Egor Dolzhenko

The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development

Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

BackgroundWhole-genome bisulfite sequencing currently provides the highest-precision view of the epigenome, with quantitative information about populations of cells down to single nucleotide resolution. Several studies have demonstrated the value of this precision: meaningful features that correlate strongly with biological functions can be found associated with only a few CpG sites. Understanding the role of DNA methylation, and more broadly the role of DNA accessibility, requires that methylation differences between populations of cells are identified with extreme precision and in complex experimental designs.ResultsIn this work we investigated the use of beta-binomial regression as a general approach for modeling whole-genome bisulfite data to identify differentially methylated sites and genomic intervals.ConclusionsThe regression-based analysis can handle medium- and large-scale experiments where it becomes critical to accurately model variation in methylation levels between replicates and account for influence of various experimental factors like cell types or batch effects.

The APOE4 allele shows opposite sex bias in microbleeds and Alzheimer's disease of humans and mice

The apolipoprotein APOE4 allele confers greater risk of Alzheimers disease (AD) for women than men, in conjunction with greater clinical deficits per unit of AD neuropathology (plaques, tangles). Cerebral microbleeds, which contribute to cognitive dysfunctions during AD, also show APOE4 excess, but sex-APOE allele interactions are not described. We report that elderly men diagnosed for mild cognitive impairment and AD showed a higher risk of cerebral cortex microbleeds with APOE4 allele dose effect in 2 clinical cohorts (ADNI and KIDS). Sex-APOE interactions were further analyzed in EFAD mice carrying human APOE alleles and familial AD genes (5XFAD (+/-) /human APOE(+/+)). At 7 months, E4FAD mice had cerebral cortex microbleeds with female excess, in contrast to humans. Cerebral amyloid angiopathy, plaques, and soluble Aβ also showed female excess. Both the cerebral microbleeds and cerebral amyloid angiopathy increased in proportion to individual Aβ load. In humans, the opposite sex bias of APOE4 allele for microbleeds versus the plaques and tangles is the first example of organ-specific, sex-linked APOE allele effects, and further shows AD as a uniquely human condition.

An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland

Pregnancy is the major modulator of mammary gland activity. It induces a tremendous expansion of the mammary epithelium and the generation of alveolar structures for milk production. Anecdotal evidence from multiparous humans indicates that the mammary gland may react less strongly to the first pregnancy than it does to subsequent pregnancies. Here, we verify that the mouse mammary gland responds more robustly to a second pregnancy, indicating that the gland retains a long-term memory of pregnancy. A comparison of genome-wide profiles of DNA methylation in isolated mammary cell types reveals substantial and long-lasting alterations. Since these alterations are maintained in the absence of the signal that induced them, we term them epigenetic. The majority of alterations in DNA methylation affect sites occupied by the Stat5a transcription factor and mark specific genes that are upregulated during pregnancy. We postulate that the epigenetic memory of a first pregnancy primes the activation of gene expression networks that promote mammary gland function in subsequent reproductive cycles. More broadly, our data indicate that physiological experience can broadly alter epigenetic states, functionally modifying the capacity of the affected cells to respond to later stimulatory events.

Modeling runtime enforcement with mandatory results automata

This paper presents a theory of runtime enforcement based on mechanism models called mandatory results automata (MRAs). MRAs can monitor and transform security-relevant actions and their results. The operational semantics of MRAs is simple and enables straightforward definitions of concrete MRAs. Moreover, the definitions of policies and enforcement with MRAs are simple and expressive. Putting all of these features together, we argue that MRAs make good general models of runtime mechanisms, upon which a theory of runtime enforcement can be based. We develop some enforceability theory by characterizing the policies deterministic and non-deterministic MRAs can and cannot enforce.

LUCApedia: a database for the study of ancient life

Organisms represented by the root of the universal evolutionary tree were most likely complex cells with a sophisticated protein translation system and a DNA genome encoding hundreds of genes. The growth of bioinformatics data from taxonomically diverse organisms has made it possible to infer the likely properties of early life in greater detail. Here we present LUCApedia, (http://eeb.princeton.edu/lucapedia), a unified framework for simultaneously evaluating multiple data sets related to the Last Universal Common Ancestor (LUCA) and its predecessors. This unification is achieved by mapping eleven such data sets onto UniProt, KEGG and BioCyc IDs. LUCApedia may be used to rapidly acquire evidence that a certain gene or set of genes is ancient, to examine the early evolution of metabolic pathways, or to test specific hypotheses related to ancient life by corroborating them against the rest of the database.

