scholarly journals Erratum: Corrigendum: A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Sandra Steyaert ◽  
Jolien Diddens ◽  
Jeroen Galle ◽  
Ellen De Meester ◽  
Sarah De Keulenaer ◽  
...  
Keyword(s):  
Zebra Finch ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

scholarly journals A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Sandra Steyaert ◽  
Jolien Diddens ◽  
Jeroen Galle ◽  
Ellen De Meester ◽  
Sarah De Keulenaer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zebra Finch ◽  
Model Organism ◽  
Rna Seq ◽  
Exon Arrays ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Upregulated Genes

Abstract Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.

scholarly journals Epigenome-Wide Study Identified Methylation Sites Associated with the Risk of Obesity

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1984
Author(s):  
Majid Nikpay ◽  
Sepehr Ravati ◽  
Robert Dent ◽  
Ruth McPherson
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Rare Variants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Risk Snps ◽  
Trait Locus ◽  
Genomic Regions ◽  
Eqtl Data

Here, we performed a genome-wide search for methylation sites that contribute to the risk of obesity. We integrated methylation quantitative trait locus (mQTL) data with BMI GWAS information through a SNP-based multiomics approach to identify genomic regions where mQTLs for a methylation site co-localize with obesity risk SNPs. We then tested whether the identified site contributed to BMI through Mendelian randomization. We identified multiple methylation sites causally contributing to the risk of obesity. We validated these findings through a replication stage. By integrating expression quantitative trait locus (eQTL) data, we noted that lower methylation at cg21178254 site upstream of CCNL1 contributes to obesity by increasing the expression of this gene. Higher methylation at cg02814054 increases the risk of obesity by lowering the expression of MAST3, whereas lower methylation at cg06028605 contributes to obesity by decreasing the expression of SLC5A11. Finally, we noted that rare variants within 2p23.3 impact obesity by making the cg01884057 site more susceptible to methylation, which consequently lowers the expression of POMC, ADCY3 and DNAJC27. In this study, we identify methylation sites associated with the risk of obesity and reveal the mechanism whereby a number of these sites exert their effects. This study provides a framework to perform an omics-wide association study for a phenotype and to understand the mechanism whereby a rare variant causes a disease.

scholarly journals A Genome-Wide Search For Susceptibility Loci to Human Essential Hypertension

Hypertension ◽  
2000 ◽  
Vol 35 (6) ◽  
pp. 1291-1296 ◽  
Author(s):  
Pankaj Sharma ◽  
Jennie Fatibene ◽  
Franco Ferraro ◽  
Haiyan Jia ◽  
Sue Monteith ◽  
...  
Keyword(s):  
Essential Hypertension ◽  
Susceptibility Loci ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

scholarly journals Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

2021 ◽  
Author(s):  
Tanzeem Fatima ◽  
Rangachari Krishnan ◽  
Ashutosh Srivastava ◽  
Vageeshbabu S. Hanur ◽  
M. Srinivasa Rao
Keyword(s):  
Transcriptome Profiling ◽  
Santalum Album ◽  
Rna Seq ◽  
Improvement Program ◽  
East Indian ◽  
Kegg Pathways ◽  
Oil Biosynthesis ◽  
Genome Wide ◽  
A Genome ◽  
Santalum Album L

East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.

Genome-Wide Prediction of Coaxial Helical Stacking Using Random Forests and Covariance Models

2014 ◽  
Vol 23 (03) ◽  
pp. 1460008
Author(s):  
Kevin Byron ◽  
Jason T. L. Wang ◽  
Dongrong Wen
Keyword(s):  
Random Forests ◽  
Life Science ◽  
Science Research ◽  
Genomic Region ◽  
Computational Approach ◽  
Search Method ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Covariance Models

Developing effective artificial intelligence tools to find motifs in DNA, RNA and proteins poses a challenging yet important problem in life science research. In this paper, we present a computational approach for finding RNA tertiary motifs in genomic sequences. Specifically, we predict genomic coordinate locations for coaxial helical stackings in 3-way RNA junctions. These predictions are provided by our tertiary motif search package, named CSminer, which utilizes two versatile methodologies: random forests and covariance models. A coaxial helical stacking tertiary motif occurs in a 3-way RNA junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Our CSminer tool first uses a genome-wide search method based on covariance models to find a genomic region that may potentially contain a coaxial helical stacking tertiary motif. CSminer then uses a random forests classifier to predict whether the genomic region indeed contains the tertiary motif. Experimental results demonstrate the effectiveness of our approach.

scholarly journals Regulation of angiogenesis through a microRNA (miR-130a) that down-regulates antiangiogenic homeobox genes GAX and HOXA5

