scholarly journals Transcriptome and Proteome Analysis Revealed Key Pathways Regulating Final Stage of Oocyte Maturation of the Turkey (Meleagris gallopavo)

2021 ◽  
Vol 22 (19) ◽  
pp. 10589
Author(s):  
Mariola Słowińska ◽  
Łukasz Paukszto ◽  
Laura Pardyak ◽  
Jan P. Jastrzębski ◽  
Ewa Liszewska ◽  
...  
Keyword(s):  
Oocyte Maturation ◽  
Regulation Of Gene Expression ◽  
Cell Communication ◽  
Meleagris Gallopavo ◽  
Proteome Analysis ◽  
Related Factor ◽  
Expression Site ◽  
Ubiquitination System ◽  
Key Pathways ◽  
Generation Sequencing

In birds, the zona pellucida (ZP) matrix that surrounds the ovulated oocyte—called the inner perivitelline layer—is involved in sperm–zona interaction and successful fertilization. To identify the important genes and proteins connected with the final step of egg development, next-generation sequencing and two-dimensional electrophoresis, combined with mass spectrometry, were used for the analysis of mature oocytes at the F1 developmental stage. A total of 8161 genes and 228 proteins were annotated. Six subfamilies of genes, with codes ZP, ZP1–4, ZPD, and ZPAX, were identified, with the dominant expression of ZPD. The main expression site for ZP1 was the liver; however, granulosa cells may also participate in local ZP1 secretion. A ubiquitination system was identified in mature oocytes, where ZP1 was found to be the main ubiquitinated protein. Analysis of transcripts classified in estrogen receptor (ESR) signaling indicated the presence of ESR1 and ESR2, as well as a set of estrogen-dependent genes involved in both genomic and nongenomic mechanisms for the regulation of gene expression by estrogen. Oxidative phosphorylation was found to be a possible source of adenosine triphosphate, and the nuclear factor erythroid 2-related factor 2 signaling pathway could be involved in the response against oxidative stress. Oocyte–granulosa cell communication by tight, adherens, and gap junctions seems to be essential for the final step of oocyte maturation.

Mutational profiling of acute myeloid leukemia with normal cytogenetics in Brazilian patients: the value of next-generation sequencing for genomic classification

2017 ◽  
Vol 65 (8) ◽  
pp. 1155-1158 ◽  
Author(s):  
Thiago Rodrigo de Noronha ◽  
Miguel Mitne-Neto ◽  
Maria de Lourdes Chauffaille
Keyword(s):  
Acute Myeloid Leukemia ◽  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Regulation Of Gene Expression ◽  
Uniparental Disomy ◽  
Driver Mutations ◽  
Next Generation ◽  
Normal Cytogenetics ◽  
Generation Sequencing ◽  
Acute Myeloid

Karyotype (KT) aberrations are important prognostic factors for acute myeloid leukemia (AML); however, around 50% of cases present normal results. Single nucleotide polymorphism array can detect chromosomal gains, losses or uniparental disomy that are invisible to KT, thus improving patients’ risk assessment. However, when both tests are normal, important driver mutations can be detected by the use of next-generation sequencing (NGS). Fourteen adult patients with AML with normal cytogenetics were investigated by NGS for 19 AML-related genes. Every patient presented at least one mutation:DNMT3Ain nine patients;IDH2in six;IDH1in three;NRASandNPM1in two; andTET2,ASXL1,PTPN11, andRUNX1in one patient. No mutations were found inFLT3,KIT,JAK2,CEBPA,GATA2,TP53,BRAF,CBL,KRAS,andWT1genes. Twelve patients (86%) had at least one mutation in genes related with DNA methylation (DNMT3A,IDH1,IDH2,andTET2), which is involved in regulation of gene expression and genomic stability. All patients could be reclassified based on genomic status and nine had their prognosis modified. In summary, NGS offers insights into the molecular pathogenesis and biology of cytogenetically normal AML in Brazilian patients, indicating that the prognosis could be further stratified by different mutation combinations. This study shows a different frequency of mutations in Brazilian population that should be confirmed.

scholarly journals miRNAs: EBV Mechanism for Escaping Host’s Immune Response and Supporting Tumorigenesis

