Biology subjects

Makova, K. D.

Publications and source records attributed to Makova, K. D..

At least 19 recordsLinked to original sources

bioRxiv2026

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

Detecting Darwinian natural selection is fundamental to evolutionary biology and functional genomics, yet standard methods based on phylogenetic models that estimate the ratio of non-synonymous to synonymous substitution rates (dN/dS) fail to scale with modern genomic volumes. Fitting continuous-time Markov substitution matrices across dense trees with hundreds of species requires extensive compute, forcing comparative genomics to rely on aggressive taxon subsampling or static whole-tree summaries that dilute transient adaptive bursts. Here we present HyphAeon, a lightweight (~1.91M parameter backbone, 2.46M across the full multi-task suite) phylogeny-informed foundation transformer trained to amortize the detection of episodic diversifying selection across 742-species mammalian coding alignments (17,186 genes, 9.77 x 10^6 codons). HyphAeon approaches the discriminative accuracy of numerical maximum-likelihood selection tests (MEME) across episodic burst regimes (ROC-AUC up to 0.942, mean 0.659; empirical Precision-Recall lift up to 25.8x, mean 7.7x; rank concordance up to rho = 0.983) while executing >1,000x faster per locus (averaging <1 ms per site across genome-wide scans) and >10,000x faster at proteome scale, generalizing outside its mammalian training distribution without retraining. Beyond accelerating classical tests, embedding molecular evolution into a differentiable geometric latent space enables analytical capabilities inaccessible to static dN/dS models: (1) targeted alignment artifact correction via counterfactual attribution; (2) macromolecular contact recovery and multi-site epistatic sectors (CESI); (3) directional phenotype-to-genotype attribution in lineage space (PARS); and (4) continuous temporal surveillance regression that tracks positive sweep velocities across longitudinal cohorts (evaluated across 12,167 timestamped genomes and benchmarked against external frequencies from >9.34 million genomes), rescuing adaptive substitutions obscured by post-fixation dilution. By bridging statistical phylogenetics with geometric representation learning, HyphAeon establishes comparative genomics as an interactive, high-throughput computational framework for evolutionary discovery.

bioinformatics↗

bioRxiv2026

Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches

Progress has been made in identifying G-quadruplexes (G4s) and other non-canonical (non-B) DNA structures in live cells. However, these experiments have been limited by methodological constraints, including low resolution and specificity, and GC-sequencing bias inherent to the short-read sequencing technologies. Direct, single-molecule, and long-read technologies have the potential to address these shortcomings. Here, we investigated the use of long-read DNA sequencing with Oxford Nanopore Technologies (ONT) to detect G4 and other non-B DNA structures. We applied ONT sequencing to oligos known to form G4s in vitro, as well as to DNA from live cells. Both experiments were probed with potassium permanganate, a chemical that preferentially oxidizes single-stranded DNA (ssDNA). We determined that G4 structures can be resolved by ONT sequencing, and a G4 motifs sequencing error profile depends on the original structural state of the G4 (as determined in vitro). We next applied machine learning algorithms (logistic regression, random forest, XGBoost, and 1D convolutional neural networks) to the raw ONT sequencing current data. Using these approaches, we could determine whether a sequencing read originated from a G4 motif in the G4 vs. B-form conformation with [~]90% accuracy. Further, we demonstrated that it is possible to sequence permanganate-modified DNA directly using ONT, with minimal effects on the read length, yield, and alignment accuracy. We conclude that at high ONT sequencing depth, this approach can identify B-folded vs. single-stranded DNA regions in cells, with ssDNA frequently present across several non-B DNA structures.

