Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1125847 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29463771_1.fastq.gz | Fastqsanger.gz | |||
| SRR29463771_2.fastq.gz | Fastqsanger.gz | |||
| SRR29463772_1.fastq.gz | Fastqsanger.gz | |||
| SRR29463772_2.fastq.gz | Fastqsanger.gz | |||
| SRR29463773_1.fastq.gz | Fastqsanger.gz |
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Project description:Flexible regulation of gene expression is essential and highly sought for synthetic biology and biotechnology. Designing regulators with specific functions remains a challenge due to the limited understanding of specific regulatory mechanisms. We design and synthesize 23,640 B-cell-specific promoters, following the design-build-test-learn pipeline in synthetic biology. Synthetic promoters exhibit B-cell-specific expression and lead to diverse expression patterns in B-cells. By conducting MPRA testing, we uncovered the factors that influence promoter strength, including core motifs and motif syntax, which shape B-cell-specific promoter strength. Finally, we developed a deep leaning model capable of predicting promoter activity directly from the sequence, and to predict promoter activity for 26,193 variants identified in the global population, indicating that polymorphisms in IgV gene promoters can influence gene expression. Our work helps to decipher the regulatory code in immunoglobulin genes and offers thousands of non-repetitive promoter elements for B-cell engineering.
2023-05-16 | GSE232161 | GEO
Project description:Genetically-engineered immune cell therapies have been in development for decades and recently have proven effective to treat some types of cancer. CRISPR-based genome editing methods enabling more flexible and targeted sequence integrations than viral transduction have potential to extend the clinical utility of cell therapies. Realization of this potential depends on improved knowledge of how coding and non-coding sites throughout the genome can be modified efficiently and on improved methods to discover novel synthetic DNA sequences that can be introduced at targeted sites to enhance critical immune cell functions. Here, we developed improved rules for non-viral genome targeting in human T cells and a pooled discovery platform to identify synthetic genome modifications that enhance therapeutically-relevant cell functions. We elucidated the breadth of targetable genomic loci by performing large knockins at 91 different genomic sites in primary human T cells, and demonstrated the power of flexible genome targeting by generating cells with Genetically Engineered Endogenous Proteins (GEEPs) that seamlessly integrate synthetic and endogenous genetic elements to alter signaling input, output, or regulatory control of genes encoding key immune receptors. Motivated by success in introducing synthetic circuits into endogenous sites, we then developed a platform to facilitate discovery of novel multi-gene circuits that reprogram both T cell specificity and function. We knocked-in barcoded pools of large DNA sequences encoding poly-cistronic gene programs. High-throughput pooled screening of targeted knock-ins to the endogenous T cell receptor (TCR) locus revealed a transcriptional regulator and novel protein chimeras that combined with a new TCR specificity to enhance T cell responses in the presence of suppressive conditions in vitro and in vivo. Overall, these pre-clinical studies provide flexible tools to discover complex synthetic gene programs that can be written into targeted genome sites to generate more effective therapeutic cells.
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Project description:Guisoni2016 - Cis-regulatory system (CRS) can
drive sustained oscillations
This model is described in the article:
Promoters Architecture-Based
Mechanism for Noise-Induced Oscillations in a Single-Gene
Circuit.
Guisoni N, Monteoliva D, Diambra
L.
PLoS ONE 2016; 11(3): e0151086
Abstract:
It is well known that single-gene circuits with negative
feedback loop can lead to oscillatory gene expression when they
operate with time delay. In order to generate these
oscillations many processes can contribute to properly timing
such delay. Here we show that the time delay coming from the
transitions between internal states of the cis-regulatory
system (CRS) can drive sustained oscillations in an
auto-repressive single-gene circuit operating in a small volume
like a cell. We found that the cooperative binding of repressor
molecules is not mandatory for a oscillatory behavior if there
are enough binding sites in the CRS. These oscillations depend
on an adequate balance between the CRS kinetic, and the
synthesis/degradation rates of repressor molecules. This
finding suggest that the multi-site CRS architecture can play a
key role for oscillatory behavior of gene expression. Finally,
our results can also help to synthetic biologists on the design
of the promoters architecture for new genetic oscillatory
circuits.
This model is hosted on
BioModels Database
and identified by:
MODEL1611030000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2016-11-03 | MODEL1611030000 | BioModels
Project description:Activation domains (ADs) within transcription factors (TFs) induce gene expression by recruiting coactivators to specific regulatory regions. Within the prevailing model, TF-coactivator recruitment is independent of DNA binding, which is consistent with direct AD-coactivator interactions seen outside cells. However, this independence was not yet tested within the genomic context. Here, we targeted two Med15-interacting ADs to hundreds of budding yeast promoters through fusions with multiple DNA binding domains (DBDs), gradually controlling their abundances using libraries of synthetic promoters. Genomic profiling revealed that AD identity influences DNA binding locations and that transcription induction and Med15 recruitment are restricted to a subset of DBD-bound promoters displaying flexible expression, multiple-TFs binding, and fuzzy nucleosome architecture. Further, when fused to a DBD, Med15 redirected binding towards promoters of fuzzy nucleosomes, overcoming DBD-based preferences. Our results demonstrate that ADs and their recruited coactivators posses an inherent preference for genomic localization and, therefore, define the subset of induced promoters.
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