Biology subjects

Makova, K. D.

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

5 recordsLinked to original sources

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↗

bioRxiv2017

Copy number variation of ampliconic genes across major human Y haplogroups

Due to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only three gene families (DATZ, RBMY, TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individuals height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

evolutionary biology↗

bioRxiv2017

Correcting palindromes in long reads after whole-genome amplification

Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long reads from technologies such as PacBio and Oxford Nanopore. Here, we present Pacasus, a tool for correcting such errors in long reads. We demonstrate on two real-world datasets that it markedly improves subsequent read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. With Pacasus long-read technologies become readily available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.

genomics↗