Biology subjects

Eichler, E.

Publications and source records attributed to Eichler, E..

At least 19 recordsLinked to original sources

bioRxiv2026

The genetic architecture of human DNA methylome variation

Population DNA methylome analyses remain largely confined to reference-defined genomic space despite extensive human genetic diversity. A central challenge is therefore to define comparable methylation phenotypes across diverse genomes and map the genetic architecture of methylome variation. Here, using 460 haplotypes from the Human Pangenome Reference Consortium Release 2, we develop two complementary pangenome-based frameworks: one compares methylation within homologous regions while retaining haplotype-specific structural configuration and CpG content; the other represents CpG island (CGI) variation at homologous loci as sequence-resolved alleles. We identified 47,039 CGI alleles, including 8,040 absent from CHM13; 62% were attributable to structural variants and 31% to small variants. Through local genealogies, we reconstructed CGI gain, loss and turnover, revealing how present-day methylation differences align with CGI evolutionary trajectories. We found that genome-wide, methylation variability was buffered against genetic diversity across more than 90% of the genome, with exceptions at extreme nucleotide diversity and locally around structural variants. Our methylation framework enabled population-scale allele-aware methylation quantitative trait locus (mQTL) mapping into non-reference and structurally complex sequence, where mQTL-associated intervals were enriched. mQTLs linked methylation to transcriptomic phenotypes, population differentiation and complex traits, supporting 8% of population differentially methylated regions and colocalizing with more than half of genome-wide association study loci. Together, our study redefines human methylome analysis and our findings reveal a genome-wide architecture of genetic-epigenetic coupling, reshaping how methylation variation is interpreted across human development and disease.

genetics↗

bioRxiv2026

Cross-species discovery of large structural variants reveals distinct evolutionary dynamics in primates

Large-scale structural variants (SVs) are major drivers of genome evolution and disease susceptibility, shaping lineage-specific gene content, genome architecture, and phenotypic diversity. Yet, their systematic detection across divergent species has been hindered by complex rearrangements and reference bias, limiting our understanding of their evolutionary impact. Here we present LGvar, a divergence-aware tool for identifying SVs in population-scale and cross-species genome assemblies, enabling up to a 7-fold increase in the detection of large deletions, insertions, inversions and complex rearrangements ([≥]10 kbp). Application of LGvar uncovers 112 previously undetected large SVs overlooked by conventional methods and quantifies the effect of evolutionary divergence on SV discovery across primate euchromatic genomes, revealing an approximately 30% overall decline in detection sensitivity with increasing phylogenetic distance. Mapping SVs from comparable syntenic regions onto the primate phylogeny shows that large deletions ([≥]10 kbp) accumulate approximately two-fold faster than insertions and eight-fold faster than inversions, in contrast to the dynamics of smaller SVs (<10 kbp). Integrating structurally divergent regions with the synteny region analysis reveals over 606 previously unreported gene gains and losses in great apes and refined the totals to 134 human-lineage-specific and 51 great-ape-lineage-specific protein coding genes. These results suggest that large SVs follow distinct evolutionary trajectories, with potential selective constraints shaping genome structure. Our study establishes a generalizable strategy for cross-species SV discovery and provides a high-resolution view of how large SVs contribute to genome evolution in primates.

