scholarly journals Abnormal Epigenetic Modifications in Surviving Somatic Cell Cloned Cattle Associated With Donor Cell Type

2021 ◽  
Author(s):  
Haoqiang Ma ◽  
Tian Huang ◽  
Jin Zhou ◽  
Jinghui Li ◽  
Shenghui Cui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Somatic Cell ◽  
High Throughput Sequencing ◽  
Formation Rate ◽  
Donor Cell ◽  
Epigenetic Modifications ◽  
Rna Seq ◽  
Fetal Fibroblasts ◽  
Cloned Bovine ◽  
Accessible Chromatin

Abstract Background Studies have shown that the efficiency of somatic cell nuclear transfer (SCNT) is related to the type of donor cell used. Previous studies have shown that fetal oviduct epithelial cells (FOVs) exhibit a higher blastocyst formation rate than fetal fibroblasts (FFBs), but they are associated with lower pregnancy, calving, and full-term rates after implantation. The reason for this difference is unclear. Result In this study, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), RNA-seq, and 5-hydroxymethylcytidine (5hmC) and 5-methylcytosine (5mC) DNA methylation sequencing methods across the whole genome to analyze the epigenetic differences between cattle cloned using FFBs or FOVs as donor nuclei. The results showed that chromatin openness, gene expression levels, and 5hmC contents were greater in cloned cattle derived from FOV donor nuclei than in those derived from FFBs. ATAC-seq and RNA-seq analyses of cloned bovine ear tissues derived from the same source of donor nuclei showed an obvious clustering tendency. In this study, we also found that the 5hmC content of surviving cloned cattle derived from FFBs was greater than 4‰, whereas it was less than 2‰ in dead cloned cattle. Conclusion We found that there were abnormalities in specific epigenetic modifications and gene expression in living somatic cell cloned cattle derived from different donor nuclei. Although cloned cattle undergo somatic reprogramming and differentiation, they retain the epigenetic imprints of their donor nuclei, and this somatic imprinting may affect the development rate of cloned blastocysts as well as the birth rate and development status of cloned fetuses after implantation.

scholarly journals The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblasts

2021 ◽  
Author(s):  
Chaoyang Li ◽  
Jiangwen Sun ◽  
Qianglin Liu ◽  
Sanjeeva Dodlapati ◽  
Hao Ming ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myocardial Infarction ◽  
High Throughput Sequencing ◽  
Cardiac Fibroblasts ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Matrix Remodeling ◽  
Rna Seq ◽  
Genome Wide ◽  
Accessible Chromatin

AbstractAfter myocardial infarction, quiescent cardiac fibroblasts are activated and undergo multiple proliferation and differentiation events, which contribute to the extracellular matrix remodeling of the infarcted myocardium. We recently found that cardiac fibroblasts of different differentiation states had distinct expression profiles closely related to their functions. Gene expression is directly regulated by chromatin state. However, the role of chromatin reorganization in the drastic gene expression changes during post-MI differentiation of cardiac fibroblast has not been revealed. In this study, the gene expression profiling and genome-wide mapping of accessible chromatin in mouse cardiac fibroblasts isolated from uninjured hearts and the infarcts at different time points were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and distal areas where enhancers might be located. A positive correlation was identified between the transcription level and promoter accessibility for many dynamically expressed genes. In addition, it was found that DNA methylation may contribute to the post-MI chromatin remodeling and gene expression in cardiac fibroblasts. Integrated analysis of ATAC-seq and RNA-seq datasets also identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.

scholarly journals Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

2021 ◽  
Author(s):  
Dennis A Sun ◽  
Nipam H Patel
Keyword(s):  
Gene Expression ◽  
Genome Annotation ◽  
Time Course ◽  
Regulatory Elements ◽  
Rna Seq ◽  
Genome Wide ◽  
Long Read ◽  
Amphipod Crustacean ◽  
Accessible Chromatin