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 353 ◽  
Author(s):  
Snježana Židovec Lepej ◽  
Maja Matulić ◽  
Paula Gršković ◽  
Mirjana Pavlica ◽  
Leona Radmanić ◽  
...  
Keyword(s):  
Immune Response ◽  
B Cell ◽  
Cell Transformation ◽  
Regulation Of Gene Expression ◽  
Cell Communication ◽  
Human Herpesvirus ◽  
Human Virus ◽  
Barr Virus ◽  
Epstein Barr

Epstein-Barr virus (EBV) or human herpesvirus 4 (HHV-4) is a ubiquitous human oncogenic virus, and the first human virus found to express microRNAs (miRNAs). Its genome contains two regions encoding more than 40 miRNAs that regulate expression of both viral and human genes. There are numerous evidences that EBV miRNAs impact immune response, affect antigen presentation and recognition, change T- and B-cell communication, drive antibody production during infection, and have a role in cell apoptosis. Moreover, the ability of EBV to induce B-cell transformation and take part in mechanisms of oncogenesis in humans is well known. Although EBV infection is associated with development of various diseases, the role of its miRNAs is still not understood. There is abundant data describing EBV miRNAs in nasopharyngeal carcinoma and several studies that have tried to evaluate their role in gastric carcinoma and lymphoma. This review aims to summarize so far known data about the role of EBV miRNAs in altered regulation of gene expression in human cells in EBV-associated diseases.

Proteome analysis of protein partners to nucleosomes containing canonical H2A or the variant histones H2A.Z or H2A.X

2012 ◽  
Vol 393 (1-2) ◽  
pp. 47-61 ◽  
Author(s):  
Satoru Fujimoto ◽  
Corrine Seebart ◽  
Tiziana Guastafierro ◽  
Jessica Prenni ◽  
Paola Caiafa ◽  
...  
Keyword(s):  
Regulation Of Gene Expression ◽  
Proteome Analysis ◽  
Strand Break ◽  
Histone Variants ◽  
Histone H2a ◽  
Systematic Analysis ◽  
Cellular Processes ◽  
Nucleosome Structure ◽  
Protein Partners ◽  
Dna Double Strand Break

Abstract Although the existence of histone variants has been known for quite some time, only recently are we grasping the breadth and diversity of the cellular processes in which they are involved. Of particular interest are the two variants of histone H2A, H2A.Z and H2A.X because of their roles in regulation of gene expression and in DNA double-strand break repair, respectively. We hypothesize that nucleosomes containing these variants may perform their distinct functions by interacting with different sets of proteins. Here, we present our proteome analysis aimed at identifying protein partners that interact with nucleosomes containing H2A.Z, H2A.X or their canonical H2A counterpart. Our development of a nucleosome-pull down assay and analysis of the recovered nucleosome-interacting proteins by mass spectrometry allowed us to directly compare nuclear partners of these variant-containing nucleosomes to those containing canonical H2A. To our knowledge, our data represent the first systematic analysis of the H2A.Z and H2A.X interactome in the context of nucleosome structure.

scholarly journals A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription

2020 ◽  
Author(s):  
Sebastian Marquardt ◽  
Xueyuan Leng ◽  
Quentin Thomas ◽  
Simon Rasmussen
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Regulation Of Gene Expression ◽  
Positioning System ◽  
Biological Functions ◽  
Post Translational Modifications ◽  
Histone Ptms ◽  
Definition Of ◽  
Generation Sequencing ◽  
Rnapii Transcription

Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNAPII transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin Immuno-precipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM “readers”, “writers” and “erasers”, with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may in part rely on the characteristic histone PTMs profiles that distinguish transcription stages.