genomics↗

bioRxiv2026

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

Complete, haplotype-resolved genome assemblies have provided unprecedented insight into the evolution of structurally complex, rapidly evolving regions of human genomes1-6; however, population-scale pangenome resources of our closest relatives, chimpanzees and bonobos (genus, Pan), are necessary to ascertain the origins and evolutionary context of these loci. Here, we sequence and assemble 58 haplotypes from four distinct Pan clades to high contiguity (median contig NG50=54 Mb), including eight near-T2T genomes. These genomes reveal previously intractable genetic variation increasing estimates of genome-wide genetic diversity 6-37% across populations compared to short-read estimates7. We identify recurrent structural polymorphisms across species impacting genes associated with immune response and host-pathogen interaction and find that structural variants (SVs) are 170- to 260-fold more likely than single nucleotide variants (SNVs) to exhibit high-impact effects across species. Contrasting SV patterns across primates we find that transposable element mutation rates differ by as much as threefold between species. We show that human disease-associated short tandem repeat (TR) loci have uniquely expanded in humans sensitizing our species to these TR-expansion disorders. Physically phased haplotypes enable reconstruction of genome-wide genealogical histories, uncovering ancient, functional genetic variation maintained by balancing selection, as well as signatures of recent adaptation in chimpanzee subspecies. Several malaria-associated loci exhibit ancient structural polymorphism, including the African great ape-specific glycophorin (GYP) gene expansion. We characterize the sequence, structure, and composition of diverse glycophorin haplotypes in humans and chimpanzees. We identify independent malaria-protective GYPA-B fusion events in humans and novel chimpanzee glycophorin genes resulting from both ancient and recent fusion events demonstrating parallel adaptations to pathogen resistance across hominins. Together, our resource highlights the critical importance of nonhuman primate population-scale pangenomics for understanding the evolution of complex genome structures and the biodiversity of our endangered closest living relatives.

evolutionary biology↗

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

A massively parallel reporter assay of MECP2 cis-regulatory elements reveals genetic candidates for male-biased autism

Autism affects males four times more often than females, yet the basis of this sex bias remains unclear. One hypothesis is that hypomorphic variants in X-linked genes--genes where loss-of-function alleles cause syndromic neurodevelopmental disorders (NDDs) predominantly in females--produce milder, non-syndromic phenotypes in hemizygous males. We tested this by investigating cis-regulatory elements (CREs) of MECP2, a dosage-sensitive X-linked gene. Using a massively parallel reporter assay in human neurons, we mapped transcription factor binding sites within MECP2 CREs and tested autism-associated variants for functional impact. We identified two noncoding variants that change CRE activity, each with a male-biased phenotype. One of these, a promoter variant, disrupts NFY binding and reduces MECP2 expression by [~]30%, a magnitude that produces autism-like phenotypes in mice. These findings suggest noncoding MECP2 variants can cause non-syndromic, male-biased autism, and provide a framework for uncovering regulatory variants in other X-linked NDD genes that may contribute to autisms missing heritability.

genetics↗

bioRxiv2026

Distinct mechanisms of CNV formation at the human 15q13.3 locus

Human chromosome 15q13.3 is a hotspot for recurrent pathogenic copy number variants (CNVs), which remain unresolved at the sequence level. We generated haplotype-resolved assemblies for 10 patient-parent trios and found that both the long ("BP4-BP5") and short ("CHRNA7") forms of 15q13.3 CNVs arise predominantly by non-allelic homologous recombination (NAHR) enabled by inversion polymorphisms. While most BP4-BP5 CNVs are structurally distinct, three breakpoints cluster in a 2 kbp PRDM9-enriched recombination hotspot. CHRNA7 CNVs originate from NAHR between CHRNA7-LCR repeats embedded within locus-spanning inversions and give rise to paired deletion/duplication events. Population analyses of 581 population haplotypes reveal at least 18 distinct structural haplotypes in 15q13.3 and more than 10-fold ancestry-stratification of BP4-BP5 CNV risk, where 68.4% of Europeans but only 5.1% of East Asians are predisposed. Comparison to six ape species indicates that the duplication architecture promoting instability expanded recently and is largely human-specific.

genetics↗

bioRxiv2026

Reshaping Organellar Translation and tRNA Metabolism: The Consequences of Photosynthesis Loss and Massive Horizontal Gene Transfer

