Faculty Opinions recommendation of Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assays.

AbstractMassively parallel reporter assays (MPRAs) are a method to probe the effects of short sequences on transcriptional regulation activity. In a MPRA, short sequences are extracted from suspected regulatory regions, inserted into reporter plasmids, transfected into cell-types of interest, and the transcriptional activity of each reporter is assayed. Recently, Ernst et al. presented MPRA data covering 15750 putative regulatory regions. We trained a multitask convolutional neural network architecture using these sequence expression readouts which predicts as output the expression level outputs across four combinations of cell types and promoters. The model allows for the assigning of importance scores to each base through in silico mutagenesis, and the resulting importance scores correlated well with regions enriched for conservation and transcription factor binding.

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Multinomial Convolutions for Joint Modeling of Sequence Motifs and Enhancer Activities

10.1101/2020.07.28.224212 ◽

2020 ◽

Author(s):

Minjun Park ◽

Salvi Singh ◽

Francisco Jose Grisanti Canozo ◽

Md. Abul Hassan Samee

Keyword(s):

De Novo ◽

Joint Modeling ◽

Chromatin Accessibility ◽

Massively Parallel ◽

Sequence Motifs ◽

Functional Variants ◽

Transcriptional Regulatory ◽

Reporter Assays ◽

Transcriptional Regulatory Mechanisms ◽

Model Sequence

AbstractMassively parallel reporter assays (MPRAs) have enabled the study of transcriptional regulatory mechanisms at an unprecedented scale and with high quantitative resolution. However, this realm lacks models that can discover sequence-specific signals de novo from the data and integrate them in a mechanistic way. We present MuSeAM (Multinomial CNNs for Sequence Activity Modeling), a convolutional neural network that overcomes this gap. MuSeAM utilizes multinomial convolutions that directly model sequence-specific motifs of protein-DNA binding. We demonstrate that MuSeAM fits MPRA data with high accuracy and generalizes over other tasks such as predicting chromatin accessibility and prioritizing potentially functional variants.

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Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assays

Translational Psychiatry ◽

10.1038/s41398-021-01493-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bernard Mulvey ◽

Joseph D. Dougherty

Keyword(s):

Transcription Factors ◽

Retinoic Acid ◽

Association Studies ◽

Massively Parallel ◽

Genome Wide Association Studies ◽

Retinoid Receptor ◽

Functional Snps ◽

Functional Variants ◽

Transcriptional Regulatory ◽

Reporter Assays

AbstractFamily and population studies indicate clear heritability of major depressive disorder (MDD), though its underlying biology remains unclear. The majority of single-nucleotide polymorphism (SNP) linkage blocks associated with MDD by genome-wide association studies (GWASes) are believed to alter transcriptional regulators (e.g., enhancers, promoters) based on enrichment of marks correlated with these functions. A key to understanding MDD pathophysiology will be elucidation of which SNPs are functional and how such functional variants biologically converge to elicit the disease. Furthermore, retinoids can elicit MDD in patients and promote depressive-like behaviors in rodent models, acting via a regulatory system of retinoid receptor transcription factors (TFs). We therefore sought to simultaneously identify functional genetic variants and assess retinoid pathway regulation of MDD risk loci. Using Massively Parallel Reporter Assays (MPRAs), we functionally screened over 1000 SNPs prioritized from 39 neuropsychiatric trait/disease GWAS loci, selecting SNPs based on overlap with predicted regulatory features—including expression quantitative trait loci (eQTL) and histone marks—from human brains and cell cultures. We identified >100 SNPs with allelic effects on expression in a retinoid-responsive model system. Functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs), with additional allelic differences unmasked by treatment with all-trans retinoic acid (ATRA). Finally, motifs overrepresented across functional SNPs corresponded to TFs highly specific to serotonergic neurons, suggesting an in vivo site of action. Our application of MPRAs to screen MDD-associated SNPs suggests a shared transcriptional-regulatory program across loci, a component of which is unmasked by retinoids.