bioinformatics↗

bioRxiv2026

Variation and selection at predicted G-quadruplexes across the human pangenome

G-quadruplexes (G4s), non-canonical DNA structures whose sequence motifs occupy approximately 1% of the human genome, are important for myriad cellular functions, including regulating transcription and replication. Yet they also contribute to genomic instability by increasing mutations and structural variation. Despite their significance, G4 motifs have not been studied in detail across multiple human genomes. Here, we conducted a comprehensive analysis of presence/absence and sequence variation, measured selection strength, and evaluated gene expression regulation potential for predicted G4s (pG4s) across population groups in the second release of the Human Pangenome Reference Consortium dataset, comprising high-quality, near-telomere-to-telomere diploid genomes from 231 individuals worldwide, along with three reference assemblies. Across the human pangenome, we identified over 353 million pG4s, including 1.15 million pG4s absent from reference assemblies but shared across other haplotypes. Our analysis revealed that pG4 sharing patterns recapitulate human population structure: African individuals displayed lower levels of pG4 sharing than non-Africans, whereas East Asian individuals exhibited higher levels of sharing. By analyzing the site frequency spectrum across various genomic annotations, we computed and compared selection coefficients (Sd) at pG4 vs. non-pG4 sites. As expected, the strongest purifying selection (Sd [≥] 10) was detected at protein-coding exons, where pG4 sites had similar or lower selection coefficients compared with those for pG4 sites. Strikingly, this pattern reversed at regulatory regions: although purifying selection was weaker overall at promoters, introns, enhancers, and replication origins (1 [≤] Sd < 10), pG4 sites at these regions experienced stronger selection than non-pG4 sites--suggesting that pG4s play functional roles outside coding sequences. Additionally, by integrating pG4 data with long-read transcriptome data profiles from this large cohort, we found that pG4s located at promoters and at (or near) exon-intron junctions may influence variation in gene expression levels and transcript isoforms, respectively, across the human pangenome individuals. Leveraging extensive population-scale data, our research illuminates the fundamental importance and functional relevance of G4s across human genomes.

genomics↗

bioRxiv2026

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The human Y chromosome is among the most structurally dynamic chromosomes in the human genome, yet much of its diversity remains unresolved because of extensive palindromes, ampliconic gene families, satellite-rich heterochromatin and large segmental duplications. What remained unclear was how these diverse forms of variation fit together across the full chromosome, how often similar structures recur in different lineages, and which aspects of organization remain constrained despite rapid sequence turnover. Here, we generated and analyzed 142 nearly complete human Y chromosome assemblies from 17 major haplogroups spanning approximately 180,000 years of evolution, creating a population-scale resource for studying Y chromosome biology and diversity. These assemblies show that structural change on the Y chromosome is recurrent but constrained, even in its most repetitive regions. In the fertility-associated azoospermia factor c (AZFc) region, recurrent inversions, deletions, and complex rearrangements generate a limited repertoire of structural haplotypes. Multicopy ampliconic gene families follow distinct evolutionary paths: DAZ paralogues differ in structural constraint, RBMY evolves within a modular array, and TSPY copy number varies mainly through local expansion and contraction. The centromere and Yq12 heterochromatin vary greatly in size but retain a stable higher-order organization, including a single hypomethylated centromeric core and conserved Yq12 repeat composition and orientation. Methylation across palindromic and ampliconic regions is likewise structured by repeat class, copy order and local architecture. Together, these results provide a population-scale resource for the human Y chromosome and show that its rapid structural evolution is repeatedly funneled into a limited set of architectural outcomes.

genomics↗

bioRxiv2026

Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification

BackgroundLong non-coding RNAs (lncRNAs) have gained significant attention in recent years, yet distinguishing them from protein-coding transcripts remains challenging. Indeed, many lncRNAs share mRNA-like processing and existing sequence-derived signals do not fully capture the coding/non-coding boundary. Recent GENCODE annotation efforts revealed tens of thousands of novel lncRNA sequences as well as the reclassification of some lncRNAs into the protein-coding class, highlighting the need to better characterize transcript features associated with classification uncertainty and errors. ResultsWe performed uncertainty-aware benchmarking by retraining and evaluating eight transcript classifiers under a controlled protocol on a label-stable GENCODE v46-v47 subset. Beyond conventional model evaluation metrics, we quantified inter-tool agreement and entropy-based uncertainty to stratify transcripts into consensus, discordant, and consensus-error groups. To expand standard sequence and ORF-derived signals, we incorporated repeat-derived features from mature transcripts and non-B DNA motif features across gene bodies. Although aggregate performance was high, [~]45% of transcripts showed inter-tool discordance, particularly among lncRNAs. Feature analyses linked low-uncertainty predictions to strong coding-like signals, whereas high-uncertainty profiles exhibited mixed signatures. Alongside classical predictors in global importance analyses, repeat-derived features appear as main contributors. ConclusionsBy combining controlled benchmarking with transcript-level agreement and uncertainty stratification, together with extended feature profiling, we identified patterns associated with classifier disagreement and misclassification. This novel framework provides practical guidance for interpreting predictions, motivating the development of more robust coding/non-coding classifiers, while also shedding light on the sequence properties that distinguish lncRNA sequences.