RMDB: An Integrated Database of Single-cytosine-resolution DNA Methylation in Oryza Sativa

2019 ◽  
Vol 14 (6) ◽  
pp. 524-531
Author(s):  
Tiansheng Zhu ◽  
Jihong Guan ◽  
Hui Liu ◽  
Shuigeng Zhou
Keyword(s):  
Dna Methylation ◽  
Oryza Sativa ◽  
Regulation Of Gene Expression ◽  
Methylation Data ◽  
Public Resource ◽  
Graphical Visualization ◽  
Visualization Tools ◽  
Next Generation Sequencing Ngs ◽  
Genome Scale ◽  
Generation Sequencing

Background: Previous studies have revealed that DNA methylation plays a crucial role in eukaryotic growth and development via involvement in the regulation of gene expression and chromosomal instability. With the advancement of biotechnology, next-generation sequencing (NGS) is emerging as a popular method to explore the functions of DNA methylation, and an increasing number of genome-scale DNA methylation datasets have been published. Several DNA methylation databases, including MethDB, NGSmethDB and MENT have been developed for storing and analyzing the DNA methylation data. However, no public resource dedicated to DNA methylation of Oryza sativa is available to date. Methods & Results: We built a comprehensive database (RMDB) for integration and analysis of DNA methylation data of Oryza sativa. A couple of functional modules were developed to identify the connections between DNA methylation and phenotypes. Moreover, rich graphical visualization tools were employed to facilitate data presentation and interpretation. Conclusion: RMDB is an integrated database dedicated to rice DNA methylation. To the best of our knowledge, this is the first integrated rice DNA methylation database. We believe that RMDB will be helpful to understand the epigenetic mechanisms of Oryza sativa. RMDB is freely available at http://admis.fudan.edu.cn/rmdb.

scholarly journals Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

PLoS Biology ◽  
2010 ◽  
Vol 8 (9) ◽  
pp. e1000475 ◽  
Author(s):  
Rami A. Dalloul ◽  
Julie A. Long ◽  
Aleksey V. Zimin ◽  
Luqman Aslam ◽  
Kathryn Beal ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Assembly ◽  
Meleagris Gallopavo ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals “Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing

BioChem ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 210-237
Author(s):  
Diane Appiasie ◽  
Daniel J. Guerra ◽  
Kyle Tanguay ◽  
Steven Jelinek ◽  
Damian D. Guerra ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Lipid Metabolism ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Viral Proteins ◽  
Next Generation ◽  
Sources Of Information ◽  
Generation Sequencing

In the race against COVID-19 for timely therapeutic developments, mass spectrometry-based high-throughput methods have been valuable. COVID-19 manifests an extremely diverse spectrum of phenotypes from asymptomatic to life-threatening, drastic elevations in immune response or cytokine storm, multiple organ failure and death. These observations warrant a detailed understanding of associated molecular mechanisms to develop therapies. In this direction, high-throughput methods that generate large datasets focusing on changes in protein interactions, lipid metabolism, transcription, and epigenetic regulation of gene expression are extremely beneficial sources of information. Hence, mass spectrometry-based methods have been employed in several studies to detect changes in interactions among host proteins, and between host and viral proteins in COVID-19 patients. The methods have also been used to characterize host and viral proteins, and analyze lipid metabolism in COVID-19 patients. Information obtained using the above methods are complemented by high-throughput analysis of transcriptomic and epigenomic changes associated with COVID-19, coupled with next-generation sequencing. Hence, this review discusses the most recent studies focusing on the methods described above. The results establish the importance of mass spectrometry-based studies towards understanding the infection process, immune imbalance, disease mechanism, and indicate the potential of the methods’ therapeutic developments and biomarker screening against COVID-19 and future outbreaks.

Regulation of Protein Synthesis by eIF4E in the Brain

2020 ◽  
Author(s):  
Kleanthi Chalkiadaki ◽  
Stella Kouloulia ◽  
Clive R. Bramham ◽  
Christos G. Gkogkas
Keyword(s):  
Protein Synthesis ◽  
Brain Function ◽  
Regulation Of Gene Expression ◽  
Mrna Translation ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Eukaryotic Mrnas ◽  
Rate Limiting ◽  
The Brain ◽  
Key Pathways

Regulation of gene expression at the level of mRNA translation is crucial for all the functions our brains carry out. eIF4E binds to the 5′-end of eukaryotic mRNAs and dictates the rate-limiting step of cap-dependent initiation. This chapter reviews the key pathways regulating eIF4E function, but also the less studied and novel mechanisms of eIF4E modulation, linked to synaptic plasticity, learning and memory, and nervous system disorders. Understanding how regulation of protein synthesis by eIF4E affects different aspects of brain function is yet elusive.

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