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Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays

10.1101/2021.03.05.434177 ◽

2021 ◽

Author(s):

Bernard Mulvey ◽

Joseph D. Dougherty

Keyword(s):

Transcription Factors ◽

Retinoic Acid ◽

Association Studies ◽

Massively Parallel ◽

Genome Wide Association Studies ◽

Retinoid Receptor ◽

Functional Snps ◽

Functional Variants ◽

Transcriptional Regulatory ◽

Reporter Assays

ABSTRACTFamily and population studies indicate clear heritability of major depressive disorder (MDD), though its underlying biology remains unclear. The majority of single-nucleotide polymorphism (SNP) linkage blocks associated with MDD by genome-wide association studies (GWASes) are believed to alter transcriptional regulators (e.g., enhancers, promoters), based on enrichment of marks correlated with these functions. A key to understanding MDD pathophysiology will be elucidation of which SNPs are functional and how such functional variants biologically converge to elicit the disease. Furthermore, retinoids can elicit MDD in patients, and promote depressive behaviors in rodent models, acting via a regulatory system of retinoid receptor transcription factors (TFs). We therefore sought to simultaneously identify functional genetic variants and assess retinoid pathway regulation of MDD risk loci. Using Massively Parallel Reporter Assays (MPRAs), we functionally screened over 1 000 SNPs prioritized from 39 neuropsychiatric trait/disease GWAS loci, with SNPs selected based on overlap with predicted regulatory features—including expression quantitative trait loci (eQTL) and histone marks—from human brains and cell cultures. We identified >100 SNPs with allelic effects on expression in a retinoid-responsive model system. Further, functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs); with additional allelic differences unmasked by treatment with all-trans retinoic acid (ATRA). Finally, motifs overrepresented across functional SNPs corresponded to TFs highly specific to serotonergic neurons, suggesting an in vivo site of action. Our application of MPRAs to screen MDD-associated SNPs suggests a shared transcriptional regulatory program across loci, a subset of which are unmasked by retinoids.

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Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma

Nature Communications ◽

10.1038/s41467-020-16590-1 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 2

Author(s):

Jiyeon Choi ◽

Tongwu Zhang ◽

Andrew Vu ◽

Julien Ablain ◽

Matthew M. Makowski ◽

...

Keyword(s):

Massively Parallel ◽

Melanoma Risk ◽

Risk Variants ◽

Reporter Assays

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Abstract 5276: Sumoylation Of Klf5 Is A Molecular Switch Regulating Ppar-δ-containing Transcriptional Programs Of Lipid Metabolism

Circulation ◽

10.1161/circ.118.suppl_18.s_518-a ◽

2008 ◽

Vol 118 (suppl_18) ◽

Author(s):

Yumiko Oishi ◽

Ichiro Manabe ◽

Kazuyuki Tobe ◽

Takashi Kadowaki ◽

Ryozo Nagai

Keyword(s):

