Biology subjects

Anderson, E. C.

Publications and source records attributed to Anderson, E. C..

8 recordsLinked to original sources

bioRxiv2026

The ChIP-FRiP pipeline quantifies co-binding and reveals how antibody background contributes to cohesin ChIP-seq patterns

Loop extruding cohesin complexes are positioned by CTCF barriers to generate locus-specific 3D genome folding patterns. Quantifying cohesin accumulation at CTCF sites is crucial for deriving insight into loop extrusion and its consequences. Here we confronted expectations from loop extrusion simulations with experimental data by developing a pipeline, ChIP-FRiP, and analysis framework to reliably quantify cohesin positioning. We used ChIP-FRiP to uniformly re-process 140 cohesin ChIP-seq datasets from 13 publicly available studies. This analysis revealed that non-specific antibody binding can skew measurements of cohesin positioning. To mitigate this bias, we developed a biochemical model of background ChIP-seq signal and a strategy to estimate and correct this background using spike-in ChIP-seq data and relative protein abundance before and after depletion. Our results establish a framework for comparative analysis, demonstrating that accurate background correction is requisite for interpreting the roles of cohesin cofactors in cohesin positioning.

genomics↗

bioRxiv2026

The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control

Enhancers have been proposed to act as privileged loading sites for cohesin, raising the idea that they actively fold the genome to engage distal target promoters for transcription. Supporting this idea, NIPBL/MAU2, which is required for cohesin loading, binds at enhancers in mouse embryonic stem cells. However, we find that driving cohesin recruitment near an enhancer strongly inhibits transcription from its target distal promoter, indicating that strong focal cohesin loading at enhancers is not compatible with their long-range regulatory functions. Quantitative experiments and biophysical modeling further indicate that cohesin loading at enhancers does not make major contributions to genome-wide cohesin binding and chromosome folding patterns. Instead, cohesin must load throughout the genome to extrude it, regardless of enhancer proximity, with the major determinants of cohesin traffic being extrusion barriers such as transcription and clustered CTCF sites. These findings indicate that enhancer function is largely ancillary to the general mechanisms of chromosome folding, informing further study of the relationship between genome architecture and transcriptional regulation.

molecular biology↗

bioRxiv2025

NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion

Genome folding is not static, but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune extrusion kinetics to achieve precise and functional chromosome folding patterns. Here we discover extrusion rate acts as a tunable biophysical parameter in cells, quantitatively dialed by the respective dosage of the cohesin cofactors NIPBL and PDS5. Modulation of extrusion rate can offset changes in cohesin lifetime to buffer steady-state chromosome structure and transcriptional states, even in the face of abnormal extrusion dynamics. These findings provide a long-sought mechanistic basis for the genetic interactions between cohesin cofactors and the molecular origin of haploinsufficiency in cohesinopathies, such as Cornelia de Lange syndrome.

molecular biology↗

bioRxiv2024

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

Enhancers are critical genetic elements controlling transcription from promoters, but the mechanisms by which they convey regulatory information across large genomic distances remain elusive. Here, we engineered pluripotent stem cells in which cohesin loop extrusion can be inducibly disrupted without causing confounding cell cycle defects. While evident, transcriptional dysregulation was cell-type specific, and not all loci with distal enhancers depend equally on cohesin extrusion. Using comparative genome editing, we demonstrate that enhancer-promoter communication across as little as 20 kilobases can rely on cohesin. However, promoter-proximal regulatory elements can support long-range, cohesin-independent enhancer action - either upon disabling extrusion or across strong CTCF insulators. Finally, transcriptional dynamics and the emergence of new embryonic cell types in response to differentiation cues remained largely robust to disrupting cohesin extrusion. Beyond establishing novel experimental strategies to study cohesin functions in enhancer biology, our work provides mechanistic insight accounting for both cell type- and genomic context-specificity.

molecular biology↗

bioRxiv2022

Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel isotype-1 β-tubulin benzimidazole resistance mutation.

