Minimal Sequence Research Articles

Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology.

Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be used to simultaneously screen multiple markers in multiple samples for a variety of variants (single nucleotide and multi nucleotide variants, insertions and deletions, gene copy number variations, and fusions). A crucial step in the workflow of targeted NGS is the enrichment of the genomic regions of interest to be sequenced, against the whole genomic background. This ensures that the NGS effort is focused to predominantly screen target regions of interest with minimal off-target sequencing, making it more accurate and economical. Polymerase chain reaction-based (PCR, or amplicon-based) and hybridization capture-based methodologies are the two prominent approaches employed for target enrichment. This review summarizes the basic principles of target enrichment utilized by these methods, their multiple variations that have evolved over time, automation approaches, overall comparison of their advantages and drawbacks, and commercially available choices for these methodologies.

Accurate Identification of Subclones in Tumor Genomes.

Understanding intratumor heterogeneity is critical for studying tumorigenesis and designing personalized treatments. To decompose the mixed cell population in a tumor, subclones are inferred computationally based on variant allele frequency (VAF) from bulk sequencing data. In this study, we showed that sequencing depth, mean VAF, and variance of VAF of a subclone are confounded. Without considering this effect, current methods require deep-sequencing data (>300× depth) to reliably infer subclones. Here, we present a novel algorithm that incorporates depth-variance and mean-variance dependencies in a clustering error model and successfully identifies subclones in tumors sequenced at depths of as low as 30×. We implemented the algorithm as a model-based adaptive grouping of subclones (MAGOS) method. Analyses of computer simulated data and empirical sequencing data showed that MAGOS outperformed existing methods on minimum sequencing depth, decomposition accuracy, and computation efficiency. The most prominent improvements were observed in analyzing tumors sequenced at depths between 30× and 200×, whereas the performance was comparable between MAGOS and existing methods on deeply sequenced tumors. MAGOS supports analysis of single-nucleotide variants and copy number variants from a single sample or multiple samples of a tumor. We applied MAGOS to whole-exome data of late-stage liver cancers and discovered that high subclone count in a tumor was a significant risk factor of poor prognosis. Lastly, our analysis suggested that sequencing multiple samples of the same tumor at standard depth is more cost-effective and robust for subclone characterization than deep sequencing a single sample. MAGOS is available at github (https://github.com/liliulab/magos).

Broadly recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles.

Sequence homology between SARS-CoV-2 and common-cold human coronaviruses (HCoVs) raises the possibility that memory responses to prior HCoV infection can affect T cell response in COVID-19. We studied T cell responses to SARS-CoV-2 and HCoVs in convalescent COVID-19 donors and identified a highly conserved SARS-CoV-2 sequence, S811-831, with overlapping epitopes presented by common MHC class II proteins HLA-DQ5 and HLA-DP4. These epitopes are recognized by low-abundance CD4 T cells from convalescent COVID-19 donors, mRNA vaccine recipients, and uninfected donors. TCR sequencing revealed a diverse repertoire with public TCRs. T cell cross-reactivity is driven by the high conservation across human and animal coronaviruses of T cell contact residues in both HLA-DQ5 and HLA-DP4 binding frames, with distinct patterns of HCoV cross-reactivity explained by MHC class II binding preferences and substitutions at secondary TCR contact sites. These data highlight S811-831 as a highly conserved CD4 T cell epitope broadly recognized across human populations.

Revision of the Oxynoemacheilus angorae group with the description of two new species (Teleostei: Nemacheilidae).

The Oxynoemacheilus angorae species group is revised and 10 species are recognised, two of which are described herein as new. Oxynoemacheilus anatolicus, O. angorae, O. eregliensis, O. germencicus, O. isauricus, O. nasreddini, O. mediterraneus, and O. theophilii are endemic to west and Central Anatolia. Oxynoemacheilus cinicus and O. mesudae, both from Byk Menderes River drainage, are synonyms of O. germencicus. As First Revisers, we give priority to Oxynoemacheilus germencicus over O. cinicus. Oxynoemacheilus atili described from Lake Beyehir basin is a synonym of O. eregliensis. Oxynoemacheilus axylos, new species, from endorheic Lake Tuz basin (Cihanbeyli, Glyaz, Melendiz, and Samsam) is distinguished by possessing an almost truncate caudal-fin, a stout caudal peduncle, and elevated dorsal and ventral adipose crests. The new species is also distinguished by a minimum K2P sequence divergence of 1.6% in the mtDNA-COI barcode region from O. eregliensis, its closest relative. Oxynoemacheilus eliasi, new species, from the Kk Menderes and Gediz River drainages, is distinguished by having small, embedded scales on the belly, a narrow suborbital groove in male, an emarginate caudal fin, the caudal peduncle depth 1.31.5 times in its length, and the body depth decreasing between the dorsal and caudal-fin bases. The new species is also distinguished by a minimum K2P sequence divergence of 2.7% in the mtDNA-COI barcode region from O. theophilii, its closest relative.

