At Last, A Complete Human Genome: Codon Index #43
Plus: CRISPR'd cat cells & a supercharged prime editor to swap DNA bases.
Hello. A complete human genome sequence adds a full chromosome’s worth of data to prior versions. An allergy-causing gene in cats is modified by CRISPR. And a tweak to prime editing boosts its efficiency by 353x, on average.
The Human Genome Sequence is Complete
About 8 percent of the human genome was “missing” from prior sequences. That’s about 200 million base pairs of DNA or roughly the length of an entire chromosome. Those gaps have now been filled in.
For a set of papers in this week’s issue of Science, DNA was extracted from CHM13hTERT human cells, first taken from a woman who conceived at Magee-Women’s Hospital in Pittsburgh, Pennsylvania. This cell line is homozygous, which means that both copies of its various chromosomes are the same, and thus easier to sequence. These cells do not carry a Y chromosome.
The completed genome sequence contains 3.055 billion base pairs of DNA and adds more than 1900 predicted genes to the prior human reference genome. About 100 of these ‘new’ genes are likely to encode proteins.
The new studies were spearheaded by the Telomere-to-Telomere (T2T) consortium, an open-source community co-chaired by Adam Phillippy at the National Institutes of Health and Karen Miga at the University of California, Santa Cruz.
Members of the consortia spent years filling in the genome sequence; mainly, these missing pieces are highly repetitive sequences or transposable elements that are difficult to sequence using current technologies, or else are difficult to ‘align’ using computational tools. The researchers used a mixture of technologies to complete the work, including sequencing machines from PacBio, Oxford Nanopore, and 10X Genomics.
Read more at Science.
Cats have a protein, called Fel d 1, that is present in their saliva and causes allergies in about 15 percent of people. For a new study, researchers used the CRISPR gene-editing tool to knock out the genes encoding Fel d 1 in cells taken from cats — but not in living, breathing animals.
Disrupting the genes did not cause the cells to die, which means those genes are likely nonessential for cats and could be a target for people who suffer from cat allergies in the future.
Read more at The CRISPR Journal.
Prime editors are modified proteins that can substitute bases in DNA (like swap a C for a T). They are not very efficient, though. For a new study, researchers modified the RNA polymer that guides a prime editor to a specific site in the genome. With the new guide, base-editing efficiency was increased by a maximum of nearly 5000-fold, or by an average of 353-fold.
Read more at Nature Communications.
(* = open access, † = review article)
Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection. Yao Y…You L. Nature Ecology & Evolution. Link
Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Patel JR…Isaacs FJ. Cell. Link
*Metabolic engineering strategies to produce medium-chain oleochemicals via acyl-ACP:CoA transacylase activity. Yan Q…Pfleger BF. Nature Communications. Link
*Synthetic 3′-UTR valves for optimal metabolic flux control in Escherichia coli. Choe D…Cho B. Nucleic Acids Research. Link
*Exploring a blue-light-sensing transcription factor to double the peak productivity of oil in Nannochloropsis oceanica. Zhang P…Xu J. Nature Communications. Link
*Harnessing phosphonate antibiotics argolaphos biosynthesis enables a synthetic biology-based green synthesis of glyphosate. Chu L…Gao J. Nature Communications. Link
†Electro-fermentation: Sustainable bioproductions steered by electricity. Virdis B…Villano M. Biotechnology Advances. Link
*Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria. Vögeli B…Jewett MC. bioRxiv (preprint). Link
†The living interface between synthetic biology and biomaterial design. Liu AP…Chaudhuri O. Nature Materials. Link
*Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles. Jones RD…Weiss R. Nature Communications. Link
Computation & Models
*†CRISPR–Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning. Konstantakos V…Paliouras G. Nucleic Acids Research. Link
*Programmable design of isothermal nucleic acid diagnostic assays through abstraction-based models. Xu G…Cooper JM. Nature Communications. Link
CRISPR & Genetic Engineering
*Guide RNAs containing universal bases enable Cas9/Cas12a recognition of polymorphic sequences. Krysler AR…Hubbard BP. Nature Communications. Link
*Phage peptides mediate precision base editing with focused targeting window. Jia K…Liu J. Nature Communications. Link
*Imperfect guide-RNA (igRNA) enables CRISPR single-base editing with ABE and CBE. Zhao D…Zhang X. Nucleic Acids Research. Link
Parameterized Computational Framework for the Description and Design of Genetic Circuits of Morphogenesis Based on Contact-Dependent Signaling and Changes in Cell–Cell Adhesion. Lam C…Morsut L. ACS Synthetic Biology. Link
*Overcoming leak sensitivity in CRISPRi circuits using antisense RNA sequestration and regulatory feedback. Specht DA, Cortes LB & Lambert G. bioRxiv (preprint). Link
Medicine & Diagnostics
Reprogramming of fibroblasts into expandable cardiovascular progenitor cells via small molecules in xeno-free conditions. Wang J…Cao N. Nature Biomedical Engineering. Link
*Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Goenka SD…Ashley EA. Nature Biotechnology. Link
*Improving the specificity of nucleic acid detection with endonuclease-actuated degradation. Zou RS…Ha T. Communications Biology. Link
The potential of eukaryotic cell-free systems as a rapid response to novel zoonotic pathogens: Analysis of SARS-CoV-2 viral proteins. Ramm F…Kubick SD. Frontiers in Bioengineering and Biotechnology. Link
Rational Design of CRISPR/Cas12a-RPA Based One-Pot COVID-19 Detection with Design of Experiments. Malcı K, Walls LE & Rios-Solis L. ACS Synthetic Biology. Link
*Optimization of CRISPR/LbCas12a-mediated gene editing in Arabidopsis. Zhang Q, Zhang Y & Chai Y. PLoS ONE. Link
Protein & Molecular Engineering
*Unleashing the Potential of Noncanonical Amino Acid Biosynthesis for Creation of Cells with Site-Specific Tyrosine Sulfation. Chen Y…Xiao H. bioRxiv (preprint). Link
Tools & Technology
Inferring gene expression from cell-free DNA fragmentation profiles. Esfahani MS…Alizadeh AA. Nature Biotechnology. Link
*Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. McCartney AM…Rhie A. Nature Methods. Link
*Reaction-diffusion patterning of DNA-based artificial cells. Leathers A…Di Michele L. bioRxiv (preprint). Link