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Article: Noncanonical DNA structures are drivers of genome evolution.

Makova, Kateryna D / Weissensteiner, Matthias H

2023 Volume 39, Issue 2, Page(s) 109–124

Abstract: In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence ... ...

Abstract	In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence is associated with elevated mutagenicity and genome instability. These discordant cellular roles fuel the enormous potential of non-B DNA to drive genomic and phenotypic evolution. Here we discuss recent studies establishing non-B DNA structures as novel functional elements subject to natural selection, affecting evolution of transposable elements (TEs), and specifying centromeres. By highlighting the contributions of non-B DNA to repeated evolution and adaptation to changing environments, we conclude that evolutionary analyses should include a perspective of not only DNA sequence, but also its structure.
MeSH term(s)	Humans ; DNA Transposable Elements/genetics ; Base Sequence ; Genomics ; Genomic Instability/genetics ; Evolution, Molecular
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2023-01-03
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2022.11.005
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Article: Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies.

Greshnova, Aleksandra / Pál, Karol / Martinez, Juan Francisco Iturralde / Canzar, Stefan / Makova, Kateryna D

bioRxiv : the preprint server for biology

2024

Abstract: ... ...

Abstract	Y
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.02.587783
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Article: Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.

Tomaszkiewicz, Marta / Sahlin, Kristoffer / Medvedev, Paul / Makova, Kateryna D

bioRxiv : the preprint server for biology

2023

Abstract: 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, ... ...

Abstract	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 (
Language	English
Publishing date	2023-03-18
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.02.530874
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Article ; Online: Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.

Tomaszkiewicz, Marta / Sahlin, Kristoffer / Medvedev, Paul / Makova, Kateryna D

Genome biology and evolution

2023 Volume 15, Issue 11

Abstract: 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 studied in great apes; however, ... ...

Abstract	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 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 data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.
MeSH term(s)	Animals ; Male ; Humans ; Pan paniscus/genetics ; Hominidae/genetics ; Y Chromosome/genetics ; Pan troglodytes/genetics ; Protein Isoforms/genetics
Chemical Substances	Protein Isoforms
Language	English
Publishing date	2023-11-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evad205
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Article: Exploring the Effects of Mitonuclear Interactions on Mitochondrial DNA Gene Expression in Humans.

Torres-Gonzalez, Edmundo / Makova, Kateryna D

Frontiers in genetics

2022 Volume 13, Page(s) 797129

Abstract: Most mitochondrial protein complexes include both nuclear and mitochondrial gene products, which coevolved to work together. This coevolution can be disrupted due to disparity in genetic ancestry between the nuclear and mitochondrial genomes in recently ... ...

Abstract	Most mitochondrial protein complexes include both nuclear and mitochondrial gene products, which coevolved to work together. This coevolution can be disrupted due to disparity in genetic ancestry between the nuclear and mitochondrial genomes in recently admixed populations. Such mitonuclear DNA discordance might result in phenotypic effects. Several nuclear-encoded proteins regulate expression of mitochondrial DNA (mtDNA) genes. We hypothesized that mitonuclear DNA discordance affects expression of genes encoded by mtDNA. To test this, we utilized the data from the GTEx project, which contains expression levels for ∼100 African Americans and >600 European Americans. The varying proportion of African and European ancestry in recently admixed African Americans provides a range of mitonuclear discordance values, which can be correlated with mtDNA gene expression levels (adjusted for age and ischemic time). In contrast, European Americans did not undergo recent admixture. We demonstrated that, for most mtDNA protein-coding genes, expression levels in energetically-demanding tissues were lower in African Americans than in European Americans. Furthermore, gene expression levels were lower in individuals with higher mitonuclear discordance, independent of population. Moreover, we found a negative correlation between mtDNA gene expression and mitonuclear discordance. In African Americans, the average value of African ancestry was higher for nuclear-encoded mitochondrial than non-mitochondrial genes, facilitating a match in ancestry with the mtDNA and more optimal interactions. These results represent an example of a phenotypic effect of mitonuclear discordance on human admixed populations, and have potential biomedical applications.
Language	English
Publishing date	2022-06-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.797129
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Article ; Online: In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq).