The transition to holoparasitism in plants precipitates the loss of photosynthesis, fundamentally altering the selective landscape acting on organellar genomes. These changes raise questions about the mechanisms by which the essential, coevolved machinery of translation responds to extreme genomic erosion and metabolic dependency. Integrating comparative genomics, tRNA sequencing, and subcellular localization assays, we elucidate the extensive rewiring of organellar translation systems and the tRNA-dependent tetrapyrrole biosynthesis pathway in the holoparasitic angiosperm family Balanophoraceae, which exhibits extreme reduction of tRNA content in plastid and mitochondrial genomes. We identified a rare evolutionary event: the putative intracellular transfer of the plastid initiator tRNA (tRNA-iMet) to the nucleus, which compensates for its loss from the plastid genome. We also demonstrate that the unusual UAG-to-Trp reassignment in the Balanophora plastid genetic code is driven by the loss of release factor pRF1 and the recruitment of a mutated nuclear tRNA-Trp. Furthermore, we reveal that the retention of organellar nuclear-encoded aminoacyl-tRNA synthetases is dictated by the presence/absence of cognate organellar tRNAs, which appear to be functional regardless of their foreign (horizontal transfer from the host plant) or native origins. Finally, we uncover a striking evolutionary asymmetry in nuclear-encoded ribosomal proteins: while plastid subunits exhibit elevated substitution rates consistent with relaxed selection and compensatory coevolution, mitochondrial subunits display high sequence conservation, likely maintaining compatibility with the extensive horizontal gene transfer observed in this lineage. Collectively, these findings represent some of the most extreme changes ever identified in the anciently conserved machinery of plant organellar translation.

evolutionary biology↗

bioRxiv2025

A global map for introgressed structural variation and selection in humans

Genetic introgression from Neanderthals and Denisovan has shaped modern human genomes; however, introgressed structural variants (SVs [≥]50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) genomes with 94 published assemblies of diverse ancestry to infer an archaic introgressed SV map. Introgressed SVs are overall enriched in genes (44%, n=1,592), including critical genomic disorder regions, and most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping across 1,363 samples reveals 16 candidate adaptive SVs, many associated with immune-related genes and their expression, in the PNG. We hypothesize that archaic SV introgression contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution.

evolutionary biology↗

bioRxiv2025

Disruption of ADNP-KDM1A-GTF2I complex drives neural differentiation imbalance in Helsmoortel-Van der Aa syndrome

Mutations in ADNP (Activity-Dependent Neuroprotective Protein) are among the most frequent monogenic causes of autism spectrum disorder (ASD) and lead to Helsmoortel-Van der Aa syndrome (HVDAS). Yet how ADNP dysfunction leads to HVDAS is unclear. We employed patient-derived induced pluripotent stem cells, cortical organoids and ADNP KO human neural stem cells (hNSCs) to clarify the cellular and molecular mechanism of HVDAS onset. We purified an ADNP-KDM1A-GTF2I (AKG) protein complex from hNSCs and show that it targets transposable elements (TEs) to repress nearby gene transcription. Upon ADNP KO, KDM1A binding is lost at promoters targeted by AKG, pointing to ADNP as the anchoring subunit of the AKG complex. HVDAS cortical organoids show impaired progenitor proliferation and accelerated neuronal differentiation, coupled with a sustained upregulation of neurogenesis transcriptional programs, including key transcription factors normally repressed by AKG. This work suggests that the AKG complex acts as the relevant ADNP unit in the molecular onset of HVDAS.

neuroscience↗

bioRxiv2024

A near telomere-to-telomere phased reference assembly for the male mountain gorilla

The endangered mountain gorilla, Gorilla beringei beringei, faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using PacBio HiFi (26.77x ave. coverage) and Oxford Nanopore Technologies (52.87x ave. coverage) data. The resulting non-scaffolded assembly exhibits exceptional contiguity, with contig N50 of [~]95 Mbp for the combined pseudohaplotype (3,540,458,497 bp), 56.5 Mbp (3.1 Gbp) and 51.0 Mbp (3.2 Gbp) for each haplotype, an average QV of 65.15 (error rate = 3.1 x 10-7), and a BUSCO score of 98.4%. These represent substantial improvements over most other available primate genomes. This first high-quality reference genome of the mountain gorilla provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species.