Blood ◽  
2008 ◽  
Vol 111 (3) ◽  
pp. 1217-1226 ◽  
Author(s):  
Yun Chen ◽  
David H. Gorski
Keyword(s):  
Binding Sites ◽  
Untranslated Region ◽  
Vascular Endothelial Cells ◽  
Homeobox Gene ◽  
Vascular Endothelial ◽  
Down Regulation ◽  
Antiangiogenic Activity ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

Abstract Angiogenesis is critical to tumor progression. The homeobox gene GAX inhibits angiogenesis in vascular endothelial cells (ECs). We have identified a microRNA (miR-130a) that regulates GAX expression and hypothesized that it plays a major role in modulating GAX activity in ECs. A 280-bp fragment from the GAX 3′-untranslated region (3′-UTR) containing 2 miR-130a targeting sites was observed to be required for the rapid down-regulation of GAX expression by serum and proangiogenic factors, whereas the activity of the GAX promoter did not vary with exposure to serum or proangiogenic factors. This same 280-bp sequence in the GAX 3′-UTR cloned into the psiCHECK2-Luciferase vector mediated serum-induced down-regulation of the reporter gene when placed 3′ of it. Finally, forced expression of miR-130a inhibits GAX expression through this specific GAX 3′-UTR sequence. A genome-wide search for other possible miR-130a binding sites revealed an miR-130a targeting site in the 3′-UTR of the antiangiogenic homeobox gene HOXA5, the expression and antiangiogenic activity of which are also inhibited by miR-130a. From these data, we conclude that miR-130a is a regulator of the angiogenic phenotype of vascular ECs largely through its ability to modulate the expression of GAX and HOXA5.

scholarly journals Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 648 ◽  
Author(s):  
Jeroen Crappé ◽  
Wim Van Criekinge ◽  
Geert Trooskens ◽  
Eisuke Hayakawa ◽  
Walter Luyten ◽  
...  
Keyword(s):  
In Silico ◽  
Ribosome Profiling ◽  
In Silico Prediction ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

A Genome-Wide Search Identifies Potential New Susceptibility Loci for Crohnʼs Disease

1999 ◽  
Vol 5 (4) ◽  
pp. 271-278 ◽  
Author(s):  
Yuanhong Ma ◽  
Jeffrey D. Ohmen ◽  
Zhiming Li ◽  
Gordon L. Bentley ◽  
Colleen McElree ◽  
...  
Keyword(s):  
Susceptibility Loci ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

scholarly journals Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice

2020 ◽  
Vol 21 (15) ◽  
pp. 5492 ◽  
Author(s):  
Yu Jin Jung ◽  
Jong Hee Kim ◽  
Hyo Ju Lee ◽  
Dong Hyun Kim ◽  
Jihyeon Yu ◽  
...  
Keyword(s):  
Gene Expression Analysis ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Loss Of Function ◽  
Amino Acid Motif ◽  
Dwarf Phenotype ◽  
Genome Wide ◽  
A Genome ◽  
Mutant Lines ◽  
Genome Wide Gene Expression

The rice SLR1 gene encodes the DELLA protein (protein with DELLA amino acid motif), and a loss-of-function mutation is dwarfed by inhibiting plant growth. We generate slr1-d mutants with a semi-dominant dwarf phenotype to target mutations of the DELLA/TVHYNP domain using CRISPR/Cas9 genome editing in rice. Sixteen genetic edited lines out of 31 transgenic plants were generated. Deep sequencing results showed that the mutants had six different mutation types at the target site of the TVHYNP domain of the SLR1 gene. The homo-edited plants selected individuals without DNA (T-DNA) transcribed by segregation in the T1 generation. The slr1-d7 and slr1-d8 plants caused a gibberellin (GA)-insensitive dwarf phenotype with shrunken leaves and shortened internodes. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two GA-related genes, GA20OX2 (Gibberellin oxidase) and GA3OX2, were increased in the edited mutant plants, suggesting that GA20OX2 acts as a convert of GA12 signaling. These mutant plants are required by altering GA responses, at least partially by a defect in the phytohormone signaling system process and prevented cell elongation. The new mutants, namely, the slr1-d7 and slr1-d8 lines, are valuable semi-dominant dwarf alleles with potential application value for molecule breeding using the CRISPR/Cas9 system in rice.

scholarly journals A genome-wide search for gene-by-obesity interaction loci of dyslipidemia in Koreans shows diverse genetic risk alleles

2019 ◽  
Vol 60 (12) ◽  
pp. 2090-2101
Author(s):  
Moonil Kang ◽  
Joohon Sung
Keyword(s):  
Genetic Risk ◽  
Risk Alleles ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search
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