Existence of minimizers for causal variational principles on compact subsets of momentum space in the homogeneous setting

We prove the existence of minimizers for the causal action in the class of negative definite measures on compact subsets of momentum space in the homogeneous setting under several side conditions (constraints). The method is to employ Prohorov’s theorem. Given a minimizing sequence of negative definite measures, we show that, under suitable side conditions, a unitarily equivalent subsequence thereof is bounded. By restricting attention to compact subsets, from Prohorov’s theorem we deduce the existence of minimizers in the class of negative definite measures.

Structural Investigation of AlsA, a Radical S‐adenosylmethionine Enzyme Involved in the Biosynthesis of the Oxetane‐containing Herbicide Albucidin

Herbicides are a class of molecules commonly employed to maintain high crop yields by targeting weeds, a particularly damaging class of pests in agriculture. Albucidin is a novel herbicide found in Streptomyces albus subsp. Chlorinus NRRL B‐24108 that shows a suspected new mode of action. Albucidin is a nucleoside analogue containing an oxetane moiety similar to the antiviral compound oxetanocin‐A (OXT‐A). OXT‐A is the only other known naturally occurring oxetane‐containing nucleoside analogue and has a biosynthetic pathway with two key enzymes: OxsA and OxsB. OsxB is a B12‐dependent radical S‐adenosylmethionine (RS) enzyme and catalyzes formation of the oxetane ring via an oxidative ring contraction. A similar reaction has been proposed to be catalyzed by the B12‐dependent RS enzyme AlsB in the biosynthetic pathway of albucidin; however, the two biosynthetic pathways appear to diverge at this point as well. While OXT‐A is formed upon subsequent reduction and OxsA catalyzed dephosphorylation of the OxsB reaction product, the chemistry leading to albucidin is much less clear. In particular, one carbon must be eliminated, and AlsA, which is a biotin synthase‐like RS enzyme also encoded in the albucidin biosynthetic cluster, has been proposed to participate in this reaction. AlsA is most closely related to BioB‐like enzymes and demonstrates high sequence similarity with the canonical TIM barrel domain; however, AlsA also contains an N‐terminal domain of about 100 amino acids that shares minimal sequence homology to other RS enzymes with known structures. Herein, recent developments in the structural analysis of AlsA using X‐ray crystallography are reported.

G protein‐coupled receptor regulation of the alpha‐arrestin ARRDC3

Adaptor proteins are an important class of proteins that help to maintain proper spatiotemporal control of cell signaling. One of the best‐studied families of adaptor proteins are the ubiquitously expressed beta‐arrestins, which are known to be key regulators of G protein‐coupled receptor (GPCR) function. Recently another family of arrestins, termed the alpha‐arrestins, were discovered and shown to be expressed in mammalian cells. While alpha‐ and beta‐arrestins share minimal sequence homology, they are predicted to be structurally similar, and therefore may be subject to common regulatory mechanisms. However, while GPCR regulation of beta‐arrestin function has been well characterized, it remains entirely unknown how GPCRs might regulate alpha‐arrestins, such as ARRDC3. We recently showed that ARRDC3 is a multifunctional adaptor that distinctly regulates protease‐activated receptor‐1 (PAR1) signaling and trafficking, but it remains unknown how these distinct ARRDC3 functions may be regulated. PAR1 is a GPCR for the protease thrombin and is known to regulate a diverse array of physiological functions in health and disease, thus, it is important to better understand the molecular mechanisms that control PAR1 function. The objective of this study is to understand the mechanisms that control ARRDC3 multifaceted functions. We hypothesize that GPCRs regulate ARRDC3 function via distinct processes that enable diverse functions. Using biochemical and microscopy‐based techniques, we show that PAR1 may regulate ARRDC3 through modulation of post‐translational modifications, including ubiquitination. We also show that ubiquitin is critical for regulating distinct ARRDC3 functions, including regulation of GPCR signaling and trafficking, through various mechanisms that may include control of protein stability, subcellular localization, and protein‐protein interactions. Additionally, ARRDC3 has previously been shown to act as a tumor suppressor in highly invasive triple‐negative breast cancers. Thus, in future studies we will assess the role of ubiquitination on ARRDC3 tumor suppressor function in vitro in vivo. The results of these studies will advance our understanding of how alpha‐arrestins may contribute to GPCR regulation and may lead to the identification of novel targets for therapeutic development to treat metastatic breast cancer.

