Comparative Methylation and RNA-Seq Expression Analysis in CpG Context to Identify Genes Involved in Backfat vs Liver Diversification in Nanchukmacdon Pig

Abstract Background: DNA methylation and demethylation at CpG island is one of the main regulatory mechanisms at the transcriptional level that give cells the possibility to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergone selection. Liver and Backfat play important role in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue stores plethora of information and their understanding are required to enhance tissue characteristics in the future generation. Results: In this study, to understand the differentiation mechanism we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis and identified 16 CpG islands were involved in differentially methylation regions (DMRs) as well differentially expressed genes (DEGs) between liver and backfat. Among the identified differentially-methylated genes (C7orf50, ACTB, MLC1) in backfat and (TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A, HOXA5) in the liver were identified. Motif analysis for DMRs was also performed to understand the major role of methylated motif for tissue-specific differentiation. Gene ontology studies revealed the association with collagen fibril organization, BMP signaling pathway in backfat and Cholesterol biosynthesis, bile acid and bile salt transport, immunity-related pathways in methylated genes expressed in the liver. Conclusion: Our finding could help in understanding how methylation on certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.

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Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig

BMC Genomics ◽

10.1186/s12864-021-08123-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Devender Arora ◽

Jong-Eun Park ◽

Dajeong Lim ◽

Bong-Hwan Choi ◽

In-Cheol Cho ◽

...

Keyword(s):

Cholesterol Biosynthesis ◽

Critical Role ◽

Cpg Islands ◽

Bmp Signaling ◽

Salt Transport ◽

Rna Seq ◽

Motif Analysis ◽

Tissue Samples ◽

Tissue Specific

Abstract Background DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. Results A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. Conclusions In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.

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PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum

10.1101/2021.04.23.441196 ◽

2021 ◽

Author(s):

Yadi Zhou ◽

Abhijit Sukul ◽

John W. Mishler-Elmore ◽

Ahmed Faik ◽

Michael A. Held

Keyword(s):

Regulatory Mechanisms ◽

Cereal Crops ◽

Data Sets ◽

Visualization Tool ◽

Rna Seq ◽

Gene Expressions ◽

Tissue Specific ◽

Network Database ◽

Meta Information ◽

Immersive Environment

AbstractGlobal gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. With the recent accumulation of RNA-seq data sets, the construction of RNA-seq-based GCNs has now become possible. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to humanity and contribute significantly to our food supply. However, co-expression network tools for these plants are outdated or lacking. In this study, we constructed global GCNs for barley and sorghum using 500 and 774 RNA-seq data sets, respectively. In addition, we curated the meta-information of these RNA-seq data sets and categorized them into four main tissue types, leaf, root, shoot, and flower/seed, and built tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus, offering an immersive environment for the exploration and visualization of gene expressions and co-expressions of barley and sorghum at the global and tissue-specific levels. PlantNexus is freely available at https://plantnexus.ohio.edu/.

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Differential Methylation Signatures in Severely Calcified Carotid Plaques by Genome-Wide Comprehensive Analysis

Current Neurovascular Research ◽

10.2174/1567202617666201029145028 ◽

2020 ◽

Vol 17 ◽

Author(s):

Hiroyuki Katano ◽

Yusuke Nishikawa ◽

Hiroshi Yamada ◽

Tomoyasu Yamanaka ◽

Mitsuhito Mase

Keyword(s):

Dna Methylation ◽

Cpg Island ◽

Principal Component ◽

Smooth Muscle Contraction ◽

Differential Methylation ◽

Promoter Regions ◽

Tissue Specific ◽

Carotid Plaques ◽

Differentially Methylated Genes ◽

Island Shore

Background: The precise cellular behaviors of calcification, including its molecular and genetic activities, have not yet been fully established for carotid plaques. Objective: We sought specific genes with tissue-specific differential methylation associated with carotid calcification status. Methods: We classified eight plaques from carotid endarterectomy patients as high- or low-calcified based on their Agatston calcium scores. We analyzed differential DNA methylation and performed bioinformatics data mining. Results: A high correlation of average methylation levels (b-values) in promoter regions between high- and low-calcified plaque groups was observed. A principal component analysis of DNA methylation values in promoters of specimens revealed two independent clusters for high- and low-calcified plaques. Volcano plots for methylation differences in promoter regions showed that significantly hypomethylated probes were more frequently found for high-calcified plaques than more methylated probes. Differential hypomethylation of receptor activity-modifying protein 1 (RAMP1) in high-calcified plaques was commonly extracted in both the promoter region and the cytosine-phosphate-guanine (CpG) island shore region, where differential methylation had been reported to be more tissue-specific. Kyoto Encyclopedia of Genes and Genomes pathway analysis annotated a pathway associated with vascular smooth muscle contraction in the differentially methylated genes of the promoter and CpG island shore regions in high-calcified plaques. Conclusion: Among the extracted differentially methylated genes, hypomethylated genes were more dominant than more methylated genes. The augmentation of RAMP1 by hypomethylation may contribute to the enhancement of antiatherosclerotic effects and hence stability in high-calcified plaques. These results contribute to our understanding of the genetic signatures associated with calcification status and cellular activity in carotid plaques.