AbstractEmerging research organisms enable the study of biology that cannot be addressed using classical “model” organisms. The development of novel data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach, including distal regulatory elements. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.Primary Findings-Omni-ATAC-Seq identifies cis-regulatory elements genome-wide during crustacean embryogenesis-Combined short- and long-read RNA-Seq improves the Parhyale genome annotation-ImpulseDE2 analysis identifies dynamically regulated candidate regulatory elements-NucleoATAC and HINT-ATAC enable inference of nucleosome occupancy and transcription factor binding-Fuzzy clustering reveals peaks with distinct accessibility and chromatin dynamics-Integration of accessibility and gene expression reveals possible enhancers and repressors-Omni-ATAC can identify known and novel regulatory elements

24 GLOBAL TRANSCRIPT PROFILING OF CLONED BOVINE BLASTOCYSTS USING AFFYMETRIX GENECHIP TECHNOLOGY

2006 ◽  
Vol 18 (2) ◽  
pp. 120
Author(s):  
Z. Beyhan ◽  
P. Ross ◽  
A. Iager ◽  
A. Kocabas ◽  
K. Cunniff ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Expression Profiles ◽  
Cell Structure ◽  
Donor Cell ◽  
Lipid Binding ◽  
Differentially Expressed ◽  
Gtp Binding ◽  
Cloned Bovine

Identification of genes implicated in the biological processes of somatic cell nuclear transfer will improve our understanding of reprogramming events, i.e. the transformation of a lineage-committed cell into a pluripotent one. In addition, the gene expression profile of cloned embryos can help explain the widely reported developmental failures in cloned animals. In this study, we investigated global gene expression profiles of bovine in vitro-fertilized and cloned embryos using Gene Chip Bovine Genome Arrays (Affymetrix, Inc., Santa Clara, CA, USA). For the generation of cloned bovine blastocysts from two adult fibroblast lines (C and D), we employed methods previously proven to generate live offspring and compared these offspring to in vitro-produced blastocysts. Total RNA isolated from groups of 10 blastocysts was amplified by a template-switching PCR. Amplified cDNAs were used to synthesize biotin-labeled antisense RNAs (aRNAs) during and in vitro transcription reaction. Labeled aRNAs were hybridized to microarrays as described by the manufacturer. Experiments were performed in four replicates. Expression data were analyzed using the Significance Analysis of Microarrays (SAM; Tusher et al. 2001 Proc. Natl. Acad. Sci. 98, 5116-5121) procedure and software. Overall, 48.4% and 46% of 23 000 bovine transcripts spotted on the arrays were present in cloned and in in vitro-produced control blastocysts, respectively. The SAM procedure identified 43 genes that changed at least 1.5-fold, with an estimated false discovery rate (FDR) of 20%. Comparison of gene expression between NT embryos produced from two different cell lines and IVF controls with the same criteria revealed 6 (clones from cell line C vs. IVF) and 46 (clones from cell line D vs. IVF) differentially expressed genes. The number of transcripts expressed differentially between the cloned embryos with different donor cell origin was 437. Of the 43 differentially expressed transcripts in cloned blastocysts, 13 have unknown functions and the rest of the genes related to cell structure (tuftelin, desmoplakin), cell cycle/mitosis (Kinesin like 4, katanin, stathmin, PCNA), energy metabolism (lactate dehydrogenase, ATPsynthase, lipid-binding protein, keto acid dehydrogenase E1, metallothionein), and cell signaling (GTP-binding protein1, GTP binding stimulatory protein). Our results indicate that expression profiles of cloned blastocysts could be affected by somatic donor cell.

scholarly journals Metabolic programming of a Warburg effect-like phenotype in donor fibroblasts prior to somatic cell nuclear transfer

2017 ◽  
Author(s):  
◽  
Bethany Rae Mordhorst
Keyword(s):  
Somatic Cell ◽  
Somatic Cell Nuclear Transfer ◽  
Nuclear Transfer ◽  
Donor Cell ◽  
Nuclear Reprogramming ◽  
In Vitro Development ◽  
Fetal Fibroblasts ◽  
Pharmaceutical Agents ◽  
Vitro Development