Quantitative structure–activity relationship modeling reveals the minimal sequence requirement and amino acid preference of sirtuin-1’s deacetylation substrates in diabetes mellitus

Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide ([Formula: see text]-dependent deacetylase involved in multiple glucose metabolism pathways and plays an important role in the pathogenesis of diabetes mellitus (DM). The enzyme specifically recognizes its deacetylation substrates' peptide segments containing a central acetyl-lysine residue as well as a number of amino acids flanking the central residue. In this study, we attempted to ascertain the minimal sequence requirement (MSR) around the central acetyl-lysine residue of SIRT1 substrate-recognition sites as well as the amino acid preference (AAP) at different residues of the MSR window through quantitative structure-activity relationship (QSAR) strategy, which would benefit our understanding of SIRT1 substrate specificity at the molecular level and is also helpful to rationally design substrate-mimicking peptidic agents against DM by competitively targeting SIRT1 active site. In this procedure, a large-scale dataset containing 6801 13-mer acetyl-lysine peptides (and their SIRT1-catalyized deacetylation activities) were compiled to train 10 QSAR regression models developed by systematic combination of machine learning methods (PLS and SVM) and five amino acids descriptors (DPPS, T-scale, MolSurf, [Formula: see text]-score, and FASGAI). The two best QSAR models (PLS+FASGAI and SVM+DPPS) were then employed to statistically examine the contribution of residue positions to the deacetylation activity of acetyl-lysine peptide substrates, revealing that the MSR can be represented by 5-mer acetyl-lysine peptides that meet a consensus motif [Formula: see text][Formula: see text][Formula: see text](AcK)0[Formula: see text]. Structural analysis found that the [Formula: see text] and (AcK)0 residues are tightly packed against the enzyme active site and confer both stability and specificity for the enzyme-substrate complex, whereas the [Formula: see text], [Formula: see text] and [Formula: see text] residues are partially exposed to solvent but can also effectively stabilize the complex system. Subsequently, a systematic deacetylation activity change profile (SDACP) was created based on QSAR modeling, from which the AAP for each residue position of MSR was depicted. With the profile, we were able to rationally design an SDACP combinatorial library with promising deacetylation activity, from which nine MSR acetyl-lysine peptides as well as two known SIRT1 acetyl-lysine peptide substrates were tested by using SIRT1 deacetylation assay. It is revealed that the designed peptides exhibit a comparable or even higher activity than the controls, although the former is considerably shorter than the latter.

Pleiotrophin Interaction with Synthetic Glycosaminoglycan Mimetics.

Chondroitin sulfate (CS) E is the natural ligand for pleiotrophin (PTN) in the central nervous system (CNS) of the embryo. Some structures of PTN in solution have been solved, but no precise location of the binding site has been reported yet. Using 15N-labelled PTN and HSQC NMR experiments, we studied the interactions with a synthetic CS-E tetrasaccharide corresponding to the minimum binding sequence. The results agree with the data for larger GAG (glycosaminoglycans) sequences and confirm our hypothesis that a synthetic tetrasaccharide is long enough to fully interact with PTN. We hypothesize that the central region of PTN is an intrinsically disordered region (IDR) and could modify its properties upon binding. The second tetrasaccharide has two benzyl groups and shows similar effects on PTN. Finally, the last measured compound aggregated but beforehand, showed a behavior compatible with a slow exchange in the NMR time scale. We propose the same binding site and mode for the tetrasaccharides with and without benzyl groups.