bioinformatics↗

bioRxiv2026

A Complete Genome for the Common Marmoset

The common marmoset is a New World monkey (NWM) commonly used as a model organism to investigate questions in primate evolution and human disease, including Alzheimers and other neurodegenerative diseases, as well as neuropsychiatric disorders. Here we present the first telomere-to-telomere (T2T) reference genome for the common marmoset, adding over 88 Mb of sequence and resolving challenging genomic regions. An additional near-T2T assembly from a second unrelated individual yields a total of four high-quality haplotypes for analysis. The improved contiguity and accuracy of these assemblies enable unprecedented insights into complex and rapidly evolving genomic regions such as centromeres, sex chromosomes, ribosomal DNA (rDNA) structure, and the major histocompatibility complex (MHC). We fully resolved all marmoset centromeres, uncovering dimeric alpha satellites with chromosomal specificity and stratified inactive layers documenting ancestral centromere turnover. We assembled six acrocentric autosomes with gene-poor, satellite-rich short arms and provide evidence that most of them can harbor rDNA and all of them share large pseudo-homologous regions (PHRs). The Y chromosome, but not the X chromosome, carries active rDNA and PHRs, and the rDNA copy number is sexually dimorphic. Chromosomes that share PHRs also share closely related centromeric satellite DNA, supporting a model of ongoing recombinational exchange between heterologous chromosomes facilitated by rDNA. We discovered multiple novel, marmoset-specific MHC genes that are predicted to protect against pathogens encountered in its environment. Leveraging this complete reference, we further identified over 500 transcribed genes with transcript models or expansions specific to the marmoset lineage. Together with additional long-read marmoset assemblies, these genomes were used to construct a marmoset pangenome, providing a robust reference framework for short-read mapping across diverse individuals. This resource will improve the utility of the common marmoset as a biomedical model organism and fill key gaps in our understanding of primate evolution.

genomics↗

bioRxiv2025

Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes

Mitochondrial sequences have integrated into the nuclear genome since the origin of eukaryotes. Recent insertions that retain homology to extant mitochondrial DNA (mtDNA), termed NUMTs, confound mtDNA sequence analysis. Here, we used great ape Telomere-to-Telomere (T2T) genomes to study NUMTs in bonobo, chimpanzee, human, gorilla, and Bornean and Sumatran orangutans. A phylogeny based on shared and lineage-specific NUMTs accurately recapitulated the great ape species tree topology. NUMTs were enriched at non-functional non-repetitive regions of the nuclear genome, and depleted within enhancers and coding sequences, suggesting negative selection. We validated the presence of a 76-kilobase-long heterozygous NUMT in chimpanzee, which was larger than any other NUMT observed in great apes, and found that dozens of NUMTs on the Pan Y chromosome expanded together with palindromes. Our study highlights NUMTs as a dynamic evolutionary force contributing to shaping ape genomes, and is valuable for characterizing mtDNA in great apes.

genomics↗

bioRxiv2024

Mitochondrial DNA mutations in human oocytes undergo frequency-dependent selection but do not increase with age

Mitochondria, cellular powerhouses, harbor DNA (mtDNA) inherited from the mothers. MtDNA mutations can cause diseases, yet whether they increase with age in human germline cells--oocytes--remains understudied. Here, using highly accurate duplex sequencing of full-length mtDNA, we detected de novo mutations in single oocytes, blood, and saliva in women between 20 and 42 years of age. We found that, with age, mutations increased in blood and saliva but not in oocytes. In oocytes, mutations with high allele frequencies ([≥]1%) were less prevalent in coding than non-coding regions, whereas mutations with low allele frequencies (<1%) were more uniformly distributed along mtDNA, suggesting frequency-dependent purifying selection. In somatic tissues, mutations caused elevated amino acid changes in protein-coding regions, suggesting positive or destructive selection. Thus, mtDNA in human oocytes is protected against accumulation of mutations having functional consequences and with aging. These findings are particularly timely as humans tend to reproduce later in life. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/627454v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@18242f6org.highwire.dtl.DTLVardef@fa5a97org.highwire.dtl.DTLVardef@51a452org.highwire.dtl.DTLVardef@1fb2374_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Non-canonical DNA in human and other ape telomere-to-telomere genomes

