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[学术文献 ] Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure 进入全文
Nature Communications
In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with structural properties of underlying DNA sequences. Our study illuminates a eukaryotic-like mechanism of domain formation in archaea and a role of intrinsic DNA structure in large-scale genome organization.
[前沿资讯 ] A generative model for complete mRNA sequences that deliver custom therapeutic payloads 进入全文
ginkgo公司
"Recent advances in AI have enabled remarkable progress in the design and optimization of messenger RNA (mRNA) for RNA vaccines and therapeutics. While recent work on mRNA design has largely focused on designing individual components of the mRNA sequence, designing end-to-end mRNA sequences presents a unique challenge. Specifically, designing functional mRNA requires joint optimization of the coding sequence (CDS) for a protein of interest in addition to the 3’ and 5’ untranslated regions (UTRs). Recently, diffusion models have emerged as a powerful generative framework for protein design and sequence generation, for example, Ginkgo's recently released antibody discrete diffusion model. Building on these advances, we introduce mRNA discrete diffusion (mDD-0), a discrete diffusion model for the generation of mRNA sequences."
[学术文献 ] biGMamAct: efficient CRISPR/Cas9-mediated docking of large functional DNA cargoes at the ACTB locus 进入全文
Synthetic Biology
Recent advances in molecular and cell biology and imaging have unprecedentedly enabled multiscale structure-functional studies of entire metabolic pathways from atomic to micrometer resolution and the visualization of macromolecular complexes in situ, especially if these molecules are expressed with appropriately engineered and easily detectable tags. However, genome editing in eukaryotic cells is challenging when generating stable cell lines loaded with large DNA cargoes. To address this limitation, here, we have conceived biGMamAct, a system that allows the straightforward assembly of a multitude of genetic modules and their subsequent integration in the genome at the ACTB locus with high efficacy, through standardized cloning steps. Our system comprises a set of modular plasmids for mammalian expression, which can be efficiently docked into the genome in tandem with a validated Cas9/sgRNA pair through homologous-independent targeted insertion. As a proof of concept, we have generated a stable cell line loaded with an 18.3-kilobase-long DNA cargo to express six fluorescently tagged proteins and simultaneously visualize five different subcellular compartments. Our protocol leads from the in silico design to the genetic and functional characterization of single clones within 6 weeks and can be implemented by any researcher with familiarity with molecular biology and access to mammalian cell culturing infrastructure.
[政策法规 ] Regulatory Horizons Council: the Governance of Engineering Biology 进入全文
Regulatory Horizons Council(UK government)
Engineering biology (EB) is an overarching, agile and rapidly evolving technology platform with the potential to spawn transformative, or disruptive, innovations across a broad range of sectors of the economy. Its increasingly sophisticated range of genetic technologies, including genetic modification, synthetic biology, and genome editing, are enabling the creation of a new bioeconomy with the potential to disrupt or displace incumbent industries. The McKinsey Global Institute claims that “as much as 60 percent of the physical inputs to the global economy could, in principle, be produced biologically. Based on our interactions with stakeholders, we concluded that our most useful course of action would be to address the question, “How can we best manage overall governance of the complex array of products arising from the EB platform,” making recommendations on the most important issues and systemic interactions to be considered in providing future answers on a sector-by-sector basis or on the basis of novel classes of product. These recommendations are therefore intended to provide the framework for future decisions on EB governance, to be undertaken on a sectoral or market basis or based on common sets of properties.This report therefore addresses the challenges surrounding the effective governance of products of this broad range of enterprises. For regulators, there is an understandable desire for simplicity, to capture as many areas of application as possible under a single regulatory system; but that approach can result in the unnecessary failure of innovative developments that would otherwise contribute to growth of the UK economy, meeting Net Zero policy commitments or curing or preventing a disease. The challenge is to find an optimal balance between simplicity in governance systems and regulatory design, and their ability to handle a range of innovation scales and complexities. This report underscores the need for a dynamic, adaptive governance framework to support translation of EB products into markets and sets out recommendations for government that will help the UK to harness the potential of EB, contributing to economic growth, environmental sustainability, and public health."
[学术文献 ] Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome 进入全文
nature communications
The Sc2.0 global consortium to design and construct a synthetic genome based on the Saccharomyces cerevisiae genome commenced in 2006, comprising 16 synthetic chromosomes and a new-to-nature tRNA neochromosome. In this paper we describe assembly and debugging of the 902,994-bp synthetic Saccharomyces cerevisiae chromosome synXVI of the Sc2.0 project. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5’ UTR of genes required for optimal growth and were identified as a systematic cause of defective growth. Based on lessons learned from analysis of Sc2.0 defects and synXVI, an in-silico redesign of the synXVI chromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. The in-silico redesign of synXVI includes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs. This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms.
[前沿资讯 ] CSHL and global collaborators map Solanum pan-genome 进入全文
Cold Spring Harbor Laboratory
CSHL researchers and colleagues around the globe have sequenced dozens of complete genomes for the plant genus that includes tomatoes, potatoes, and eggplants. In a process they deem “pan-genetics,” the biologists use their new, high-quality pan-genome to map the genes behind specific traits of agricultural significance across the genus, and target those genes to create desirable mutations. Their research reveals the importance of understanding the evolution of paralog genes—those that arise through gene duplication—in predicting genome editing outcomes. Importantly, their biggest breakthroughs didn’t come from plants in Lippman’s backyard. Instead, it was African eggplant. A tomato relative indigenous to the sub-Saharan region, African eggplant varies highly in fruit shape, color, and size.