Existence of solution for a class of activator–inhibitor systems

AbstractWe prove the existence of a solution for a class of activator–inhibitor system of type $- \Delta u +u = f(u) -v$ , $-\Delta v+ v=u$ in $\mathbb{R}^{N}$ . The function f is a general nonlinearity which can grow polynomially in dimension $N\geq 3$ or exponentiallly if $N=2$ . We are able to treat f when it has critical growth corresponding to the Sobolev space we work with. We transform the system into an equation with a nonlocal term. We find a critical point of the corresponding energy functional defined in the space of functions with norm endowed by a scalar product that takes into account such nonlocal term. For that matter, and due to the lack of compactness, we deal with weak convergent minimizing sequences and sequences of Lagrange multipliers of an action minima problem.

Phosphate-Solubilizing Microorganisms for Agricultural Sustainability

Identification, evaluation and optimization of a minimum simple sequence repeat marker set for triticale breedingW.C. Botes and D. Bitalo

An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms

Designing oligonucleotide-sensing ribozymes using computational approaches is advantageous to in vitro selection methods for efficiency and accuracy. Allosteric ribozymes can be computationally designed for various applications in gene therapy, designer gene control systems, biosensors, and molecular computation. Here we present two programs, the allosteric Ribozyme Generator (RG) and the Inverse Folding Ribozyme Generator (IFRG), engineered to generate allosteric ribozymes with YES logic. The RG computes allosteric ribozyme sequences’ secondary structure using the minimal sequence of the hammerhead ribozyme by inserting oligonucleotide binding site (OBS) elements in the second stem. The IFRG program uses inverse folding to generate allosteric ribozyme sequences with OBS bearing distinct sequences and similar folding. For the generation of the OBS sequences, random search algorithms are employed. Allosteric ribozyme sequences generated by the RG can be used as a matrix for the IFRG program. This approach applies RNA-folding algorithms based on applying thermodynamic parameters using the partition function of the RNAfold, and the RNAinverse source codes from the Vienna RNA folding package. The two algorithms apply dynamic programming and random search algorithms to generate in silico allosteric ribozymes with predefined properties within minutes using a personal computer with over 90% accuracy, without high computation power as experimentally validated and published by us previously.

Multi-step interval prediction of ultra-short-term wind power based on CEEMDAN-FIG and CNN-BiLSTM.

Aiming at the uncertainty of wind power and the low accuracy of multi-step interval prediction, an ultra-short-term wind power multi-step interval prediction method based on complete ensemble empirical mode decomposition with adaptive noise-fuzzy information granulation (CEEMDAN-FIG) and convolutional neural network-bidirectional long short-term memory (CNN-BiLSTM) is proposed. Firstly, the CEEMDAN is used to decompose the wind power time series into several sub-components to reduce the non-stationary characteristics of the wind power time series. Then, different components are selected for FIG, and the maximum value sequence, average value sequence, minimum value sequence gotten from FIG, and the remaining components without FIG are combined with the wind speed data, wind direction data, and the temperature data. They all are input into the CNN-BiLSTM combined prediction model to obtain the initial wind power prediction interval. The prediction results of the maximum value sequence, the average value sequence, and the minimum value sequence are respectively superimposed on the prediction results of the remaining components to obtain the upper limit, point prediction, and lower limit of the initial prediction interval. Finally, the improved coverage width criterion is used as the objective function to optimize the interval, and the forecast interval of wind power under a given confidence level is generated. Taking the actual operating data of a certain unit of a wind farm as an example, the validity of the proposed model is verified.

Rapid Donor-Specific Single Nucleotide Variation Detection by Nanopore Sequencing of Ex Vivo Lung Perfusate