Non-canonical (non-B) DNA structures--e.g., bent DNA, hairpins, G-quadruplexes (G4s), Z-DNA, etc.--which form at certain sequence motifs (e.g., A-phased repeats, inverted repeats, etc.), have emerged as important regulators of cellular processes and drivers of genome evolution. Yet, they have been understudied due to their repetitive nature and potentially inaccurate sequences generated with short-read technologies. Here we comprehensively characterize such motifs in the long-read telomere-to-telomere (T2T) genomes of human, bonobo, chimpanzee, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. Non-B DNA motifs are enriched at the genomic regions added to T2T assemblies, and occupy 9-15%, 9-11%, and 12-38% of autosomes, and chromosomes X and Y, respectively. G4s and Z-DNA are enriched at promoters and enhancers, as well as at origins of replication. Repetitive sequences harbor more non-B DNA motifs than non-repetitive sequences, especially in the short arms of acrocentric chromosomes. Most centromeres and/or their flanking regions are enriched in at least one non-B DNA motif type, consistent with a potential role of non-B structures in determining centromeres. Our results highlight the uneven distribution of predicted non-B DNA structures across ape genomes and suggest their novel functions in previously inaccessible genomic regions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/610891v3_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1a359forg.highwire.dtl.DTLVardef@b66b36org.highwire.dtl.DTLVardef@38dae8org.highwire.dtl.DTLVardef@abdf84_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies

The mammalian Y chromosome is an evolutionary paradox: it cannot recombine across most of its length and has lost many genes, yet it retains multicopy gene families required for sperm production. How these genes survive has been difficult to resolve because their near-identical copies collapse in most genome assemblies and are difficult to analyze accurately with short RNA reads. Using telomere-to-telomere assemblies of seven ape genomes together with long-read testis transcriptomes, protein-structure predictions, and selection tests, we show that these gene families vary extensively but encode structurally conserved proteins. We demonstrate that, while copy number varies across and within species, palindromes and tandem arrays are equally effective in homogenizing copies via gene conversion--a result we could obtain only with complete assemblies. We detect extensive transcript variation arising from alternative splicing and inter-copy sequence differences. Yet this variation collapses into only a few predicted protein-structure clusters per family. Furthermore, we find evidence of purifying selection acting on gene families (and domains) encoding ordered protein structures--the majority of multicopy families on the human Y. Thus, copy number and (to a lesser degree) sequence, and transcript structure and sequence all vary, whereas protein structure, which is important for spermatogenic function, is held nearly constant. Together, our results show that palindrome- and array-mediated homogenization and purifying selection aimed at preserving protein structure jointly enable the survival of fertility-related genes on the non-recombining Y chromosome. These results will inform diagnostic approaches to human Y-linked infertility and studies of the conservation of non-human great apes.

genomics↗

bioRxiv2023

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

Apes possess two sex chromosomes--the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility1. The X chromosome carries genes vital for reproduction and cognition2. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosomes. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies allowed us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the Xs, the ape Ys vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements, and satellites. Our analysis of Y chromosome genes revealed expansions of multi-copy gene families and signatures of purifying selection. Thus, the Y exhibits dynamic evolution, while the X is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of >100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species.

genomics↗

bioRxiv2023

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes

Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been recently studied in great apes, however, the diversity of splicing variants remains unexplored. Here we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture-probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this dataset resulted in several findings. First, we uncovered a high diversity of YAG transcripts across great apes. Second, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Our results suggest that BPY2 transcripts and predicted proteins in several great ape species (bonobo and the two orangutans) have independent evolutionary origins and are not homologous to human reference transcripts and proteins. In contrast, our results suggest that the PRY gene family, having the highest representation of transcripts without open reading frames, has been undergoing pseudogenization. Third, even though we have identified many species-specific protein-coding YAG transcripts, we have not detected any signatures of positive selection. Overall, our work illuminates the YAG isoform landscape and its evolutionary history, and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.