Gene edited pigs serve as excellent models for biomedicine and agriculture. Currently, the most efficient way to make a reliably-edited transgenic animal is through somatic cell nuclear transfer (SCNT) also known as cloning. This process involves using cells from a donor (which may have been gene edited) that are typically grown in culture and using their nuclear content to reconstruct a new zygote. To do this, the cell may be placed in the perivitelline space of an enucleated oocyte and activated artificially by a calcium-containing media and electrical pulse waves. While it is remarkable that this process works, it is highly inefficient. In pigs the success of transferred embryos becoming live born piglets is only 1-3%. The creation of more cloned pigs enables further study for the benefit of both A) biomedicine in the development of prognosis and treatments and B) agriculture, whether it be for disease resistance, feed efficiency, gas emissions, etc. Two decades of research has not drastically improved the cloning efficiency of most mammals. One of the main impediments to successful cloning is thought to be due to inefficient nuclear reprogramming and remodeling of the donor cell nucleus. In the following chapters we detail our efforts to improve nuclear reprogramming of porcine fetal fibroblasts by altering the metabolism to be more blastomere-like in nature. We used two methods to alter metabolism 1) pharmaceutical agents and 2) hypoxia. After treating donor cells both methods were used in nuclear transfer. Pharmaceutical agents did not improve in vitro development of gestational survival of clones. Hypoxia did improve in vitro development and we are currently awaiting results of gestation.

scholarly journals Transcriptome-based Selection and Validation of Optimal House-keeping Genes for Skin Research in Goats (Capra hircus)

2020 ◽  
Author(s):  
Jipan Zhang ◽  
Chengchen Deng ◽  
Jialu Li ◽  
Yong-Ju Zhao
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
High Throughput Sequencing ◽  
Comprehensive Analysis ◽  
Skin Tissue ◽  
Capra Hircus ◽  
Meat Industry ◽  
Rna Seq ◽  
Tissue Samples ◽  
Target Gene Expression

Abstract Background : In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat ( Capra hircus ) is an economically important livestock species and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology. Results: Based on the transcriptome dataset of 39 goat skin tissue samples, 8 genes ( SRP68 , NCBP3 , RRAGA , EIF4H , CTBP2 , PTPRA , CNBP , and EEF2 ) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes ( ACTB and GAPDH ) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was shown that NCBP3+SDHA+PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released. Conclusion: This study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3+SDHA+PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.

20 Aggregation of yak heterospecific somatic cell nuclear transfer embryos improves cloning efficiency

2020 ◽  
Vol 32 (2) ◽  
pp. 135
Author(s):  
M. Yauri Felipe ◽  
M. Duque Rodríguez ◽  
A. De Stéfano ◽  
D. Salamone
Keyword(s):  
Somatic Cell ◽  
Somatic Cell Nuclear Transfer ◽  
Nuclear Transfer ◽  
Bos Taurus ◽  
Formation Rate ◽  
Donor Cell ◽  
Blastocyst Formation ◽  
Fluid Medium ◽  
Exact Test ◽  
Significant Difference