<h3>Purpose</h3> Donor-derived cell-free DNA (cfDNA) has been shown to be useful to monitor the health of the lung graft. To distinguish donor from recipient cfDNA in the blood, single nucleotide variations (SNV) between the genome of the donor and recipient are generally used. However, this requires whole genome sequencing which is time-consuming and costly. A recently developed sequencing technology known as nanopore sequencing may prove to be a solution. Nanopore sequencing requires minimal preparation and sequences are read out in real-time. When combined with ex vivo lung perfusion (EVLP), we hypothesize that we can rapidly generate a donor-specific SNV map by nanopore sequencing of the perfusate cfDNA. In this study, we investigated the feasibility of using the nanopore sequencer to call donor SNVs from EVLP perfusate cfDNA (<b>Fig A</b>). <h3>Methods</h3> EVLP perfusate samples from 4 clinical cases were collected at 4h of perfusion. DNA was extracted and library preparation performed using the Oxford Nanopore Rapid Sequencing Kit (<b>Fig B</b>). To correct for the low accuracy of nanopore sequencing, identified SNVs were compared to publicly accessible databases of common SNVs (dbSNP) in the population. We further compared the SNVs identified by nanopore sequencing with short-read sequencing of the same sample in 1 case. <h3>Results</h3> The mean and range of reads generated in the four cases were 69k and 6k-247k respectively. The average dbSNP overlap was 16,116, with a range of 907-57,558 (<b>Fig C</b>). In the case where we compared to short-read sequencing, we obtained 13,976 SNV overlaps. All sequencing was possible within 4 hours of preparation from perfusate samples. <h3>Conclusion</h3> The nanopore sequencer allowed us to quickly search for donor SNVs from cfDNA in EVLP perfusate. In addition, comparison with short-read sequencing data demonstrated overlap and supports this approach. Further optimization of library preparation and validation with short-read sequencing is needed.

Automata and finite order elements in the Nottingham group

The Nottingham group at 2 is the group of (formal) power series t+a2t2+a3t3+⋯ in the variable t with coefficients ai from the field with two elements, where the group operation is given by composition of power series. The depth of such a series is the largest d⩾1 for which a2=…=ad=0.Only a handful of power series of finite order (forcedly a power of 2) are explicitly known through a formula for their coefficients. We argue in this paper that it is advantageous to describe such series in closed computational form through automata, based on effective versions of proofs of Christol's theorem identifying algebraic and automatic series.Up to conjugation, there are only finitely many series σ of order 2n with fixed break sequence (i.e. the sequence of depths of σ∘2i). Starting from Witt vector or Carlitz module constructions, we give an explicit automaton-theoretic description of: (a) representatives up to conjugation for all series of order 4 with break sequence (1,m) for m<10; (b) representatives up to conjugation for all series of order 8 with minimal break sequence (1,3,11); and (c) an embedding of the Klein four-group into the Nottingham group at 2.We study the complexity of the new examples from the algebro-geometric properties of the equations they satisfy. For this, we generalise the theory of sparseness of power series to a four-step hierarchy of complexity, for which we give both Galois-theoretic and combinatorial descriptions. We identify where our different series fit into this hierarchy. We construct sparse representatives for the conjugacy class of elements of order two and depth 2μ±1(μ⩾1). Series with small state complexity can end up high in the hierarchy. This is true, for example, for a new automaton we found, representing a series of order 4 with 5 states (the minimal possible number for such a series).

Unique peptide signatures of SARS-CοV-2 virus against human proteome reveal variants’ immune escape and infectiveness

SARS-CoV-2 pandemic has necessitated the identification of sequence areas in the viral proteome that are capable to serve as antigenic sites and treatment targets. In the present study, we have applied a novel approach for mechanistically illuminating the virus-host organism interactions, by analyzing the Unique Peptides (UPs) of the virus featured by a minimum amino acid sequence length being defined as Core Unique Peptides (CrUPs), not of the virus per se, but against the entire proteome of the host organism. This approach resulted in the identification of CrUPs of the virus itself, which could not be recognized in the host organism proteome. Thereby, we analyzed the SARS-CoV-2 proteome for identification of CrUPs against the human proteome, which have been defined as C/H-CrUPs. We herein reveal that SARS-CoV-2 include 7.503 C/H-CrUPs, with the SPIKE_SARS2 being detected as the protein with the highest density of C/H-CrUPs. Extensive analysis has indicated that the critical P681R mutation produces new C/H-CrUPs around the R685 cleavage site, while the L452R mutation causes loss of antigenicity of the NF9 peptide and strong(er) binding of the virus to its ACE2 receptor protein. Simultaneous formation of these mutations in detrimental variants like Delta leads to the immune escape of the virus, its massive entrance into the host cell, a notable increase in virus formation, and its massive release and thus elevated infectivity of human target cells.

Minimal bad sequences are necessary for a uniform Kruskal theorem

Kruskal's theorem on trees is a classical result of combinatorics with important applications in computer science. The minimal bad sequence argument of Nash-Williams yields a proof that is very elegant but not as elementary as possible, by previous results from mathematical logic. In the present paper, we formulate a uniform Kruskal theorem, which extends the original theorem from trees to general recursive data types. Our main result shows that the minimal bad sequence argument does yield the most elementary proof of this uniform Kruskal theorem. So in the uniform case, the elegant proof coincides with the most elementary one. In more precise and technical terms, we work in the framework of reverse mathematics, where we show that the uniform Kruskal theorem is equivalent to Π11-comprehension, over RCA0 extended by the chain-antichain principle. As a by-product of our investigation, we obtain uniform proofs of several Kruskal-type independence results.

