Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single-cell RNA-seq DOI Creative Commons
Jeremy A. Schofield, Steven Hahn

Cell Reports, Journal Year: 2024, Volume and Issue: 43(8), P. 114593 - 114593

Published: Aug. 1, 2024

We describe a time-resolved nascent single-cell RNA sequencing (RNA-seq) approach that measures gene-specific transcriptional noise and the fraction of active genes in S. cerevisiae. Most are expressed with near-constitutive behavior, while subset show high mRNA variance suggestive transcription bursting. Transcriptional is highest cofactor/coactivator-redundant (CR) gene class (dependent on both SAGA TFIID) strongest TATA-containing CR genes. Using this approach, we also find histone switches from low-level, low-noise constitutive mode during M M/G1 to an activated state S phase shows increase promoters switch noisy bursty mode. Rapid depletion cofactors MED Tail indicates factors play important role stimulating at genes, more modest noise.

Language: Английский

Accelerating Diverse Cell-Based Therapies Through Scalable Design DOI
Emma L. Peterman, Deon Ploessl, Kate E. Galloway

et al.

Annual Review of Chemical and Biomolecular Engineering, Journal Year: 2024, Volume and Issue: 15(1), P. 267 - 292

Published: April 10, 2024

Augmenting cells with novel, genetically encoded functions will support therapies that expand beyond natural capacity for immune surveillance and tissue regeneration. However, engineering at scale transgenic cargoes remains a challenge in realizing the potential of cell-based therapies. In this review, we introduce range applications primary stem We highlight tools advances have launched mammalian cell from bioproduction to precision editing therapeutically relevant cells. Additionally, examine how transgenesis methods genetic cargo designs can be tailored performance. Altogether, offer vision accelerating translation innovative by harnessing diverse types, integrating expanding array synthetic biology tools, building cellular through advanced genome writing techniques.

Language: Английский

Citations

6
DNA topology: A central dynamic coordinator in chromatin regulation DOI

Shuai Li,

Charan Vemuri,

Chongyi Chen

et al.

Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 87, P. 102868 - 102868

Published: June 14, 2024

Language: Английский

Citations

6
STRAIGHT-IN Dual: a platform for dual, single-copy integrations of DNA payloads and gene circuits into human induced pluripotent stem cells DOI Creative Commons
Albert Blanch-Asensio, Deon Ploessl, Nathan Wang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 17, 2024

Abstract Targeting DNA payloads into human (h)iPSCs involves multiple time-consuming, inefficient steps that must be repeated for each construct. Here, we present STRAIGHT-IN Dual, which enables simultaneous, allele-specific, single-copy integration of two with 100% efficiency within one week. Notably, Dual leverages the platform to allow near-scarless cargo integration, facilitating recycling components subsequent cellular modifications. Using investigated how promoter choice and gene syntax influences transgene silencing, demonstrate impact these design features on forward programming hiPSCs neurons. Furthermore, designed a grazoprevir-inducible synZiFTR system complement widely-used tetracycline-inducible system, providing independent, tunable, temporally controlled expression both transcription factors functional reporters. The unprecedented speed generates homogenous genetically engineered hiPSC populations represents major advancement synthetic biology in stem cell applications opens opportunities precision engineering.

Language: Английский

Citations

4
High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation DOI Open Access
Porter M. Hall, Lauren A. Mayse,

Lu Bai

et al.

Published: Feb. 18, 2025

Torsional stress in chromatin plays a fundamental role cellular functions, influencing key processes such as transcription, replication, and organization. Transcription other may generate be regulated by torsional stress. In the genome, interplay of these creates complicated patterns both positive (+) negative (-) torsion. However, challenge generating an accurate torsion map is determining zero-torsion baseline signal, which conflated with accessibility. Here, we introduce high-resolution method based on intercalator trimethylpsoralen (TMP) to address this challenge. We describe establish while preserving state genome S. cerevisiae . This approach enables mapping accessibility cell. Our analysis shows transcription-generated domains consistent twin-supercoiled-domain model transcription suggests for recruiting topoisomerases regulating 3D architecture via cohesin. Significantly, reveal that insulator sequence-specific factors decouple between divergent promoters, whereas spreads promoters lacking factors, suggesting serves regulatory mechanism regions. Although insulators are known gene expression, our finding provides physical explanation how decoupling occur. new potential path forward using TMP measure without confounding contribution chromatin.