genomics↗

bioRxiv2022

Altered sequencing success at non-B-DNA motifs

Modern sequencing technologies are not error-free, and might have elevated error rates at some locations of the genome. A potential cause for such elevated error rates is the formation of alternative DNA structures (non-B DNA), such as G-quadruplexes (G4s), Z-DNA, or cruciform structures, during sequencing. Approximately 13% of the human genome has the potential to form such structures, which have been previously shown to affect the activity of DNA polymerases and helicases. Here we tested whether motifs with the potential to form non-B DNA (non-B motifs) influence the sequencing success of three major sequencing technologies--Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT). We estimated sequencing success by computing the rates of single-nucleotide, insertion, and deletion errors, as well as by evaluating mean read depth and mean base quality. Overall, all technologies exhibited altered sequencing success for most non-B motif types. Single-nucleotide error rates were generally increased for G-quadruplexes (G4s) and Z-DNA motifs in all three technologies. Illumina and PacBio HiFi deletion error rates were also increased for all non-B types except for Z-DNA motifs, while in ONT they were increased substantially only for G4 motifs. Insertion error rates for non-B motifs were highly elevated in Illumina, moderately elevated in PacBio HiFi, and only slightly elevated in ONT. Using Poisson regression modeling, we evaluated how non-B DNA motifs and other factors influence sequencing error profiles. Using the error rates at non-B motifs, we developed a probabilistic approach to determine the number of false-positive single-nucleotide variants (SNVs) in different sample size and variant frequency cutoff scenarios, as well as in previously generated sequencing data sets (1000Genomes, Simons Genome Diversity Project, and gnomAD). Overall, the effect of non-B DNA on sequencing should be considered in downstream analyses, particularly in studies with limited read depth--e.g., single-cell and ancient DNA sequencing, as well as sequencing of pooled population samples--and when scoring variants with low frequency (e.g., singletons). Because each sequencing technology analyzed has a unique error profile at non-B motifs, a combination of different technologies should be considered in future sequencing studies of such motifs, to maximize accuracy.

genomics↗

bioRxiv2019

Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity

Obesity is highly heritable, yet only a small fraction of its heritability has been attributed to specific genetic variants. These variants are traditionally ascertained from genome-wide association studies (GWAS), which utilize samples with tens or hundreds of thousands of individuals for whom a single summary measurement (e.g., BMI) is collected. An alternative approach is to focus on a smaller, more deeply characterized sample in conjunction with advanced statistical models that leverage detailed phenotypes. Here we use novel functional data analysis (FDA) techniques to capitalize on longitudinal growth information and construct a polygenic risk score (PRS) for obesity in children followed from birth to three years of age. This score, comprised of 24 single nucleotide polymorphisms (SNPs), is significantly higher in children with (vs. without) rapid infant weight gain--a predictor of obesity later in life. Using two independent cohorts, we show that genetic variants identified in early childhood are also informative in older children and in adults, consistent with early childhood obesity being predictive of obesity later in life. In contrast, PRSs based on SNPs identified by adult obesity GWAS are not predictive of weight gain in our cohort of children. Our research provides an example of a successful application of FDA to GWAS. We demonstrate that a deep, statistically sophisticated characterization of a longitudinal phenotype can provide increased statistical power to studies with relatively small sample sizes. This study shows how FDA approaches can be used as an alternative to the traditional GWAS. Author SummaryFinding genetic variants that confer an increased risk of developing a particular disease has long been a focus of modern genetics. Genome wide association studies (GWAS) have catalogued single nucleotide polymorphisms (SNPs) associated with a variety of complex diseases in humans, including obesity, but by and large have done so using increasingly large samples-- tens or even hundreds of thousands of individuals, whose phenotypes are thus often only superficially characterized. This, in turn, may hide the intricacies of the genetic influence on disease. GWAS findings are also usually study-population dependent. We found that genetic risk scores based on SNPs from large adult obesity studies are not predictive of the propensity to gain weight in very young children. However, using a small cohort of a few hundred children deeply characterized with growth trajectories between birth and two years, and leveraging such trajectories through novel functional data analysis (FDA) techniques, we were able to produce a strong childhood obesity genetic risk score.

