Application of Shotgun Proteomics to Transcriptional Regulatory Pathways

Abstract The onset of labour is a culmination of a series of highly coordinated and preparatory physiological events that take place throughout the gestational period. In order to produce the associated contractions needed for fetal delivery, smooth muscle cells in the muscular layer of the uterus (i.e. myometrium) undergo a transition from quiescent to contractile phenotypes. Here, we present the current understanding of the roles transcription factors play in critical labour-associated gene expression changes as part of the molecular mechanistic basis for this transition. Consideration is given to both transcription factors that have been well-studied in a myometrial context, i.e. activator protein 1 (AP-1), progesterone receptors (PRs), estrogen receptors (ERs), and nuclear factor kappa B (NF-κB), as well as additional transcription factors whose gestational event-driving contributions have been demonstrated more recently. These transcription factors may form pregnancy- and labour- associated transcriptional regulatory networks in the myometrium to modulate the timing of labour onset. A more thorough understanding of the transcription factor-mediated, labour-promoting regulatory pathways holds promise for the development of new therapeutic treatments that can be used for the prevention of preterm labour in at-risk women.

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Transcriptional regulation of metabolism in disease: From transcription factors to epigenetics

PeerJ ◽

10.7717/peerj.5062 ◽

2018 ◽

Vol 6 ◽

pp. e5062 ◽

Cited By ~ 4

Author(s):

Liam J. Hawkins ◽

Rasha Al-attar ◽

Kenneth B. Storey

Keyword(s):

Transcriptional Regulation ◽

Genomic Sequence ◽

Regulatory Elements ◽

Regulatory Pathways ◽

Transcriptional Dysregulation ◽

Disease States ◽

Specific Subset ◽

Transcriptional Regulatory ◽

Cis And Trans ◽

Or Genes

Every cell in an individual has largely the same genomic sequence and yet cells in different tissues can present widely different phenotypes. This variation arises because each cell expresses a specific subset of genomic instructions. Control over which instructions, or genes, are expressed is largely controlled by transcriptional regulatory pathways. Each cell must assimilate a huge amount of environmental input, and thus it is of no surprise that transcription is regulated by many intertwining mechanisms. This large regulatory landscape means there are ample possibilities for problems to arise, which in a medical context means the development of disease states. Metabolism within the cell, and more broadly, affects and is affected by transcriptional regulation. Metabolism can therefore contribute to improper transcriptional programming, or pathogenic metabolism can be the result of transcriptional dysregulation. Here, we discuss the established and emerging mechanisms for controling transcription and how they affect metabolism in the context of pathogenesis. Cis- and trans-regulatory elements, microRNA and epigenetic mechanisms such as DNA and histone methylation, all have input into what genes are transcribed. Each has also been implicated in diseases such as metabolic syndrome, various forms of diabetes, and cancer. In this review, we discuss the current understanding of these areas and highlight some natural models that may inspire future therapeutics.

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Developmental stage-dependent transcriptional regulatory pathways control neuroblast lineage progression

Development ◽

10.1242/dev.098723 ◽

2013 ◽

Vol 140 (18) ◽

pp. 3838-3847 ◽

Cited By ~ 27

Author(s):

G. Feng ◽

P. Yi ◽

Y. Yang ◽

Y. Chai ◽

D. Tian ◽

...

Keyword(s):

Developmental Stage ◽

Regulatory Pathways ◽

Transcriptional Regulatory

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The CHK-2 antagonizing phosphatase PPM-1.D regulates meiotic entry via catalytic and non-catalytic activities

10.1101/2021.08.02.453806 ◽

2021 ◽

Author(s):

Antoine Baudrimont ◽

Dimitra Paouneskou ◽

Ariz Mohammad ◽

Raffael Lichtenberger ◽

Joshua Blundon ◽

...

Keyword(s):

Meiotic Prophase ◽

Nuclear Periphery ◽

Dna Double Strand Breaks ◽

Timely Initiation ◽

Regulatory Pathways ◽

Strand Breaks ◽

Catalytic Activities ◽

C Elegans ◽

Transcriptional Regulatory ◽

Meiotic Entry

The transition from the stem cell/progenitor fate to meiosis is mediated by several redundant post-transcriptional regulatory pathways in C. elegans. Interfering with all three branches causes tumorous germlines. SCFPROM-1 comprises one branch and mediates a scheduled degradation step at entry into meiosis. prom-1 mutants show defects in timely initiation of events of meiotic prophase I, resulting in high rates of embryonic lethality. Here, we identify a crucial substrate for PROM-1, encoded by the phosphatase PPM-1.D/Wip1. We report that it antagonizes CHK-2 kinase, a key regulator for meiotic prophase initiation e.g., DNA double strand breaks, chromosome pairing and synaptonemal complex formation. We propose that PPM-1.D controls the amount of active CHK-2 by both catalytic and non-catalytic activities, where strikingly the non-catalytic regulation seems to be crucial at meiotic entry. PPM-1.D sequesters CHK-2 at the nuclear periphery and programmed SCFPROM-1 mediated degradation of PPM-1.D liberates the kinase and promotes meiotic entry.

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Use of L- arginine in the treatment of comorbid pathology in neurological patients

East European Journal of Neurology ◽

10.33444/2411-5797.2017.1(13).4-8 ◽

2017 ◽

pp. 4-8

Author(s):

N. Svyrydova ◽

N. Zhhilova

Keyword(s):

Amino Acids ◽

Ischemia Reperfusion Injury ◽

Ischemia Reperfusion ◽

Essential Amino Acids ◽

The Body ◽

Special Importance ◽

Post Translational Modification ◽

Regulatory Pathways ◽

Transcriptional Regulatory ◽

Neurological Patients

Amino acids are the structural chemical units that make up proteins. The special importance of amino acids is that some of them - precursors of neurotransmitters which are necessary for normal functioning of the brain. The absence one of essential amino acid suspend the formation of protein. Correction of deficiency of essential amino acids and replacement carried out by different drugs. Recently, interest in preparations that contain arginine significantly increased. This interest caused by the importance of L- arginine in the body functioning, as L- Arginine is a precursor of nitric oxide (NO). Arginine (Valagyn) is a common post-translational modification of proteins tsytoplazmatycheskyh that has a unique transcriptional regulatory pathways. L-arginine showed a protective effect in ischemia / reperfusion injury, which can be widely used in various diseases of the cardio-sudinnoyi system and metabolic disorders

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RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism

International Journal of Molecular Sciences ◽

10.3390/ijms21010167 ◽

2019 ◽

Vol 21 (1) ◽

pp. 167 ◽

Cited By ~ 1

Author(s):

Isiaka Ibrahim Muhammad ◽

Sze Ling Kong ◽

Siti Nor Akmar Abdullah ◽

Umaiyal Munusamy

Keyword(s):

Transcriptional Regulation ◽

Regulatory Networks ◽

Data Sets ◽

Rna Seq ◽

Transcriptional Regulatory Networks ◽

Regulatory Pathways ◽

Specific Biological Process ◽

Transcriptional Regulatory ◽

Chromatin Immunoprecipitation Sequencing ◽

Sequencing Platforms

The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.

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