Strand asymmetry in MPRA Signal
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE156857 | GEO | 2020/12/04
REPOSITORIES: GEO
Similar Datasets
Project description:Strand asymmetry in MPRA Signal
| PRJNA659269 | ENA
Project description:Enhancers play important roles in evolution and disease. However, traditional assays to test enhancers are low throughput and not scalable to the >100,000 enhancers in the human genome. To better prioritize variants associated with disease and to study the role of enhancers, our group and others developed massively parallel reporter assays (MPRAs), which functionally screen thousands of sequences for regulatory activity in parallel. Although MPRAs have been applied to address diverse questions in gene regulation, there has been no systematic comparison of how differences in experimental design influence findings, making it difficult to interpret results and compare between groups. Here, we screen a library of 2,440 sequences, representing candidate liver enhancers and controls, in HepG2 cells for regulatory activity using nine different approaches (including conventional episomal, STARR-seq, and lentiviral MPRA designs). We identify subtle but significant differences in the resulting measurements that correlate with epigenetic and sequence-level features. We also test this library in both orientations with respect to the promoter, validating en masse that enhancer activity is robustly independent of orientation. Finally, we develop and apply a novel method to assemble and functionally test libraries of the same putative enhancers as 192-mers, 354-mers, and 678-mers, and observe surprisingly large differences in functional activity. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.
2019-12-30 | GSE142696 | GEO
Project description:Gene regulation occurs through trans-acting factors (e.g. transcription factors) acting on cis-regulatory elements (e.g. enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers of cis-regulatory elements for regulatory potential, but do not identify the trans-acting factors that mediate any observed effects. Here we include preliminary data from a pilot transMPRA experiment — a reporter assay that efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to identify trans-acting factors that modulate the regulatory activity of specific enhancers.
2020-09-30 | GSE157430 | GEO
Project description:Asymmetric selection of single-stranded guide RNAs from double-stranded RNA (dsRNA) precursors is crucial for RNA silencing-mediated gene regulation. However, the precise mechanisms for small RNA asymmetry remain unclear, especially since asymmetric selection can still occur under depletion of putative asymmetry sensors, Drosophila R2D2 and mammalian Dicer. Here we report direct contribution of mammalian Argonaute 2 (Ago2) to microRNA (miRNA) asymmetry. Ago2 selects strands with 5´-uridine/adenosine and thermodynamically unstable 5´-ends in parallel through its two sensor regions, which contact 5´-nucleobase and 5´-phosphate(s) of the prospective guide strands, respectively. Consistently, miRNA asymmetry shows characteristic digital-analog superposed patterns reflecting 5'-end nucleotide identity and thermodynamic stability. Furthermore, we demonstrate that cancer-associated miRNA variations reprogram asymmetric selection. Finally, our study presents a model of this universal principle that will aid a comprehensive understanding of miRNA function and therapeutic reinvention of RNA silencing in precision medicine. Immunoprecipitation of WT or mutant Ago2 in mouse ES cells (Ago-null background) and small RNA sequencing
2015-06-15 | E-GEOD-66022 | biostudies-arrayexpress
Project description:Non-syndromic facial asymmetry is commonly found in dentofacial deformity populations with skeletal malocclusions. Asymmetry of this type may result from imbalanced growth and function of both the jaw and associated muscles. Among the multiple genes that interact to affect the craniofacial musculoskeletal complex during pre and postnatal growth and development, NODAL signaling pathwy (NSP) genes are active in adult skeletal muscle and may be key factors in development, growth and maintenance of facial asymmetry. It is of interest to determine whether expression of NODAL pathway genes might differ in masseter muscles between individuals with malocclusion that have facial asymmetry and normal symmetry. Human Transcriptome 2.0 GeneChips (HTA2.0) were used to examine global gene expression in masster muscles between malocclusion subjects with posterior facial asymmetry and with normal facial symmetry. Eleven patients undergoing orthoganthic surgery were selected for comparison of masseter muscle gene expression on microarrays. Two subjects had posterior facial asymmetry (one with class II open bite and one with class III open bite malocclusion) and nine subjects had normal facial symmetry (three with class II open bite, two with class III open bite and four with class II deep bite malocclusion). RNA representative of total gene expression in masseter muscles of the malocclusion subjects with and without posterior facial asymmetry was prepared for labeling and hybridization on HTA2.0 chips. The two subjects with facial asymmetry clustered separately from eight other malocclusion subjects by a principle component analysis (PCA), even though one had a class II and the other a class III malocclusion. Sample 4L_Open_II is from a subject who has sleep apnea. Data from 4L_Open_II clustered independent of the asymmetry group and the eight other subjects of the symmetry group by PCA and was not included in analysis of differential expression with facial symmetry. Masseter muscles are paired jaw muscles (i.e. right and left masseter). In some cases, there was not sufficient quantity/quality of RNA from one side, thus the other side was used. Please note that the following information is provided in the 'source name' field of each sample record; subject ID number; either left or right masseter; J CRANIOFAC SURG_ID# corresponding to the data presented in the manuscript
2014-05-20 | E-GEOD-57775 | biostudies-arrayexpress
Project description:Asymmetric selection of single-stranded guide RNAs from double-stranded RNA (dsRNA) precursors is crucial for RNA silencing-mediated gene regulation. However, the precise mechanisms for small RNA asymmetry remain unclear, especially since asymmetric selection can still occur under depletion of putative asymmetry sensors, Drosophila R2D2 and mammalian Dicer. Here we report direct contribution of mammalian Argonaute 2 (Ago2) to microRNA (miRNA) asymmetry. Ago2 selects strands with 5´-uridine/adenosine and thermodynamically unstable 5´-ends in parallel through its two sensor regions, which contact 5´-nucleobase and 5´-phosphate(s) of the prospective guide strands, respectively. Consistently, miRNA asymmetry shows characteristic digital-analog superposed patterns reflecting 5'-end nucleotide identity and thermodynamic stability. Furthermore, we demonstrate that cancer-associated miRNA variations reprogram asymmetric selection. Finally, our study presents a model of this universal principle that will aid a comprehensive understanding of miRNA function and therapeutic reinvention of RNA silencing in precision medicine.