genetics↗

bioRxiv2018

High inter- and intraspecific turnover of satellite repeats in great apes

BackgroundSatellite repeats are a structural component of centromeres and telomeres, and in some instances their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads.\n\nResultsThe density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: (1) the (AATGG)n repeat (critical for heat shock response) and its derivatives; and (2) subtelomeric 32-mers. Using the densities of abundant repeats, individuals could be classified into species. However clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males vs. females; using existing Y chromosome assemblies or FIuorescent In Situ Hybridization, we validated location for some of them on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences.\n\nConclusionsOur results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.

evolutionary biology↗

bioRxiv2018

Mito-nuclear effects uncovered in admixed populations

To function properly, mitochondria utilize products of 37 and >1,000 genes encoded by the mitochondrial and nuclear genomes, respectively, which should be compatible with each other. Discordance between mitochondrial and nuclear genetic ancestry could contribute to phenotypic variation in admixed populations. Here we explored potential mito-nuclear incompatibility in six admixed human populations from the Americas: African Americans, African Caribbeans, Colombians, Mexicans, Peruvians, and Puerto Ricans. For individuals in these populations, we determined nuclear genome proportions derived from Africans, Europeans, and Native Americans, the geographic origins of the mitochondrial DNA (mtDNA), as well as mtDNA copy number in lymphoblastoid cell lines. By comparing nuclear vs. mitochondrial ancestry in admixed populations, we show that, first, mtDNA copy number decreases with increasing discordance between nuclear and mitochondrial DNA ancestry, in agreement with mito-nuclear incompatibility. The direction of this effect is consistent across mtDNA haplogroups of different geographic origins. This observation suggests suboptimal regulation of mtDNA replication when its components are encoded by nuclear and mtDNA genes with different ancestry. Second, while most populations analyzed exhibit no such trend, in Puerto Ricans and African Americans we find a significant enrichment of ancestry at nuclear-encoded mitochondrial genes towards the source populations contributing the most prevalent mtDNA haplogroups (Native American and African, respectively). This likely reflects compensatory effects of selection in recovering mito-nuclear interactions optimized in the source populations. Our results provide the first evidence of mito-nuclear effects in human admixed populations and we discuss its implications for human health and disease.

genetics↗

bioRxiv2018

IsoCon: Deciphering highly similar multigene family transcripts from Iso-Seq data

A significant portion of genes in vertebrate genomes belongs to multigene families, with each family containing several gene copies whose presence/absence can be highly variable across individuals. For example, each Y chromosome ampliconic gene family harbors several nearly identical (up to 99.99%) gene copies. Existing de novo techniques for assaying the sequences of such highly-similar gene families fall short of reconstructing end to end transcripts with nucleotide-level precision or assigning them to their respective gene copies. We present IsoCon, a novel approach that combines experimental and computational techniques that leverage the power of long PacBio Iso-Seq reads to determine the full-length transcripts of highly similar multicopy gene families. IsoCon uses a cautiously iterative process to correct errors, followed by a statistical framework that allows it to distinguish errors from true variants with high precision. IsoCon outperforms existing methods for transcriptome analysis of Y ampliconic gene families in both simulated and real human data and is able to detect rare transcripts that differ by as little as one base pair from much more abundant transcripts. IsoCon has allowed us to detect an unprecedented number of novel isoforms, as well as to derive estimates on the number of gene copies in human Y ampliconic gene families.

genomics↗

bioRxiv2017

Non-B DNA affects polymerization speed and error rate in sequencers and living cells

DNA conformation may deviate from the classical B-form in ~13% of the human genome. Non-B DNA regulates many cellular processes; however, its effects on DNA polymerization speed and accuracy have not been investigated genome-wide. Such an inquiry is critical for understanding neurological diseases and cancer genome instability. Here we present the first simultaneous examination of DNA polymerization kinetics and errors in the human genome sequenced with Single-Molecule-Real-Time technology. We show that polymerization speed differs between non-B and B-DNA: it decelerates at G-quadruplexes and fluctuates periodically at disease-causing tandem repeats. Analyzing polymerization kinetics profiles, we predict and validate experimentally non-B DNA formation for a novel motif. We demonstrate that several non-B motifs affect sequencing errors (e.g., G-quadruplexes increase error rates) and that sequencing errors are positively associated with polymerase slowdown. Finally, we show that highly divergent G4 motifs have pronounced polymerization slowdown and high sequencing error rates, suggesting similar mechanisms for sequencing errors and germline mutations.

genomics↗