genomics↗

bioRxiv2024

The Platinum Pedigree: A long-read benchmark for genetic variants

Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance since existing standards often focus on specificity, neglecting completeness in difficult to analyze regions. To create a more comprehensive truth set, we used Mendelian inheritance in a large pedigree (CEPH-1463) to filter variants across Illumina, PacBio high-fidelity (HiFi), and Oxford Nanopore Technologies platforms. This generated a variant map with over 4.7 million single-nucleotide variants, 767,795 indels, 537,486 tandem repeats, and 24,315 structural variants, covering 2.77 Gb of the GRCh38 genome. This work adds [~]200 Mb of high-confidence regions, including 8% more small variants, and introduces the first tandem repeat and structural variant truth sets for NA12878. As an example of the value of this improved benchmark, we retrained DeepVariant using this data to reduce genotyping errors by [~]34%.

genomics↗

bioRxiv2024

Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans

TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 nonhuman primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on chromosome 17. We find that most humans vary along two TBC1D3 clusters where human haplotypes are highly variable in copy number, differing by as many as 20 copies, and structure (structural heterozygosity 90%). We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Lastly, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL. These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.

genetics↗

bioRxiv2023

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of Oxford Nanopore Technologies (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.

bioinformatics↗

bioRxiv2022

Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation

Immunoglobulins (IGs), crucial components of the adaptive immune system, are encoded by three genomic loci. However, the complexity of the IG loci severely limits the effective use of short read sequencing, limiting our knowledge of population diversity in these loci. We leveraged existing long read whole-genome sequencing (WGS) data, fosmid technology, and IG targeted single-molecule, real-time (SMRT) long-read sequencing (IG-Cap) to create haplotype-resolved assemblies of the IG Lambda (IGL) locus from 6 ethnically diverse individuals. In addition, we generated 10 diploid assemblies of IGL from a diverse cohort of individuals utilizing IG-cap. From these 16 individuals, we identified significant allelic diversity, including 37 novel IGLV alleles. In addition, we observed highly elevated single nucleotide variation (SNV) in IGLV genes relative to IGL intergenic and genomic background SNV density. By comparing SNV calls between our high quality assemblies and existing short read datasets from the same individuals, we show a high propensity for false-positives in the short read datasets. Finally, for the first time, we nucleotide-resolved common 5-10 Kb duplications in the IGLC region that contain functional IGLJ and IGLC genes. Together these data represent a significant advancement in our understanding of genetic variation and population diversity in the IGL locus.

genetics↗

bioRxiv2021

From telomere to telomere: the transcriptional and epigenetic state of human repeat elements

Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific genomic innovation and fingerprint individual genomes. Comprehensive analyses of large, composite or arrayed repeat elements and those found in more complex regions of the genome require a complete, linear genome assembly. Here we present the first de novo repeat discovery and annotation of a complete human reference genome, T2T-CHM13v1.0. We identified novel satellite arrays, expanded the catalog of variants and families for known repeats and mobile elements, characterized new classes of complex, composite repeats, and provided comprehensive annotations of retroelement transduction events. Utilizing PRO-seq to detect nascent transcription and nanopore sequencing to delineate CpG methylation profiles, we defined the structure of transcriptionally active retroelements in humans, including for the first time those found in centromeres. Together, these data provide expanded insight into the diversity, distribution and evolution of repetitive regions that have shaped the human genome.