2015-06-15 | GSE66022 | GEO
Project description:Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we determine epigenetic changes and genes involved in hemispheric asymmetry in the healthy and PD brain. Neurons of healthy individuals exhibit numerous hemispheric differences in DNA methylation, affecting genes implicated in neurodegenerative diseases. In PD patients, hemispheric asymmetry in DNA methylation is even greater and involves many PD risk genes. Moreover, the lateralization of clinical PD symptoms involves epigenetic, transcriptional, and proteomic differences across hemispheres that affect neurodevelopment, immune activation, and synaptic transmission. In aging, healthy neurons demonstrate a progressive loss of hemisphere asymmetry in epigenomes that is amplified in PD. For PD patients, a long disease course is associated with retaining more hemispheric asymmetry in neuronal epigenomes. Hemispheric differences in epigenetic gene regulation are prevalent in neurons and may affect the progression and symptoms of PD.
2020-03-26 | PXD015239 | Pride
Project description:Non-syndromic facial asymmetry is commonly found in dentofacial deformity populations with skeletal malocclusions. Asymmetry of this type may result from imbalanced growth and function of both the jaw and associated muscles. Among the multiple genes that interact to affect the craniofacial musculoskeletal complex during pre and postnatal growth and development, NODAL signaling pathwy (NSP) genes are active in adult skeletal muscle and may be key factors in development, growth and maintenance of facial asymmetry. It is of interest to determine whether expression of NODAL pathway genes might differ in masseter muscles between individuals with malocclusion that have facial asymmetry and normal symmetry. Human Transcriptome 2.0 GeneChips (HTA2.0) were used to examine global gene expression in masster muscles between malocclusion subjects with posterior facial asymmetry and with normal facial symmetry.
2014-05-20 | GSE57775 | GEO
Project description:Background Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in isolated prefrontal cortex neurons from control and PD brain hemispheres. DNA methylation is fine-mapped at enhancers and promoters, genome-wide, by targeted bisulfite sequencing in two independent sample cohorts. Results We find that neurons of the human prefrontal cortex exhibit hemispheric differences in DNA methylation. Hemispheric asymmetry in neuronal DNA methylation patterns is largely mediated by differential CpH methylation, and chromatin conformation analysis finds that it targets thousands of genes. With aging, there is a loss of hemispheric asymmetry in neuronal epigenomes, such that hemispheres epigenetically converge in late life. In neurons of PD patients, hemispheric asymmetry in DNA methylation is greater than in controls and involves many PD risk genes. Epigenetic, transcriptomic, and proteomic differences between PD hemispheres correspond to the lateralization of PD symptoms, with abnormalities being most prevalent in the hemisphere matched to side of symptom predominance. Hemispheric asymmetry and symptom lateralization in PD is linked to genes affecting neurodevelopment, immune activation, and synaptic transmission. PD patients with a long disease course have greater hemispheric asymmetry in neuronal epigenomes than those with a short disease course. Conclusions Hemispheric differences in epigenetic gene regulation are prevalent in neurons and may affect the progression and symptoms of PD.
2020-02-12 | GSE135037 | GEO
Project description:Human Accelerated Regions (HARs) are the fastest-evolving regions of the human genome and many are hypothesized to function as regulatory elements that drive human-specific gene regulatory programs. We interrogate the in vitro enhancer activity of >3,100 HARs in massively parallel reporter assays (MPRAs), demonstrating that many HARs appear to act as neural enhancers and that sequence divergence at HARs has largely augmented their neuronal enhancer activity.
2021-07-24 | GSE180714 | GEO