Biology subjects

Shleizer-Burko, S.

Publications and source records attributed to Shleizer-Burko, S..

7 recordsLinked to original sources

bioRxiv2025

Systematic evaluation of the impact of promoter proximal short tandem repeats on expression

Genetic variation at thousands of short tandem repeats (STRs), which consist of consecutive repeated sequences of 1-6bp, has been statistically associated with gene expression and other molecular phenotypes in humans. However, the causality and regulatory mechanisms for most of these STRs remains unknown. Massively parallel reporter assays (MPRA) enable testing the regulatory activity of a large number of synthesized variants, but have not been applied to STRs due to experimental and computational challenges. Here, we optimized an MPRA framework based on random barcoding to study the impact of variation in repeat copy number on expression. We first performed an MPRA on sequences derived from 30,516 promoter-proximal STR loci along with up to 152bp of genomic context, testing 3-4 variants with differing repeat copy numbers for each locus in HEK293T cells. We identified 1,366 loci with significant associations between repeat copy number and expression, which were enriched for positive effect sizes (P=2.08e-110). We then designed a second MPRA in which we performed deeper perturbations, including systematic manipulation of the repeat unit sequence, orientation, and copy number, with 200-300 perturbations for each of the 300 loci with the strongest signals. Our results revealed that the repeat unit sequence is the primary driver of differences in the relationship between copy number and expression across loci, whereas orientation and flanking sequence have weaker effects, primarily for AT-rich repeat units. The high resolution of these perturbations enabled us to detect non-linear effects, most notably for AAAC/GTTT repeats, which emerge only beyond a certain copy number threshold. Finally, we observed that a subset of STRs in our library show expression levels that are tightly linked with predicted DNA secondary structure formation. We repeated our perturbation MPRA in HeLa S3 cells under wildtype and RNase H1 knockdown conditions, which, via reduction in RNase H1 activity, are expected to hinder resolution of R-loops. This demonstrated that associations between copy number and expression at G-quadruplex-forming CCCCG/CGGGG repeats are particularly sensitive to loss of RNase H1, providing support for an R-loop mediated mechanism for these repeats. Altogether, we establish STRs as a critical component of the non-coding regulatory grammar and provide a framework for understanding how this dynamic form of genetic variation shapes gene expression.

genomics↗

bioRxiv2020

Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium

Morphogenesis and differentiation are important stages in organ development and shape determination. However, how they are balanced and tuned during development is not fully understood. In the compound leaved tomato, an extended morphogenesis phase allows for the initiation of leaflets, resulting in the compound form. Maintaining a prolonged morphogenetic phase in early stages of compound-leaf development is dependent on delayed activity of several factors that promote differentiation, including CIN-TCP transcription factor (TF) LA, the MYB TF CLAU and the plant hormone Gibberellin (GA). Here, we investigated the genetic regulation of the morphogenesis-differentiation balance by studying the relationship between LA, CLAU and GA. Our genetic and molecular examination suggest that LA is expressed more broadly than CLAU and determines the spatio-temporal context of CLAU activity. We demonstrate that both LA and CLAU affect the Cytokinin/Gibberellin (CK/GA) balance. LA reduces the sensitivity of the leaf margin to CK, shown before to be also affected by CLAU. CLAU affects leaf active GA content and sensitivity, shown previously to be also influenced by LA. Therefore, LA and CLAU likely function in parallel pathways to promote leaf differentiation by converging on common downstream processes, including the CK/GA balance.

plant biology↗

bioRxiv2020

Variable Number Tandem Repeats mediate the expression of proximal genes

Variable Number Tandem Repeats (VNTRs) account for a significant amount of human genetic variation. VNTRs have been implicated in both Mendelian and Complex disorders, but are largely ignored by whole genome analysis pipelines due to the complexity of genotyping and the computational expense. We describe adVNTR-NN, a method that uses shallow neural networks for fast read recruitment. On 55X whole genome data, adVNTR-NN genotyped each VNTR in less than 18 cpu-seconds, while maintaining 100% accuracy on 76% of VNTRs. We used adVNTR-NN to genotype 10,264 VNTRs in 652 individuals from the GTEx project and associated VNTR length with gene expression in 46 tissues. We identified 163 eVNTR loci that were significantly associated with gene expression. Of the 22 eVNTRs in blood where independent data was available, 21 (95%) were replicated in terms of significance and direction of association. 49% of the eVNTR loci showed a strong and likely causal impact on the expression of genes and 80% had maximum effect size at least 0.3. The impacted genes have important role in complex phenotypes including Alzheimers, obesity and familial cancers. Our results point to the importance of studying VNTRs for understanding the genetic basis of complex diseases.