Lahnsteiner, Angelika / Craig, Sarah J C / Kamali, Kaivan / Weissensteiner, Bernadette / McGrath, Barbara / Risch, Angela / Makova, Kateryna D

Methods in enzymology

2024 Volume 695, Page(s) 159–191

Abstract: DNA secondary structures are essential elements of the genomic landscape, playing a critical role in regulating various cellular processes. These structures refer to G-quadruplexes, cruciforms, Z-DNA or H-DNA structures, amongst others (collectively ... ...

Abstract	DNA secondary structures are essential elements of the genomic landscape, playing a critical role in regulating various cellular processes. These structures refer to G-quadruplexes, cruciforms, Z-DNA or H-DNA structures, amongst others (collectively called 'non-B DNA'), which DNA molecules can adopt beyond the B conformation. DNA secondary structures have significant biological roles, and their landscape is dynamic and can rearrange due to various factors, including changes in cellular conditions, temperature, and DNA-binding proteins. Understanding this dynamic nature is crucial for unraveling their functions in cellular processes. Detecting DNA secondary structures remains a challenge. Conventional methods, such as gel electrophoresis and chemical probing, have limitations in terms of sensitivity and specificity. Emerging techniques, including next-generation sequencing and single-molecule approaches, offer promise but face challenges since these techniques are mostly limited to only one type of secondary structure. Here we describe an updated version of a technique permanganate/S1 nuclease footprinting, which uses potassium permanganate to trap single-stranded DNA regions as found in many non-B structures, in combination with S1 nuclease digest and adapter ligation to detect genome-wide non-B formation. To overcome technical hurdles, we combined this method with direct adapter ligation and sequencing (PDAL-Seq). Furthermore, we established a user-friendly pipeline available on Galaxy to standardize PDAL-Seq data analysis. This optimized method allows the analysis of many types of DNA secondary structures that form in a living cell and will advance our knowledge of their roles in health and disease.
MeSH term(s)	DNA/chemistry ; G-Quadruplexes ; Oxides ; Manganese Compounds ; Oligonucleotides
Chemical Substances	permanganic acid (14333-13-2) ; DNA (9007-49-2) ; Oxides ; Manganese Compounds ; Oligonucleotides
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2023.12.003
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Article ; Online: Investigating mitonuclear interactions in human admixed populations.

Zaidi, Arslan A / Makova, Kateryna D

Nature ecology & evolution

2019 Volume 3, Issue 2, Page(s) 213–222

Abstract: To function properly, mitochondria utilize products of 37 mitochondrial and >1,000 nuclear genes, which should be compatible with each other. Discordance between mitochondrial and nuclear genetic ancestry could contribute to phenotypic variation in ... ...

Abstract	To function properly, mitochondria utilize products of 37 mitochondrial and >1,000 nuclear genes, 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 mitonuclear incompatibility in six admixed human populations from the Americas: African Americans, African Caribbeans, Colombians, Mexicans, Peruvians and Puerto Ricans. By comparing nuclear versus mitochondrial ancestry in these populations, we first show that mitochondrial DNA (mtDNA) copy number decreases with increasing discordance between nuclear and mtDNA ancestry. The direction of this effect is consistent across mtDNA haplogroups of different geographic origins. This observation indicates suboptimal regulation of mtDNA replication when its components are encoded by nuclear and mtDNA genes with different ancestry. Second, while most populations analysed exhibit no such trend, in African Americans and Puerto Ricans, we find a significant enrichment of ancestry at nuclear-encoded mitochondrial genes towards the source populations contributing the most prevalent mtDNA haplogroups (African and Native American, respectively). This possibly reflects compensatory effects of selection in recovering mitonuclear interactions optimized in the source populations. Our results provide evidence of mitonuclear interactions in human admixed populations and we discuss their implications for human health and disease.
MeSH term(s)	Caribbean Region ; Cell Nucleus/genetics ; Colombia ; DNA Copy Number Variations ; DNA, Mitochondrial/genetics ; Genetic Variation ; Humans ; Mexico ; Peru ; Puerto Rico ; United States
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2019-01-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-018-0766-1
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Article: Methylation profiles at birth linked to early childhood obesity.