Ancylostoma caninum is an important zoonotic gastrointestinal nematode of dogs worldwide and a close relative of human hookworms. We recently reported that racing greyhounds in the USA are infected with A. caninum that are commonly resistant to multiple anthelmintics. Benzimidazole resistance in A. caninum in greyhounds was associated with a high frequency of the canonical F167Y(TTC>TAC) isotype-1 {beta}-tubulin mutation. In this work, we show that benzimidazole resistance is remarkably widespread in A. caninum from domestic dogs across the USA. First, we identified and showed the functional significance of a novel benzimidazole isotype-1 {beta}-tubulin resistance mutation, Q134H(CAA>CAT). Several benzimidazole resistant A. caninum isolates from greyhounds with a low frequency of the F167Y(TTC>TAC) mutation had a high frequency of a Q134H(CAA>CAT) mutation not previously reported from any eukaryotic pathogen in the field. Structural modeling predicted that the Q134 residue is directly involved in benzimidazole drug binding and that the 134H substitution would significantly reduce binding affinity. Introduction of the Q134H substitution into the C. elegans {beta}-tubulin gene ben-1, by CRISPR-Cas9 editing, conferred similar levels of resistance as a ben-1 null allele. Deep amplicon sequencing on A. caninum eggs from 685 hookworm positive pet dog fecal samples revealed that both mutations were widespread across the USA, often at high frequency, with prevalences of 49.7% (overall frequency 54.0%) and 31.1% (overall frequency 16.4%) for F167Y(TTC>TAC) and Q134H(CAA>CAT), respectively. Canonical codon 198 and 200 benzimidazole resistance mutations were absent. The F167Y(TTC>TAC) mutation had a significantly higher prevalence and frequency in Western USA than in other regions, which we hypothesize is due to differences in refugia. This work has important implications for companion animal parasite control and the potential emergence of drug resistance in human hookworms. Author SummaryAlthough increasingly common in livestock, no reports of widespread anthelmintic resistance are confirmed in any companion animal or human gastrointestinal nematode parasite to date. The canine hookworm is a common intestinal zoonotic parasite of dogs with severe clinical impacts in young dogs, and for which control is dependent on regular anthelmintic use. We recently reported multiple anthelmintic drug resistance in A. caninum isolates from greyhounds derived from multiple locations in the USA likely caused by long standing intensive treatment regimens in kennels. In this study, we investigated benzimidazole resistance in A. caninum in pet dogs across the USA. We also identified and showed the functional significance of a novel benzimidazole isotype-1 {beta}-tubulin resistance mutation in A. caninum from greyhounds that has not been previously reported in the field for any organism. We then determined that this novel mutation, as well as a previously characterized resistance mutation, were present, often at high frequency, in many A. caninum populations across the USA. This study reports the first evidence of widespread drug resistance for any parasitic nematode of companion animals and illustrates the power of molecular approaches to rapidly assess anthelmintic resistance in a region.

genomics↗

bioRxiv2021

Simplifying the development of portable, scalable, and reproducible workflows

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tools inputs, outputs, and other execution details in a manner that fosters use of shared computational methods and reproducibility of complex analyses. CWL documents can include instructions for executing tools inside software containers--isolated, operating-system environments. Accordingly, CWL tools are portable--they can be executed on diverse computers--including personal workstations, high-performance clusters, or the cloud. This portability enables easier adoption of bioinformatics pipelines. CWL supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents confirm to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create "input-object" files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine.

bioinformatics↗

bioRxiv2020

The genomic landscape of divergence across the speciation continuum in island-colonising silvereyes (Zosterops lateralis)

A goal of the genomic era is to infer the evolutionary dynamics at play during the process of speciation by analysing the genomic landscape of divergence. However, empirical assessments of genomic landscapes under varying evolutionary scenarios are few, limiting the ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape in the silvereye (Zosterops lateralis). Using comparisons matched for divergence timeframe and gene flow context, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. Furthermore, we modelled the transition from localised to genome-wide levels of divergence using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process. DATA ACCESSION NUMBERSResequencing data from this study have been submitted to the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov) under accession number PRJNA489169.

evolutionary biology↗

bioRxiv2018

Sex-dependent dominance maintains migration supergene in rainbow trout

Traits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolved in these species is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 56 Mb double-inversion supergene that mediates sex-specific migration through sex-dependent dominance, a mechanism that reduces sexual conflict. The double-inversion contains key photosensory, circadian rhythm, adiposity, and sexual differentiation genes and displays frequency clines associated with latitude and temperature, revealing environmental dependence. Our results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.

evolutionary biology↗