Four-regular graphs with rigid vertices associated to DNA recombination

Genome rearrangement and homological recombination processes have been modeled by Angeleska et al. [A. Angeleska, N. Jonoska, M. Saito, DNA recombinations through assembly graphs, Discrete Appl. Math. 157 (2009) 3020-3037] as 4-regular spacial graphs with rigid vertices, called assembly graphs. These graphs can also be represented by double occurrence words called assembly words. The rearranged DNA segments are modeled by certain types of paths in the assembly graphs called polygonal paths. The minimum number of polygonal paths visiting all vertices in a graph is called an assembly number for the graph. In this paper, we give formulas for counting certain types of assembly graphs and assembly words. Some of these formulas produce sequences not previously reported at the Online Encyclopedia of Integer Sequences (http://oeis.org). We provide a sharp upper bound for the number of polygonal paths in Hamiltonian sets of polygonal paths, and present a family of graphs that achieves this bound. We investigate changes in the assembly numbers as a result of graph compositions. Finally, we introduce a polynomial invariant for assembly graphs and show properties of this invariant.

Transducer generated arrays of robotic nano-arms

We consider sets of two-dimensional arrays, called here transducer generated languages, obtained by iterative applications of transducers (finite state automata with output). Each transducer generates a set of blocks of symbols such that the bottom row of a block is an input string accepted by the transducer and, by iterative application of the transducer, each row of the block is an output of the transducer on the preceding row. We show how these arrays can be implemented through molecular assembly of triple crossover DNA molecules. Such assembly could serve as a scaffold for arranging molecular robotic arms capable of simultaneous movements. We observe that transducer generated languages define a class of languages which is a proper subclass of recognizable picture languages, but it contains the class of all factorial local two-dimensional languages. By taking the average growth rate of the number of blocks in the language as a measure of its complexity, we further observe that arrays with high complexity patterns can be generated in this way.

Molecular characterization of the transition from acute to chronic kidney injury following ischemia/reperfusion

Though an acute kidney injury (AKI) episode is associated with an increased risk of chronic kidney disease (CKD), the mechanisms determining the transition from acute to irreversible chronic injury are not well understood. To extend our understanding of renal repair, and its limits, we performed a detailed molecular characterization of a murine ischemia/reperfusion injury (IRI) model for 12 months after injury. Together, the data comprising RNA-sequencing (RNA-seq) analysis at multiple time points, histological studies, and molecular and cellular characterization of targeted gene activity provide a comprehensive profile of injury, repair, and long-term maladaptive responses following IRI. Tubular atrophy, interstitial fibrosis, inflammation, and development of multiple renal cysts were major long-term outcomes of IRI. Progressive proximal tubular injury tracks with de novo activation of multiple Krt genes, including Krt20, a biomarker of renal tubule injury. RNA-seq analysis highlights a cascade of temporal-specific gene expression patterns related to tubular injury/repair, fibrosis, and innate and adaptive immunity. Intersection of these data with human kidney transplant expression profiles identified overlapping gene expression signatures correlating with different stages of the murine IRI response. The comprehensive characterization of incomplete recovery after ischemic AKI provides a valuable resource for determining the underlying pathophysiology of human CKD.

On Complexity of Two Dimensional Languages Generated by Transducers

We consider two-dimensional languages, called here 2d transducer languages, generated by iterative applications of transducers (finite state automata with output). To each transducer a two-dimensional language consisting of blocks of symbols is associated: the bottom row of a block is an input string accepted by the transducer and, by iterative application of the transducer, each row of the block is an output of the transducer on the preceding row. We observe that this class of languages is a proper subclass of recognizable picture languages containing the class of all factorial local 2d languages. By taking the average growth rate of the number of blocks in the language as a measure of its complexity, also known as the entropy of the language, we show that every entropy value of a one-dimensional regular language can be obtained as an entropy value of a 2d transducer language.