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Genomic context sensitizes regulatory elements to genetic disruption

Ordoñez, Raquel; Zhang, Weimin; Ellis, Gwen; Zhu, Yinan; Ashe, Hannah J; Ribeiro-Dos-Santos, André M; Brosh, Ran; Huang, Emily; Hogan, Megan S; Boeke, Jef D; Maurano, Matthew T
Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis. Thus it remains unclear to what extent enhancer function at native loci relies on surrounding genomic context. Using the Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the murine Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting the activity of payloads delivered to the endogenous locus or to a safe harbor locus (Hprt) revealed that the Igf2/H19 locus includes additional, previously unknown long-range regulatory elements. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate the relationship between locus architecture and function.
PMID: 37781588
CID: 5606642

Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae

Cheng, Li; Zhao, Shijun; Li, Tianyi; Hou, Sha; Luo, Zhouqing; Xu, Jinsheng; Yu, Wenfei; Jiang, Shuangying; Monti, Marco; Schindler, Daniel; Zhang, Weimin; Hou, Chunhui; Ma, Yingxin; Cai, Yizhi; Boeke, Jef D; Dai, Junbiao
Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we construct SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes. SCRaMbLE of SparLox83R produces versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, when combined with synthetic chromosomes, SCRaMbLE of hetero-diploids with SparLox83R leads to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to hetero-diploids only with wild-type chromosomes. Analysis of the SCRaMbLEd strain with increased tolerance to nocodazole demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool for studying the consequence of genomic rearrangements and accelerating strain engineering in Saccharomyces cerevisiae.
PMID: 38278805
ISSN: 2041-1723
CID: 5625492

Manipulating the 3D organization of the largest synthetic yeast chromosome

Zhang, Weimin; Lazar-Stefanita, Luciana; Yamashita, Hitoyoshi; Shen, Michael J; Mitchell, Leslie A; Kurasawa, Hikaru; Lobzaev, Evgenii; Fanfani, Viola; Haase, Max A B; Sun, Xiaoji; Jiang, Qingwen; Goldberg, Gregory W; Ichikawa, David M; Lauer, Stephanie L; McCulloch, Laura H; Easo, Nicole; Lin, S Jiaming; Camellato, Brendan R; Zhu, Yinan; Cai, Jitong; Xu, Zhuwei; Zhao, Yu; Sacasa, Maya; ,; Noyes, Marcus B; Bader, Joel S; Deutsch, Samuel; Stracquadanio, Giovanni; Aizawa, Yasunori; Dai, Junbiao; Boeke, Jef D
Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes.
PMID: 37944526
ISSN: 1097-4164
CID: 5612832

Building a eukaryotic chromosome arm by de novo design and synthesis

Jiang, Shuangying; Luo, Zhouqing; Wu, Jie; Yu, Kang; Zhao, Shijun; Cai, Zelin; Yu, Wenfei; Wang, Hui; Cheng, Li; Liang, Zhenzhen; Gao, Hui; Monti, Marco; Schindler, Daniel; Huang, Linsen; Zeng, Cheng; Zhang, Weimin; Zhou, Chun; Tang, Yuanwei; Li, Tianyi; Ma, Yingxin; Cai, Yizhi; Boeke, Jef D; Zhao, Qiao; Dai, Junbiao
The genome of an organism is inherited from its ancestor and continues to evolve over time, however, the extent to which the current version could be altered remains unknown. To probe the genome plasticity of Saccharomyces cerevisiae, here we replace the native left arm of chromosome XII (chrXIIL) with a linear artificial chromosome harboring small sets of reconstructed genes. We find that as few as 12 genes are sufficient for cell viability, whereas 25 genes are required to recover the partial fitness defects observed in the 12-gene strain. Next, we demonstrate that these genes can be reconstructed individually using synthetic regulatory sequences and recoded open-reading frames with a "one-amino-acid-one-codon" strategy to remain functional. Finally, a synthetic neochromsome with the reconstructed genes is assembled which could substitute chrXIIL for viability. Together, our work not only highlights the high plasticity of yeast genome, but also illustrates the possibility of making functional eukaryotic chromosomes from entirely artificial sequences.
PMID: 38036514
ISSN: 2041-1723
CID: 5589872