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Lamin A/C Is Dispensable to Mechanical Repression of Adipogenesis

International Journal of Molecular Sciences ◽

10.3390/ijms22126580 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6580

Author(s):

Matthew Goelzer ◽

Amel Dudakovic ◽

Melis Olcum ◽

Buer Sen ◽

Engin Ozcivici ◽

...

Keyword(s):

Cell Structure ◽

Nuclear Architecture ◽

Focal Adhesions ◽

Protein Translation ◽

Lamin A ◽

Transcriptional Level ◽

Rna Seq ◽

Interferon Signaling ◽

Regulate Protein ◽

Low Intensity Vibration

Mesenchymal stem cells (MSCs) maintain the musculoskeletal system by differentiating into multiple lineages, including osteoblasts and adipocytes. Mechanical signals, including strain and low-intensity vibration (LIV), are important regulators of MSC differentiation via control exerted through the cell structure. Lamin A/C is a protein vital to the nuclear architecture that supports chromatin organization and differentiation and contributes to the mechanical integrity of the nucleus. We investigated whether lamin A/C and mechanoresponsiveness are functionally coupled during adipogenesis in MSCs. siRNA depletion of lamin A/C increased the nuclear area, height, and volume and decreased the circularity and stiffness. Lamin A/C depletion significantly decreased markers of adipogenesis (adiponectin, cellular lipid content) as did LIV treatment despite depletion of lamin A/C. Phosphorylation of focal adhesions in response to mechanical challenge was also preserved during loss of lamin A/C. RNA-seq showed no major adipogenic transcriptome changes resulting from LIV treatment, suggesting that LIV regulation of adipogenesis may not occur at the transcriptional level. We observed that during both lamin A/C depletion and LIV, interferon signaling was downregulated, suggesting potentially shared regulatory mechanism elements that could regulate protein translation. We conclude that the mechanoregulation of adipogenesis and the mechanical activation of focal adhesions function independently from those of lamin A/C.

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Exploring Differentially Methylated Genes in Vulvar Squamous Cell Carcinoma

Cancers ◽

10.3390/cancers13143580 ◽

2021 ◽

Vol 13 (14) ◽

pp. 3580

Author(s):

Shatavisha Dasgupta ◽

Patricia C. Ewing-Graham ◽

Sigrid M. A. Swagemakers ◽

Thierry P. P. van den Bosch ◽

Peggy N. Atmodimedjo ◽

...

Keyword(s):

Dna Methylation ◽

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Dna Sequences ◽

Cpg Island ◽

Epigenetic Modification ◽

Vulvar Squamous Cell Carcinoma ◽

Differentially Methylated Genes ◽

Methylation Profiling

DNA methylation is the most widely studied mechanism of epigenetic modification, which can influence gene expression without alterations in DNA sequences. Aberrations in DNA methylation are known to play a role in carcinogenesis, and methylation profiling has enabled the identification of biomarkers of potential clinical interest for several cancers. For vulvar squamous cell carcinoma (VSCC), however, methylation profiling remains an under-studied area. We sought to identify differentially methylated genes (DMGs) in VSCC, by performing Infinium MethylationEPIC BeadChip (Illumina) array sequencing, on a set of primary VSCC (n = 18), and normal vulvar tissue from women with no history of vulvar (pre)malignancies (n = 6). Using a false-discovery rate of 0.05, beta-difference (Δβ) of ± 0.5, and CpG-island probes as cut-offs, 199 DMGs (195 hyper-methylated, 4 hypo-methylated) were identified for VSCC. Most of the hyper-methylated genes were found to be involved in transcription regulator activity, indicating that disruption of this process plays a vital role in VSCC development. The majority of VSCCs harbored amplifications of chromosomes 3, 8, and 9. We identified a set of DMGs in this exploratory, hypothesis-generating study, which we hope will facilitate epigenetic profiling of VSCCs. Prognostic relevance of these DMGs deserves further exploration in larger cohorts of VSCC and its precursor lesions.

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The BET Inhibitor JQ1 Augments the Antitumor Efficacy of Gemcitabine in Preclinical Models of Pancreatic Cancer

Cancers ◽

10.3390/cancers13143470 ◽

2021 ◽

Vol 13 (14) ◽

pp. 3470

Author(s):

Aubrey L. Miller ◽

Patrick L. Garcia ◽

Samuel C. Fehling ◽

Tracy L. Gamblin ◽

Rebecca B. Vance ◽

...