Longitudinal personalized urinary tumor DNA analysis in muscle-invasive bladder cancer from the neoadjuvant immunotherapy trial RJBLC-I2N003.

552 Background: RJBLC-I2N003 is an investigator-initiated study to evaluate the clinical activity and predictive biomarkers for neoadjuvant immunotherapy with toripalimab (anti-PD-1) in muscle invasive bladder cancer (MIBC). Methods: Twenty patients with pathologically confirmed MIBC were enrolled and received toripalimab (3 mg/kg Q2W, 4 cycles) before radical cystectomy. The safety and efficacy of neoadjuvant toripalimab were assessed. Serial urinary cell-free DNA (ucfDNA) and blood cell-free DNA (bcfDNA) were obtained at baseline and after each cycle of toripalimab treatment. Personalized minimal residual disease (MRD) assays and low-pass whole genome sequencing (LP-WGS) were applied to analyze liquid biopsy samples. Results: Eighteen patients (90%) completed all 4 cycles of neoadjuvant treatment. Grade 3-4 immune-related adverse events occurred in two patients (10%). Eight patients (40%) achieved a pathological complete response (pCR). Thirteen patients (65%) had no remaining invasive disease (pCR or pTisN0/pTaN0). Pre-treatment somatic variants and copy number abnormalities were prevalently detected in ucfDNA as compared to bcfDNA. On-treatment urinary tumor DNA (utDNA) clearance was associated with objective responses. Preliminary concordance was observed between molecular and pathological MRD status. Conclusions: These findings suggest that neoadjuvant administration of PD-1 blockade followed by surgical resection represents a feasible and efficacious approach to treat MIBC. The exploratory biomarker assessment demonstrates the potential utility of longitudinal personalized utDNA analysis to complement existing trial endpoints.

Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis.

Single-cell RNA sequencing is a powerful technique that continues to expand across various biological applications. However, incomplete 3′-UTR annotations can impede single-cell analysis resulting in genes that are partially or completely uncounted. Performing single-cell RNA sequencing with incomplete 3′-UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single-cell isoform sequencing in tandem with single-cell RNA sequencing can rapidly improve 3′-UTR annotations. Using threespine stickleback fish (Gasterosteus aculeatus), we show that gene models resulting from a minimal embryonic single-cell isoform sequencing dataset retained 26.1% greater single-cell RNA sequencing reads than gene models from Ensembl alone. Furthermore, pooling our single-cell sequencing isoforms with a previously published adult bulk Iso-Seq dataset from stickleback, and merging the annotation with the Ensembl gene models, resulted in a marginal improvement (+0.8%) over the single-cell isoform sequencing only dataset. In addition, isoforms identified by single-cell isoform sequencing included thousands of new splicing variants. The improved gene models obtained using single-cell isoform sequencing led to successful identification of cell types and increased the reads identified of many genes in our single-cell RNA sequencing stickleback dataset. Our work illuminates single-cell isoform sequencing as a cost-effective and efficient mechanism to rapidly annotate genomes for single-cell RNA sequencing.

Cell scientist to watch – Mounia Lagha

ABSTRACT Mounia Lagha studied Biology at the Grande École AGRO-INA-PG in Paris (now AgroParisTech). She then pursued her PhD in the lab of Margaret Buckingham at the Institut Pasteur, where she worked on the regulation of myogenesis by the transcription factor Pax3. In 2010, she joined the lab of Michael Levine at UC Berkeley, USA for her postdoc; there, she discovered that minimal promoter sequences control RNA polymerase II pausing, which is essential for transcriptional synchrony and coordinated cell behaviour during gastrulation in the fly embryo. Mounia started her independent research group in 2015, funded by an ERC starting grant, at the Institute of Molecular Genetics of Montpellier (IGMM), French National Centre for Scientific Research (CNRS). Using live imaging approaches in Drosophila, her lab studies the coordination of transcription and transcriptional memory, and more recently the dynamics of translation. In 2021, Mounia was selected as an EMBO Young Investigator.