Cloning endangered species has the limitation that generally the number of available oocytes is limited. Reprogramming the nuclei heterospecifically using an enucleated oocyte from a different species is an alternative. Aggregation of SCNT (somatic cell nuclear transfer) embryos from the same specie results in improved embryo development. However, after aggregation of heterospecific SCNT embryos from different genera, no effects were observed (Moro et al. 2015 Reproduction 50, 1-10). The objective of this study was to evaluate the influence of aggregation of yak (Bos grunniens) embryos produced by heterospecific SCNT using enucleated oocytes from an animal from the same genus Bos taurus. As control homospecific SCNT of Bos taurus, parthenogenic zone-free embryos and IVF embryos were used. Cumulus-oocyte complexes were recovered from bovine slaughterhouse ovaries by follicular aspiration. The cumulus-oocyte complexes were matured in tissue culture medium 199 containing 10% fetal bovine serum, 10μgmL−1 FSH, 0.3mM sodium pyruvate, 100mM cysteamine, and 2% antibiotic-antimycotic for 22h, at 6.5% CO2 in humidified air and 38.5°C. After denudation, mature oocytes were stripped of the zona pellucida using a protease and then enucleated by micromanipulation. Staining was performed with Hoechst 33342 to observe MII. Enucleated oocytes were placed in phytohemagglutinin to induce adherence with the donor cell followed by electrofusion. All reconstituted embryos were activated using ionomcine. This was followed by a treatment with 6-dimethylaminopurine for 3h. Zona-free reconstituted cloned embryos were cultured in the wells of the well system, placing one (1×) or two (2×) per microwell, in synthetic oviductal fluid medium. The experimental groups were parthenogenic zone free; IVF; reconstituted embryos bull fibroblast-enucleated oocyte from cow (BC1×); reconstituted embryos yak fibroblast-enucleated oocyte from cow (YC1×); and reconstituted embryos aggregated yak fibroblast-enucleated oocyte from cow (YC2×). In all experimental groups, cleavage of at least one embryo in the wells and blastocyst formation at Day 7 were assessed. The effect of cloned embryo aggregation on blastocyst rates was analysed using Fisher exact tests (GraphPad Prisma 8), and results are shown on Table 1. Results demonstrated that aggregation of two SCNT heterospecific embryos increased the blastocyst formation rate of yak (P<0.05). In conclusion aggregation in yak heterospecific SCNT embryos from species of the same genus (Bos) can improve development to blastocyst. Table 1.Aggregation of yak heterospecific somatic cell nuclear transfer embryos Experimental group1 No. of embryos No. of embryos-wells2 Cleavage (%) Blastocyst (%) PZF 68 68 66 (97.06%)a 17 (25.00%)acd IVF 89 - 81 (91.01%)ab 39 (43.82%)b BC1× 45 45 41 (91.11%)b 6 (13.33%)cd YC1× 101 101 77 (76.24%)c 14 (13.86%)c YC2× 134 67 61 (91.04%)ab 21 (31.34%)ab a-dDifferent superscripts in the same column indicate significant difference (Fisher's exact test, P<0.05). 1PZF, parthenogenetic zone free; IFV, IVF fecundation; BC1×, clone of bovine; YC1×, clone of yak-bovine; YC2×, clone of yak-bovine added. 2Wells used with embryos.

ISOFORM ABUNDANCE INFERENCE PROVIDES A MORE ACCURATE ESTIMATION OF GENE EXPRESSION LEVELS IN RNA-SEQ

2010 ◽  
Vol 08 (supp01) ◽  
pp. 177-192 ◽  
Author(s):  
XI WANG ◽  
ZHENGPENG WU ◽  
XUEGONG ZHANG
Keyword(s):  
Gene Expression ◽  
High Throughput Sequencing ◽  
Transcript Abundance ◽  
Accurate Estimation ◽  
Rna Seq ◽  
Estimation Errors ◽  
Expression Levels ◽  
Or Gene ◽  
Read Distribution ◽  
Gene Expression Levels

Due to its unprecedented high-resolution and detailed information, RNA-seq technology based on next-generation high-throughput sequencing significantly boosts the ability to study transcriptomes. The estimation of genes' transcript abundance levels or gene expression levels has always been an important question in research on the transcriptional regulation and gene functions. On the basis of the concept of Reads Per Kilo-base per Million reads (RPKM), taking the union-intersection genes (UI-based) and summing up inferred isoform abundance (isoform-based) are the two current strategies to estimate gene expression levels, but produce different estimations. In this paper, we made the first attempt to compare the two strategies' performances through a series of simulation studies. Our results showed that the isoform-based method gives not only more accurate estimation but also has less uncertainty than the UI-based strategy. If taking into account the non-uniformity of read distribution, the isoform-based method can further reduce estimation errors. We applied both strategies to real RNA-seq datasets of technical replicates, and found that the isoform-based strategy also displays a better performance. For a more accurate estimation of gene expression levels from RNA-seq data, even if the abundance levels of isoforms are not of interest, it is still better to first infer the isoform abundance and sum them up to get the expression level of a gene as a whole.