Keyword(s):

Pancreatic Cancer ◽

Dna Damage ◽

Cholesterol Biosynthesis ◽

Antitumor Efficacy ◽

Rna Seq ◽

Bet Inhibitor ◽

Bet Inhibitors ◽

Xenograft Models

Gemcitabine is used to treat pancreatic cancer (PC), but is not curative. We sought to determine whether gemcitabine + a BET bromodomain inhibitor was superior to gemcitabine, and identify proteins that may contribute to the efficacy of this combination. This study was based on observations that cell cycle dysregulation and DNA damage augment the efficacy of gemcitabine. BET inhibitors arrest cells in G1 and allow increases in DNA damage, likely due to inhibition of expression of DNA repair proteins Ku80 and RAD51. BET inhibitors (JQ1 or I-BET762) + gemcitabine were synergistic in vitro, in Panc1, MiaPaCa2 and Su86 PC cell lines. JQ1 + gemcitabine was more effective in vivo than either drug alone in patient-derived xenograft models (P < 0.01). Increases in the apoptosis marker cleaved caspase 3 and DNA damage marker γH2AX paralleled antitumor efficacy. Notably, RNA-seq data showed that JQ1 + gemcitabine selectively inhibited HMGCS2 and APOC1 ~6-fold, compared to controls. These proteins contribute to cholesterol biosynthesis and lipid metabolism, and their overexpression supports tumor cell proliferation. IPA data indicated that JQ1 + gemcitabine selectively inhibited the LXR/RXR activation pathway, suggesting the hypothesis that this inhibition may contribute to the observed in vivo efficacy of JQ1 + gemcitabine.

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Expression of the genes for the ferritin H and L subunits in rat liver and heart. Evidence for tissue-specific regulations at pre- and post-translational levels

Biochemical Journal ◽

10.1042/bj2750813 ◽

1991 ◽

Vol 275 (3) ◽

pp. 813-816 ◽

Cited By ~ 38

Author(s):

G Cairo ◽

E Rappocciolo ◽

L Tacchini ◽

L Schiaffonati

Keyword(s):

Translational Regulation ◽

Specific Pattern ◽

Regulatory Mechanisms ◽

Mrna Accumulation ◽

Tissue Specific ◽

Protein Levels ◽

Ferritin Gene ◽

Ferritin H ◽

Translational Mechanisms ◽

Different Tissues

The proportion of ferritin light-chain and heavy-chain subunits (L and H) present in the ferritin multimeric shell varies between different tissues. To identify the regulatory mechanisms responsible for the greater amount of L in liver than in heart isoferritins, we analysed ferritin-gene expression at the RNA and protein levels in these two tissues of the rat. In the heart the ratio between the amount of L and H, at the level both of synthesis and accumulation, is about 1 and is the same as the ratio between their respective mRNAs. In contrast, in the liver, the ratio between the L- and H-mRNAs is approx. 2 and cannot entirely explain the large predominance of L in isoferritins in this tissue. Since in the liver the L-mRNA is neither preferentially associated with polyribosomes nor translated more efficiently than its H- counterpart, it seems that the liver-specific isoferritin profile is determined by a combination of pre- and post-translational mechanisms, whereas in heart the post-translational regulation does not seem to be relevant and the tissue-specific pattern is determined at the level of mRNA accumulation.

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Methylation of the Cyclin A1 Promoter Correlates with Gene Silencing in Somatic Cell Lines, while Tissue-Specific Expression of Cyclin A1 Is Methylation Independent

Molecular and Cellular Biology ◽

10.1128/mcb.20.9.3316-3329.2000 ◽

2000 ◽

Vol 20 (9) ◽

pp. 3316-3329 ◽

Cited By ~ 55

Author(s):

Carsten Müller ◽

Carol Readhead ◽

Sven Diederichs ◽

Gregory Idos ◽

Rong Yang ◽

...

Keyword(s):

Gene Expression ◽

Cell Lines ◽

Promoter Methylation ◽

Cpg Island ◽

Trichostatin A ◽

Specific Gene ◽

Cyclin A1 ◽

Specific Expression ◽

Tissue Specific ◽

Tissue Specific Expression

ABSTRACT Gene expression in mammalian organisms is regulated at multiple levels, including DNA accessibility for transcription factors and chromatin structure. Methylation of CpG dinucleotides is thought to be involved in imprinting and in the pathogenesis of cancer. However, the relevance of methylation for directing tissue-specific gene expression is highly controversial. The cyclin A1 gene is expressed in very few tissues, with high levels restricted to spermatogenesis and leukemic blasts. Here, we show that methylation of the CpG island of the human cyclin A1 promoter was correlated with nonexpression in cell lines, and the methyl-CpG binding protein MeCP2 suppressed transcription from the methylated cyclin A1 promoter. Repression could be relieved by trichostatin A. Silencing of a cyclin A1 promoter-enhanced green fluorescent protein (EGFP) transgene in stable transfected MG63 osteosarcoma cells was also closely associated with de novo promoter methylation. Cyclin A1 could be strongly induced in nonexpressing cell lines by trichostatin A but not by 5-aza-cytidine. The cyclin A1 promoter-EGFP construct directed tissue-specific expression in male germ cells of transgenic mice. Expression in the testes of these mice was independent of promoter methylation, and even strong promoter methylation did not suppress promoter activity. MeCP2 expression was notably absent in EGFP-expressing cells. Transcription from the transgenic cyclin A1 promoter was repressed in most organs outside the testis, even when the promoter was not methylated. These data show the association of methylation with silencing of the cyclin A1 gene in cancer cell lines. However, appropriate tissue-specific repression of the cyclin A1 promoter occurs independently of CpG methylation.

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