Lariviere, Delphine / Craig, Sarah J C / Paul, Ian M / Hohman, Emily E / Savage, Jennifer S / Wright, Robert O / Chiaromonte, Francesca / Makova, Kateryna D / Reimherr, Matthew L

medRxiv : the preprint server for health sciences

2024

Abstract: Childhood obesity represents a significant global health concern and identifying risk factors is crucial for developing intervention programs. Many 'omics' factors associated with the risk of developing obesity have been identified, including genomic, ... ...

Abstract	Childhood obesity represents a significant global health concern and identifying risk factors is crucial for developing intervention programs. Many 'omics' factors associated with the risk of developing obesity have been identified, including genomic, microbiomic, and epigenomic factors. Here, using a sample of 48 infants, we investigated how the methylation profiles in cord blood and placenta at birth were associated with weight outcomes (specifically, conditional weight gain, body mass index, and weight-for-length ratio) at age six months. We characterized genome-wide DNA methylation profiles using the Illumina Infinium MethylationEpic chip, and incorporated information on child and maternal health, and various environmental factors into the analysis. We used regression analysis to identify genes with methylation profiles most predictive of infant weight outcomes, finding a total of 23 relevant genes in cord blood and 10 in placenta. Notably, in cord blood, the methylation profiles of three genes (
Language	English
Publishing date	2024-01-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.12.24301172
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Article ; Online: Methylation profiles at birth linked to early childhood obesity.

Lariviere, Delphine / Craig, Sarah J C / Paul, Ian M / Hohman, Emily E / Savage, Jennifer S / Wright, Robert O / Chiaromonte, Francesca / Makova, Kateryna D / Reimherr, Matthew L

Journal of developmental origins of health and disease

2024 Volume 15, Page(s) e7

Abstract: Childhood obesity represents a significant global health concern and identifying its risk factors is crucial for developing intervention programs. Many "omics" factors associated with the risk of developing obesity have been identified, including genomic, ...

Abstract	Childhood obesity represents a significant global health concern and identifying its risk factors is crucial for developing intervention programs. Many "omics" factors associated with the risk of developing obesity have been identified, including genomic, microbiomic, and epigenomic factors. Here, using a sample of 48 infants, we investigated how the methylation profiles in cord blood and placenta at birth were associated with weight outcomes (specifically, conditional weight gain, body mass index, and weight-for-length ratio) at age six months. We characterized genome-wide DNA methylation profiles using the Illumina Infinium MethylationEpic chip, and incorporated information on child and maternal health, and various environmental factors into the analysis. We used regression analysis to identify genes with methylation profiles most predictive of infant weight outcomes, finding a total of 23 relevant genes in cord blood and 10 in placenta. Notably, in cord blood, the methylation profiles of three genes (PLIN4, UBE2F, and PPP1R16B) were associated with all three weight outcomes, which are also associated with weight outcomes in an independent cohort suggesting a strong relationship with weight trajectories in the first six months after birth. Additionally, we developed a Methylation Risk Score (MRS) that could be used to identify children most at risk for developing childhood obesity. While many of the genes identified by our analysis have been associated with weight-related traits (e.g., glucose metabolism, BMI, or hip-to-waist ratio) in previous genome-wide association and variant studies, our analysis implicated several others, whose involvement in the obesity phenotype should be evaluated in future functional investigations.
MeSH term(s)	Humans ; Female ; DNA Methylation ; Pediatric Obesity/genetics ; Pregnancy ; Male ; Infant, Newborn ; Infant ; Fetal Blood/metabolism ; Placenta/metabolism ; Body Mass Index ; Epigenesis, Genetic ; Adult
Language	English
Publishing date	2024-04-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2554780-X
ISSN	2040-1752 ; 2040-1744
ISSN (online)	2040-1752
ISSN	2040-1744
DOI	10.1017/S2040174424000060
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Article ; Online: Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data.

Harris, Robert S / Cechova, Monika / Makova, Kateryna D

Bioinformatics (Oxford, England)

2019 Volume 35, Issue 22, Page(s) 4809–4811

Abstract: Summary: Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat ... ...

Abstract	Summary: Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response. Availability and implementation: NCRF is implemented in C, supported by several python scripts, and is available in bioconda and at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Nanopores ; Sequence Analysis, DNA ; Software ; Tandem Repeat Sequences
Language	English
Publishing date	2019-07-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz484
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