scholarly journals Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)

2020 ◽  
Vol 21 (8) ◽  
pp. 2800 ◽  
Author(s):  
Xi Wu ◽  
Yang Yang ◽  
Chaoyue Zhong ◽  
Yin Guo ◽  
Tengyu Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Sex Reversal ◽  
Open Chromatin ◽  
Specific Marker ◽  
Epinephelus Coioides ◽  
Rna Seq ◽  
Accessible Chromatin

Chromatin structure plays a pivotal role in maintaining the precise regulation of gene expression. Accessible chromatin regions act as the binding sites of transcription factors (TFs) and cis-elements. Therefore, information from these open regions will enhance our understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. We employed an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq analyses in the gonads of protogynous hermaphroditic orange-spotted groupers during sex reversal to profile open chromatin regions and TF binding sites. We focused on several crucial TFs, including ZNF263, SPIB, and KLF9, and analyzed the networks of TF-target genes. We identified numerous transcripts exhibiting sex-preferred expression among their target genes, along with their associated open chromatin regions. We then investigated the expression patterns of sex-related genes as well as the mRNA localization of certain genes during sex reversal. We found a set of sex-related genes that—upon further study—might be identified as the sex-specific or cell-specific marker genes that trigger sex reversal. Moreover, we discovered the core genes (gnas, ccnb2, and cyp21a) of several pathways related to sex reversal that provide the guideposts for future study.

scholarly journals Characterization of the rat developmental liver transcriptome

2013 ◽  
Vol 45 (8) ◽  
pp. 301-311 ◽  
Author(s):  
Richard H. Chapple ◽  
Polyana C. Tizioto ◽  
Kevin D. Wells ◽  
Scott A. Givan ◽  
JaeWoo Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput Sequencing ◽  
Mitochondrial Gene ◽  
Probe Design ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Biologically Relevant ◽  
Gradual Process ◽  
Intergenic Regions ◽  
Sequencing Platforms

Gene regulation and transcriptome studies have been enabled by the development of RNA-Seq applications for high-throughput sequencing platforms. Next generation sequencing is remarkably efficient and avoids many issues inherent in hybridization-based microarray methodologies including the exon-specific dependence of probe design. Biologically relevant transcripts including messenger and regulatory RNAs may now be quantified and annotated regardless of whether they have previously been observed. We used RNA-Seq to investigate global patterns of gene expression in early developing rat liver. Liver samples from timed-pregnant Lewis rats were collected at six fetal and neonatal stages [embryonic day (E)14, E16, E18, E20, postnatal day (P)1, P7], transcripts were sequenced using an Illumina HiSeq 2000, and data analysis was performed with the Tuxedo software suite. Genes and isoforms differing in abundance were queried for enrichment within functionally related gene groups using the Functional Annotation Tool of the DAVID Bioinformatics Database. While hematopoietic gene expression is initiated by E14, hepatocyte maturation is a gradual process involving clusters of genes responsible for response to nutrients and enzymes responsible for glycolysis and fatty acid catabolism. Following birth, a large cluster of differentially abundant genes was enriched for mitochondrial gene expression and cholesterol synthesis indicating that by 1 wk of age, the liver is engaged in lipid sensing and bile production. Clustering results for differentially abundant genes and isoforms were similar with the greatest difference for the E14/E16 comparison. Finally, a bioinformatic approach was used to annotate 1,307 novel liver transcripts assembled from sequences that aligned to intergenic regions of the rat genome.

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