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions

Zhao, Yu; Coelho, Camila; Hughes, Amanda L; Lazar-Stefanita, Luciana; Yang, Sandy; Brooks, Aaron N; Walker, Roy S K; Zhang, Weimin; Lauer, Stephanie; Hernandez, Cindy; Cai, Jitong; Mitchell, Leslie A; Agmon, Neta; Shen, Yue; Sall, Joseph; Fanfani, Viola; Jalan, Anavi; Rivera, Jordan; Liang, Feng-Xia; Bader, Joel S; Stracquadanio, Giovanni; Steinmetz, Lars M; Cai, Yizhi; Boeke, Jef D
The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe the consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS," to map phenotypic variants caused by specific designer modifications, known as "bugs." We first fine-mapped a bug in synthetic chromosome II (synII) and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism, and tRNASer
PMID: 37944511
ISSN: 1097-4172
CID: 5590882

Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains

McCulloch, Laura H; Sambasivam, Vijayan; Hughes, Amanda L; Annaluru, Narayana; Ramalingam, Sivaprakash; Fanfani, Viola; Lobzaev, Evgenii; Mitchell, Leslie A; Cai, Jitong; ,; Jiang, Hua; LaCava, John; Taylor, Martin S; Bishai, William R; Stracquadanio, Giovanni; Steinmetz, Lars M; Bader, Joel S; Zhang, Weimin; Boeke, Jef D; Chandrasegaran, Srinivasan
We describe the complete synthesis, assembly, debugging, and characterization of a synthetic 404,963 bp chromosome, synIX (synthetic chromosome IX). Combined chromosome construction methods were used to synthesize and integrate its left arm (synIXL) into a strain containing previously described synIXR. We identified and resolved a bug affecting expression of EST3, a crucial gene for telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains, we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. Both steps of this chromosome substitution method were efficient. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these chromosomes.
PMID: 38020974
ISSN: 2666-979x
CID: 5617102

Context-dependent neocentromere activity in synthetic yeast chromosome VIII

Lauer, Stephanie; Luo, Jingchuan; Lazar-Stefanita, Luciana; Zhang, Weimin; McCulloch, Laura H; Fanfani, Viola; Lobzaev, Evgenii; Haase, Max A B; Easo, Nicole; Zhao, Yu; Yu, Fangzhou; Cai, Jitong; ,; Bader, Joel S; Stracquadanio, Giovanni; Boeke, Jef D
Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synthetic eukaryotic organism by assembling the genome of Saccharomyces cerevisiae. With the completion of synthetic chromosome VIII (synVIII) described here, this goal is within reach. In addition to writing the yeast genome, we sought to manipulate an essential functional element: the point centromere. By relocating the native centromere sequence to various positions along chromosome VIII, we discovered that the minimal 118-bp CEN8 sequence is insufficient for conferring chromosomal stability at ectopic locations. Expanding the transplanted sequence to include a small segment (∼500 bp) of the CDEIII-proximal pericentromere improved chromosome stability, demonstrating that minimal centromeres display context-dependent functionality.
PMID: 38020969
ISSN: 2666-979x
CID: 5617072

Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function

Luo, Jingchuan; Vale-Silva, Luis A; Raghavan, Adhithi R; Mercy, Guillaume; Heldrich, Jonna; Sun, Xiaoji; Li, Mingyu Kenneth; Zhang, Weimin; Agmon, Neta; Yang, Kun; Cai, Jitong; Stracquadanio, Giovanni; Thierry, Agnès; Zhao, Yu; Coelho, Camila; McCulloch, Laura H; Lauer, Stephanie; ,; Kaback, David B; Bader, Joel S; Mitchell, Leslie A; Mozziconacci, Julien; Koszul, Romain; Hochwagen, Andreas; Boeke, Jef D
We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.
PMID: 38020967
ISSN: 2666-979x
CID: 5617052