Cardiovascular Disease ◽

Metabolic Syndrome ◽

Lipid Metabolism ◽

Cardiovascular Diseases ◽

Transcriptional Control ◽

Uncoupling Protein ◽

Molecular Switch ◽

Atherosclerotic Cardiovascular Disease ◽

Transcriptional Regulatory ◽

Reporter Assays

Metabolic syndrome is increasingly recognized as a major risk factor for cardiovascular disease. We have previously shown that a zinc finger transcription factor, Krüppel-like factor 5 (KLF5), plays an important role in cardiovascular diseases, such as atherosclerosis and cardiac hypertrophy. Interestingly, KLF5 is also expressed in metabolic tissues, such as adipose tissue, skeletal muscle and pancreatic β-cells. Moreover, we found that KLF5 is crucial for adipocyte differentiation. Therefore, it is very likely that KLF5 plays multiple roles in development and progression of metabolic syndrome and its cardiovascular and metabolic consequences including atherosclerotic cardiovascular disease. Indeed, KLF5 heterozygous knockout ( KLF5 +/− ) mice were resistant to high-fat-induced obesity and metabolic syndrome, despite consuming more food than wild-type mice. This appears to in part reflect their enhanced energy expenditure. Expression of the genes involved in lipid oxidation and energy uncoupling, including uncoupling protein (UCP) and carnitine-palmitoyl transferase 1b (CPT1b) was upregulated in the soleus muscles of KLF5 +/− mice. KLF5 could be reversibly modified by small ubiquitin-like modifier 1 (SUMO1), after which SUMOylated KLF5 strongly inhibited CPT1b , UCP3 and UCP2 promoter activity. Results of chromatin immunoprecipitation, two-hybrid, and reporter assays showed that under basal conditions SUMOylated KLF5 associated with transcriptionally repressive regulatory complexes containing unliganded PPARδ and corepressors. However, upon agonist stimulation of PPARδ, the deSUMOylating enzyme was recruited and KLF5 was deSUMOylated. The unSUMOylated KLF5 now formed transactivating complexes with liganded PPARδ and CBP. Thus, SUMOylation appears to be a molecular switch affecting function of KLF5 and the transcriptional regulatory programs governing lipid metabolism. Moreover, KLF5 is essential for the PPARδ agonist-dependent transcriptional control. Results of the present study have established KLF5 as a novel key molecule in lipid metabolism and suggest that the posttranscriptional modification of KLF5 is an attractive novel therapeutic target for both metabolic and cardiovascular diseases.

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Transcriptional Regulation of gga-miR-451 by AhR:Arnt in Mycoplasma gallisepticum (HS Strain) Infection

International Journal of Molecular Sciences ◽

10.3390/ijms20123087 ◽

2019 ◽

Vol 20 (12) ◽

pp. 3087 ◽

Cited By ~ 4

Author(s):

Yabo Zhao ◽

Yali Fu ◽

Yingfei Sun ◽

Mengyun Zou ◽

Xiuli Peng

Keyword(s):

Aryl Hydrocarbon Receptor ◽

Chromatin Immunoprecipitation ◽

Regulatory Region ◽

Mycoplasma Gallisepticum ◽

Luciferase Reporter ◽

Binding Motif ◽

Aryl Hydrocarbon ◽

Transcriptional Regulatory ◽

Reporter Assays ◽

Transcriptional Regulatory Region

MicroRNAs (miRNAs) have been determined to be important regulators for pathogenic microorganism infection. However, it is largely unclear how miRNAs are triggered during pathogen infection. We previously reported that the up-regulation of gga-miR-451 negatively regulates the Mycoplasma gallisepticum (MG)-induced production of inflammatory cytokines via targeting tyrosine3-monooxygenase/tryptophan5-monooxygenase activation protein zeta (YWHAZ). The aim of this study was to investigate the mechanism regulating gga-miR-451 in MG infection in chickens. Analysis of gga-miR-451 precursor, pri-miR-451, and pre-miR-451 indicated that the regulation occurred transcriptionally. We also identified the transcriptional regulatory region of gga-miR-451 that contained consensus-binding motif for aryl hydrocarbon receptor (AhR) and aryl hydrocarbon receptor nuclear translocator (Arnt) complex, which is known as the transcription factor that regulates gene expression. Luciferase reporter assays combined with chromatin immunoprecipitation (ChIP) demonstrated that AhR:Arnt bound directly to the promoter elements of gga-miR-451, which were responsible for gga-miR-451 transcription in the context of MG infection. Furthermore, upregulation of AhR:Arnt significantly induced gga-miR-451 and inhibited YWHAZ expression, suggesting that AhR:Arnt may play an anti-inflammatory role in MG infection. This discovery suggests that induced gga-miR-451 expression is modulated by AhR:Arnt in response to MG infection.

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