Encoding of odors by mammalian olfactory receptors

Olfactory receptors (ORs) constitute the largest multi-gene family in the mammalian genome, with hundreds to thousands of loci in humans and mice respectively. The rapid expansion of this massive family of genes has been generated by numerous duplication and diversification events throughout evolutionary history. This size, similarity, and diversity has made it challenging to define the principles by which ORs encode olfactory stimuli. Here, we performed a broad surveying of OR responses, using an in vivo strategy, against a diverse panel of odorants. We then used the resulting interaction profiles to uncover relationships between OR responses, odorants, odor molecular properties, and OR sequences. Our data and analyses revealed that ORs generally exhibited sparse tuning towards odorants and their molecular properties. Odor molecular property similarity between pairs of odorants was informative of odor response similarity. Finally, ORs sharing response to an odorant possessed amino acids at poorly conserved sites that exhibited both, predictive power towards odorant selectivity and convergent evolution. The localization of these residues occurred primarily at the interface of the upper halves of the transmembrane domains, implying that canonical positions govern odor selectivity across ORs. Altogether, our results provide a basis for translating odorants into receptor neuron responses for the unraveling of mammalian odor coding.

Find and cut-and-transfer (FiCAT) mammalian genome engineering

While multiple technologies for small allele genome editing exist, robust technologies for targeted integration of large DNA fragments in mammalian genomes are still missing. Here we develop a gene delivery tool (FiCAT) combining the precision of a CRISPR-Cas9 (find module), and the payload transfer efficiency of an engineered piggyBac transposase (cut-and-transfer module). FiCAT combines the functionality of Cas9 DNA scanning and targeting DNA, with piggyBac donor DNA processing and transfer capacity. PiggyBac functional domains are engineered providing increased on-target integration while reducing off-target events. We demonstrate efficient delivery and programmable insertion of small and large payloads in cellulo (human (Hek293T, K-562) and mouse (C2C12)) and in vivo in mouse liver. Finally, we evolve more efficient versions of FiCAT by generating a targeted diversity of 394,000 variants and undergoing 4 rounds of evolution. In this work, we develop a precise and efficient targeted insertion of multi kilobase DNA fragments in mammalian genomes.

EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality

Background To select the most complete, continuous, and accurate assembly for an organism of interest, comprehensive quality assessment of assemblies is necessary. We present a novel tool, called Evaluation of De Novo Assemblies (EvalDNA), which uses supervised machine learning for the quality scoring of genome assemblies and does not require an existing reference genome for accuracy assessment. Results EvalDNA calculates a list of quality metrics from an assembled sequence and applies a model created from supervised machine learning methods to integrate various metrics into a comprehensive quality score. A well-tested, accurate model for scoring mammalian genome sequences is provided as part of EvalDNA. This random forest regression model evaluates an assembled sequence based on continuity, completeness, and accuracy, and was able to explain 86% of the variation in reference-based quality scores within the testing data. EvalDNA was applied to human chromosome 14 assemblies from the GAGE study to rank genome assemblers and to compare EvalDNA to two other quality evaluation tools. In addition, EvalDNA was used to evaluate several genome assemblies of the Chinese hamster genome to help establish a better reference genome for the biopharmaceutical manufacturing community. EvalDNA was also used to assess more recent human assemblies from the QUAST-LG study completed in 2018, and its ability to score bacterial genomes was examined through application on bacterial assemblies from the GAGE-B study. Conclusions EvalDNA enables scientists to easily identify the best available genome assembly for their organism of interest without requiring a reference assembly. EvalDNA sets itself apart from other quality assessment tools by producing a quality score that enables direct comparison among assemblies from different species.