Mouse genome rewriting and tailoring of three important disease loci

Zhang, Weimin; Golynker, Ilona; Brosh, Ran; Fajardo, Alvaro; Zhu, Yinan; Wudzinska, Aleksandra M; Ordoñez, Raquel; Ribeiro-Dos-Santos, André M; Carrau, Lucia; Damani-Yokota, Payal; Yeung, Stephen T; Khairallah, Camille; Vela Gartner, Antonio; Chalhoub, Noor; Huang, Emily; Ashe, Hannah J; Khanna, Kamal M; Maurano, Matthew T; Kim, Sang Yong; tenOever, Benjamin R; Boeke, Jef D
Genetically engineered mouse models (GEMMs) help us to understand human pathologies and develop new therapies, yet faithfully recapitulating human diseases in mice is challenging. Advances in genomics have highlighted the importance of non-coding regulatory genome sequences, which control spatiotemporal gene expression patterns and splicing in many human diseases1,2. Including regulatory extensive genomic regions, which requires large-scale genome engineering, should enhance the quality of disease modelling. Existing methods set limits on the size and efficiency of DNA delivery, hampering the routine creation of highly informative models that we call genomically rewritten and tailored GEMMs (GREAT-GEMMs). Here we describe 'mammalian switching antibiotic resistance markers progressively for integration' (mSwAP-In), a method for efficient genome rewriting in mouse embryonic stem cells. We demonstrate the use of mSwAP-In for iterative genome rewriting of up to 115 kb of a tailored Trp53 locus, as well as for humanization of mice using 116 kb and 180 kb human ACE2 loci. The ACE2 model recapitulated human ACE2 expression patterns and splicing, and notably, presented milder symptoms when challenged with SARS-CoV-2 compared with the existing K18-hACE2 model, thus representing a more human-like model of infection. Finally, we demonstrated serial genome writing by humanizing mouse Tmprss2 biallelically in the ACE2 GREAT-GEMM, highlighting the versatility of mSwAP-In in genome writing.
PMID: 37914927
ISSN: 1476-4687
CID: 5606842

Two differentially stable rDNA loci coexist on the same chromosome and form a single nucleolus

Lazar-Stefanita, Luciana; Luo, Jingchuan; Haase, Max A B; Zhang, Weimin; Boeke, Jef D
The nucleolus is the most prominent membraneless compartment within the nucleus-dedicated to the metabolism of ribosomal RNA. Nucleoli are composed of hundreds of ribosomal DNA (rDNA) repeated genes that form large chromosomal clusters, whose high recombination rates can cause nucleolar dysfunction and promote genome instability. Intriguingly, the evolving architecture of eukaryotic genomes appears to have favored two strategic rDNA locations-where a single locus per chromosome is situated either near the centromere (CEN) or the telomere. Here, we deployed an innovative genome engineering approach to cut and paste to an ectopic chromosomal location-the ~1.5 mega-base rDNA locus in a single step using CRISPR technology. This "megablock" rDNA engineering was performed in a fused-karyotype strain of Saccharomyces cerevisiae. The strategic repositioning of this locus within the megachromosome allowed experimentally mimicking and monitoring the outcome of an rDNA migratory event, in which twin rDNA loci coexist on the same chromosomal arm. We showed that the twin-rDNA yeast readily adapts, exhibiting wild-type growth and maintaining rRNA homeostasis, and that the twin loci form a single nucleolus throughout the cell cycle. Unexpectedly, the size of each rDNA array appears to depend on its position relative to the CEN, in that the locus that is CEN-distal undergoes size reduction at a higher frequency compared to the CEN-proximal counterpart. Finally, we provided molecular evidence supporting a mechanism called paralogous cis-rDNA interference, which potentially explains why placing two identical repeated arrays on the same chromosome may negatively affect their function and structural stability.
PMID: 36821584
ISSN: 1091-6490
CID: 5432312