 102593 - 102593

Опубликована: Апрель 24, 2023

Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances opened this previously underexplored area the human interactome to high-throughput protein–protein discovery. In article, we discuss SLiM-based represent significant blind spot in current interactomics data, introduce methods illuminating elusive SLiM-mediated cell on large scale, implications for field.

Язык: Английский

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Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Май 5, 2023

Abstract Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying DNA binding and functional specificity homo- versus heterodimers remains elusive. To address this gap, we present double Affinity Purification-sequencing (dDAP-seq) technique that maps sites on endogenous genomic DNA. Using dDAP-seq profile twenty pairs C/S1 bZIP S1 homodimers in Arabidopsis show heterodimerization significantly expands preferences these TFs. Analysis reveals function bZIP9 abscisic acid response role bZIP53 heterodimer-specific seed maturation. The distinct ACGT elements recognized by plant bZIPs motifs resembling yeast GCN4 cis -elements. This study demonstrates potential deciphering specificities interacting key combinatorial regulation.

Язык: Английский

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An activity-specificity trade-off encoded in human transcription factors

Nature Cell Biology, Год журнала: 2024, Номер 26(8), С. 1309 - 1321

Опубликована: Июль 5, 2024

Abstract Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off the in human TFs encoded as submaximal dispersion aromatic residues their intrinsically disordered protein regions. We identified approximately 500 that encode short periodic blocks regions, resembling imperfect prion-like sequences. Mutation reduced transcriptional activity, whereas increasing multiple enhanced reprogramming efficiency, promoted liquid–liquid phase separation vitro more promiscuous DNA binding cells. Together with recent work on enhancer elements, results suggest important role suboptimal control. propose rational engineering amino acid alter may be strategy to optimize TF-dependent processes, including cellular reprogramming.

Язык: Английский

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Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Май 17, 2024

Abstract Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective perturbing regulatory elements in pooled assays. However, current CRISPRi screening approaches limited targeting one three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation stabilizes the ribonucleoprotein–DNA complex via nicking. The multiAsCas12a-KRAB fusion improves activity over DNase-dead AsCas12a-KRAB fusions, often rescuing activities of lentivirally delivered RNAs (crRNA) inactive when used with latter. supports 6-plex crRNA arrays high-throughput screens. Using multiAsCas12a-KRAB, we discover enhancer dissect combinatorial function cis -regulatory human cells. These results instantiate group framework efficiently surveying numerous combinations biological discovery engineering.

Язык: Английский

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Development of compact transcriptional effectors using high-throughput measurements in diverse contexts

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 1, 2024

Язык: Английский

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Single-molecule chromatin configurations link transcription factor binding to expression in human cells

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

Опубликована: Фев. 4, 2024

The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence TF binding, promoter state, and levels remain opaque. We applied single-molecule footprinting (SMF) measure simultaneous occupancy TFs, nucleosomes, components machinery on engineered enhancer/promoter constructs with variable numbers sites for both a synthetic an endogenous TF. find activation domains enhance TF's capacity compete nucleosomes DNA BAF-dependent manner, nucleosome-free is consistent independent between average linearly contributes rates. also decompose strength into separable terms, which can be tuned perturbed independently. Finally, we develop thermodynamic kinetic models quantitatively predict microstates observed at subsequent time-dependent expression. This work provides template quantitative dissection distinct contributors activation, including activity chromatin remodelers, domains, acetylation, concentration, affinity, site configuration.

Язык: Английский

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Relocalizing transcriptional kinases to activate apoptosis

Science, Год журнала: 2024, Номер 386(6717)

Опубликована: Окт. 3, 2024

Kinases are critical regulators of cellular function that commonly implicated in the mechanisms underlying disease. Most drugs target kinases molecules inhibit their catalytic activity, but here we used chemically induced proximity to convert kinase inhibitors into activators therapeutic genes. We synthesized bivalent link ligands transcription factor B cell lymphoma 6 (BCL6) cyclin-dependent (CDKs). These relocalized CDK9 BCL6-bound DNA and directed phosphorylation RNA polymerase II. The resulting expression pro-apoptotic, BCL6-target genes caused killing diffuse large cells specific ablation BCL6-regulated germinal center response. Genomics proteomics corroborated a gain-of-function mechanism which global activity was not inhibited rather redirected. Thus, can be context-specifically activate transcription.

Язык: Английский

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