Demethylation of Non-CpG Sites in DNA Is Initiated by TET2 5-Methylcytosine Dioxygenase

In the mammalian genome, cytosine methylation predominantly occurs at CpG sites. In addition, a number of recent studies have uncovered extensive C5 cytosine methylation (5mC) at non-CpG (5mCpH, where H = A/C/T) sites. Little is known about the enzyme responsible for active demethylation of 5mCpH sites. Using a very sensitive and quantitative LC–MS/MS method, we demonstrate that the human TET2, an iron (II)- and 2OG-dependent dioxygenase, which is a frequently mutated gene in several myeloid malignancies, as well as in a number of other types of cancers, can oxidize 5mCpH sites in double-stranded DNA in vitro. Similar to oxidation of 5mCpG, oxidation of 5mC at CpH sites produces 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC) bases in DNA. After 5mCpG, which is the most preferred substrate, TET2 prefers 5mCpC as a substrate, followed by 5mCpA and then 5mCpT. Since the TDG/BER pathway and deformylation or decarboxylation of 5fC or 5caC, respectively, can convert 5fCpH and 5caCpH to an unmodified cytosine base in DNA, our results suggest a novel demethylation pathway of 5mCpH sites initiated by TET2 dioxygenase.

Mechanism of broad-spectrum Cas9 inhibition by AcrIIA11

Mobile genetic elements evade CRISPR-Cas adaptive immunity by encoding anti-CRISPR proteins (Acrs). Acrs inactivate CRISPR-Cas systems via diverse mechanisms but are generally specific for a narrow subset of Cas nucleases that share high sequence similarity. Here, we demonstrate that AcrIIA11 inhibits diverse Cas9 sub-types in vitro and human cells. Single-molecule fluorescence imaging reveals that AcrIIA11 interferes with the first steps of target search by reducing S. aureus Cas9′s diffusion on non-specific DNA. DNA cleavage is inhibited because the AcrIIA11:Cas9 complex is kinetically trapped at PAM-rich decoy sites, preventing Cas9 from reaching its target. This work establishes that DNA trapping can be used to inhibit a broad spectrum of Cas9 orthologs in vitro and during mammalian genome editing.

Pleiotropy data resource as a primer for investigating co-morbidities/multi-morbidities and their role in disease

Most current biomedical and protein research focuses only on a small proportion of genes, which results in a lost opportunity to identify new gene-disease associations and explore new opportunities for therapeutic intervention. The International Mouse Phenotyping Consortium (IMPC) focuses on elucidating gene function at scale for poorly characterized and/or under-studied genes. A key component of the IMPC initiative is the implementation of a broad phenotyping pipeline, which is facilitating the discovery of pleiotropy. Characterizing pleiotropy is essential to identify gene-disease associations, and it is of particular importance when elucidating the genetic causes of syndromic disorders. Here we show how the IMPC is effectively uncovering pleiotropy and how the new mouse models and gene function hypotheses generated by the IMPC are increasing our understanding of the mammalian genome, forming the basis of new research and identifying new gene-disease associations.

Receptor guanylyl cyclase (RGC) family in GtoPdb v.2021.3

The mammalian genome encodes seven guanylyl cyclases, GC-A to GC-G, that are homodimeric transmembrane receptors activated by a diverse range of endogenous ligands. These enzymes convert guanosine-5'-triphosphate to the intracellular second messenger cyclic guanosine-3',5'-monophosphate (cyclic GMP). GC-A, GC-B and GC-C are expressed predominantly in the cardiovascular system, skeletal system and intestinal epithelium, respectively. GC-D and GC-G are found in the olfactory neuropepithelium and Grueneberg ganglion of rodents, respectively. GC-E and GC-F are expressed in retinal photoreceptors.

Fishing for Genes: How the Largest Gene Family in the Mammalian Genome was Found (and Why Idiosyncrasy in Exploration Matters)

In 1991, Linda Buck and Richard Axel identified the multigene family expressing odor receptors. Their discovery transformed research on olfaction overnight, and Buck and Axel were awarded the 2004 Nobel Prize in Physiology or Medicine. Behind this success lies another, less visible study about the methodological ingenuity of Buck. This hidden tale holds the key to answering a fundamental question in discovery analysis: What makes specific discovery tools fit their tasks? Why do some strategies turn out to be more fruitful than others? The fit of a method with an experimental system often establishes the success of a discovery. However, the underlying reasoning of discovery is hard to codify. These difficulties point toward an element of discovery analysis routinely sidelined as a mere biographical element in the philosophical analysis of science: the individual discoverer’s role. I argue that the individual researcher is not a replaceable epistemic element in discovery analysis. This article draws on contemporary oral history, including interviews with Buck and other actors key to developments in late 1980s olfaction.