genomics↗

bioRxiv2020

The contribution of de novo tandem repeat mutations to autism spectrum disorders

Autism Spectrum Disorder (ASD) is an early onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive behaviors1,2. Family studies demonstrate that ASD has a significant genetic basis3 with contributions both from inherited and de novo variants. While the majority of variance in liability to ASD is estimated to arise from common genetic variation4, it has been estimated that de novo mutations may contribute to 30% of all simplex cases, in which only a single child is affected per family5. Tandem repeats (TRs), consisting of approximately 1-20bp motifs repeated in tandem, comprise one of the largest sources of de novo mutations in humans6. Yet, largely due to technical challenges they present, de novo TR mutations have not yet been characterized on a genome-wide scale, and their contribution to ASD remains unexplored. Here, we develop novel bioinformatics tools for identifying and prioritizing de novo TR mutations from whole genome sequencing (WGS) data and use these to perform a genome-wide characterization of de novo TR mutations in ASD-affected probands and unaffected siblings. Compared to recent work on TRs in ASD7, we explicitly infer mutation events and their precise changes in repeat copy number, and primarily focus on more prevalent stepwise copy number changes rather than large or complex expansions. Our results demonstrate a significant genome-wide excess of TR mutations in ASD probands. TR mutations in probands tend to be larger, enriched in fetal brain regulatory regions, and predicted to be more evolutionarily deleterious compared to mutations observed in unaffected siblings. Overall, our results highlight the importance of considering repeat variants in future studies of de novo mutations.

genomics↗

bioRxiv2018

Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits

Short tandem repeats (STRs) have been implicated in a variety of complex traits in humans. However, genome-wide studies of the effects of STRs on gene expression thus far have had limited power to detect associations and provide insights into putative mechanisms. Here, we leverage whole genome sequencing and expression data for 17 tissues from the Genotype-Tissue Expression Project (GTEx) to identify STRs for which repeat number is associated with expression of nearby genes (eSTRs). Our analysis reveals more than 28,000 eSTRs. We employ fine-mapping to quantify the probability that each eSTR is causal and characterize a group of the top 1,400 fine-mapped eSTRs. We identify hundreds of eSTRs linked with published GWAS signals and implicate specific eSTRs in complex traits including height and schizophrenia, inflammatory bowel disease, and intelligence. Overall, our results support the hypothesis that eSTRs contribute to a range of human phenotypes and will serve as a valuable resource for future studies of complex traits.

genomics↗

bioRxiv2018

Profiling the genome-wide landscape of tandem repeat expansions

Tandem Repeat (TR) expansions have been implicated in dozens of genetic diseases, including Huntingtons Disease, Fragile X Syndrome, and hereditary ataxias. Furthermore, TRs have recently been implicated in a range of complex traits, including gene expression and cancer risk. While the human genome harbors hundreds of thousands of TRs, analysis of TR expansions has been mainly limited to known pathogenic loci. A major challenge is that expanded repeats are beyond the read length of most next-generation sequencing (NGS) datasets. We present GangSTR, a novel algorithm for genome-wide profiling of both normal and expanded TRs. GangSTR extracts information from paired-end reads into a unified model to estimate maximum likelihood TR lengths. We validated GangSTR on real and simulated TR expansions and show that GangSTR outperforms alternative methods. We applied GangSTR to more than 150 individuals to profile the landscape of TR expansions in a healthy population and validated novel expansions using orthogonal technologies. Our analysis revealed that each individual harbors dozens of TR alleles longer than standard read lengths and identified hundreds of potentially mis-annotated TRs in the reference genome. GangSTR is packaged as a standalone tool that will likely enable discovery of novel pathogenic variants not currently accessible from NGS.

genomics↗

bioRxiv2017

Targeted Genotyping of Variable Number Tandem Repeats with adVNTR

Whole Genome Sequencing is increasingly used to identify Mendelian variants in clinical pipelines. These pipelines focus on single nucleotide variants (SNVs) and also structural variants, while ignoring more complex repeat sequence variants. We consider the problem of genotyping Variable Number Tandem Repeats (VNTRs), composed of inexact tandem duplications of short (6-100bp) repeating units. VNTRs span 3% of the human genome, are frequently present in coding regions, and have been implicated in multiple Mendelian disorders. While existing tools recognize VNTR carrying sequence, genotyping VNTRs (determining repeat unit count and sequence variation) from whole genome sequenced reads remains challenging. We describe a method, adVNTR, that uses Hidden Markov Models to model each VNTR, count repeat units, and detect sequence variation. adVNTR models can be developed for short-read (Illumina) and single molecule (PacBio) whole genome and exome sequencing, and show good results on multiple simulated and real data sets. adVNTR is available at https://github.com/mehrdadbakhtiari/adVNTR

bioinformatics↗