Language: Английский

Citations

0
Statistical mechanics of multiplectoneme phases in DNA DOI
Midas Segers, Enrico Skoruppa, Helmut Schiessel

et al.

Physical review. E, Journal Year: 2025, Volume and Issue: 111(4)

Published: April 17, 2025

Language: Английский

Citations

0
U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation DOI Creative Commons
Gyeungyun Kim, Christine L. Carroll,

Zachary Peters Wakefield

et al.

Molecular Cell, Journal Year: 2025, Volume and Issue: 85(10), P. 1968 - 1981.e7

Published: May 1, 2025

Language: Английский

Citations

0
Transcriptional coregulation in cis around a contact insulation site revealed by single-molecule microscopy DOI Open Access
Maciej A. Kerlin,

Ilham Aboulfath-Ladid,

Julia Roensch

et al.

Published: May 16, 2025

Abstract Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, transcription occurs sporadic bursts, transcriptional coordination has been observed between proximal but how folding of mammalian chromosomes influences coregulation cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent from three adjacent located around a strong contact insulation site FOS locus, during estrogen response human breast cancer cells. To interpret this data, developed two new analysis approaches dissect sources (co)variation activities: one separate allele-extrinsic, allele-intrinsic, gene-autonomous components; another quantify contributions burst co-occurrence size correlations. We find that variability largely gene-autonomous, yet correlations display distinct patterns occur almost exclusively cis. Correlations stronger less insulated genes. However, unexpectedly, substantial also and, under certain on same side can exhibit uncorrelated occurrences. By disentangling correlations, reveal coregulatory influenced by chromosome folding.

Language: Английский

Citations

0
Transcriptional coregulation in cis around a contact insulation site revealed by single-molecule microscopy DOI Open Access
Maciej A. Kerlin,

Ilham Aboulfath-Ladid,

Julia Roensch

et al.

Published: May 16, 2025

Abstract Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, transcription occurs sporadic bursts, transcriptional coordination has been observed between proximal but how folding of mammalian chromosomes influences coregulation cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent from three adjacent located around a strong contact insulation site FOS locus, during estrogen response human breast cancer cells. To interpret this data, developed two new analysis approaches dissect sources (co)variation activities: one separate allele-extrinsic, allele-intrinsic, gene-autonomous components; another quantify contributions burst co-occurrence size correlations. We find that variability largely gene-autonomous, yet correlations display distinct patterns occur almost exclusively cis. Correlations stronger less insulated genes. However, unexpectedly, substantial also and, under certain on same side can exhibit uncorrelated occurrences. By disentangling correlations, reveal coregulatory influenced by chromosome folding.

Language: Английский

Citations

0
Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome DOI Creative Commons
Yumi Minyi Yao,

Irina Miodownik,

Michael O’Hagan

et al.

Transcription, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 25

Published: July 20, 2024

Transcription factors (TFs) intricately navigate the vast genomic landscape to locate and bind specific DNA sequences for regulation of gene expression programs. These interactions occur within a dynamic cellular environment, where both TF proteins experience continual chemical structural perturbations, including epigenetic modifications, damage, mechanical stress, post-translational modifications (PTMs). While many these impact TF-DNA binding interactions, understanding their effects remains challenging incomplete. This review explores existing literature on changes potential interactions.

Language: Английский

Citations

3
Enhancers: A Focus on Synthetic Biology and Correlated Gene Expression DOI
Christopher H. Bohrer, Nadezda A. Fursova, Daniel R. Larson

et al.

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 14, 2024

Enhancers are central for the regulation of metazoan transcription but have proven difficult to study, primarily due a myriad interdependent variables shaping their activity. Consequently, synthetic biology has emerged as main approach dissecting mechanisms enhancer function. We start by reviewing simple highly parallel reporter assays, which been successful in quantifying complexity activator/coactivator at enhancers. then describe studies that examine how enhancers function genomic context and combination with other enhancers, revealing they activate genes through variety different mechanisms, working together system. Here, we focus on can quantify dynamics time. end considering consequences having many within 'local environment', believe leads correlated gene expression likely reports general principles biology.

Language: Английский

Citations

3