genomics↗

bioRxiv2021

Epigenetic Patterns in a Complete Human Genome

The completion of the first telomere-to-telomere human genome, T2T-CHM13, enables exploration of the full epigenome, removing limitations previously imposed by the missing reference sequence. Existing epigenetic studies omit unassembled and unmappable genomic regions (e.g. centromeres, pericentromeres, acrocentric chromosome arms, subtelomeres, segmental duplications, tandem repeats). Leveraging the new assembly, we were able to measure enrichment of epigenetic marks with short reads using k-mer assisted mapping methods. This granted array-level enrichment information to characterize the epigenetic regulation of these satellite repeats. Using nanopore sequencing data, we generated base level maps of the most complete human methylome ever produced. We examined methylation patterns in satellite DNA and revealed organized patterns of methylation along individual molecules. When exploring the centromeric epigenome, we discovered a distinctive dip in centromere methylation consistent with active sites of kinetochore assembly. Through long-read chromatin accessibility measurements (nanoNOMe) paired to CUT&RUN data, we found the hypomethylated region was extremely inaccessible and paired to CENP-A/B binding. With long-reads we interrogated allele-specific, longrange epigenetic patterns in complex macro-satellite arrays such as those involved in X chromosome inactivation. Using the single molecule measurements we can clustered reads based on methylation status alone distinguishing epigenetically heterogeneous and homogeneous areas. The analysis provides a framework to investigate the most elusive regions of the human genome, applying both long and short-read technology to grant new insights into epigenetic regulation.

genomics↗

bioRxiv2020

SMRT sequencing yields the chromosome-scale reference genome of tea tree, Camellia sinensis var. sinensis

Tea is the oldest and most popular nonalcoholic beverage consumed in the world. It provides abundant secondary metabolites that account for its diverse flavors and health benefits. Here we present the first high-quality chromosome-length reference genome of C. sinensis var. sinensis using long read single-molecule real time (SMRT) sequencing and Hi-C technologies to anchor the [~]2.85-Gb genome assembly into 15 pseudo-chromosomes with a scaffold N50 length of [~]195.68 Mb. We annotated at least 2.17 Gb ([~]74.13%) of repetitive sequences and high-confidence prediction of 40,812 protein-coding genes in the [~]2.92-Gb genome assembly. This accurately assembled genome allows us to comprehensively annotate functionally important gene families such as those involved in the biosynthesis of catechins, theanine and caffeine. The contiguous genome assembly provides the first view of the repetitive landscape allowing us to accurately characterize retrotransposon diversity. The large tea tree genome is dominated by a handful of Ty3-gypsy long terminal repeat (LTR) retrotransposon families that recently expanded to high copy numbers. We uncover the latest bursts of numerous non-autonomous LTR retrotransposons that may interfere with the propagation of autonomous retroelements. This reference genome sequence will largely facilitate the improvement of agronomically important traits relevant to the tea quality and production.

genomics↗

bioRxiv2019

Exome sequencing of 457 autism families recruited online provides evidence for novel ASD genes

Autism spectrum disorder (ASD) is a genetically heterogeneous condition, caused by a combination of rare de novo and inherited variants as well as common variants in at least several hundred genes. However, significantly larger sample sizes are needed to identify the complete set of genetic risk factors. We conducted a pilot study for SPARK (SPARKForAutism.org) of 457 families with ASD, all consented online. Whole exome sequencing (WES) and genotyping data were generated for each family using DNA from saliva. We identified variants in genes and loci that are clinically recognized causes or significant contributors to ASD in 10.4% of families without previous genetic findings. Additionally, we identified variants that are possibly associated with autism in an additional 3.4% of families. A meta-analysis using the TADA framework at a false discovery rate (FDR) of 0.2 provides statistical support for 34 ASD risk genes with at least one damaging variant identified in SPARK. Nine of these genes (BRSK2, DPP6, EGR3, FEZF2, ITSN1, KDM1B, NR4A2, PAX5 and RALGAPB) are newly emerging genes in autism, of which BRSK2 has the strongest statistical support as a risk gene for autism (TADA q-value = 0.0015). Future studies leveraging the thousands of individuals with ASD that have enrolled in SPARK are likely to further clarify the genetic risk factors associated with ASD as well as allow accelerate autism research that incorporates genetic etiology.

genetics↗