scholarly journals Milestones in transcription and chromatin published in the Journal of Biological Chemistry

2019 ◽  
Vol 294 (5) ◽  
pp. 1652-1660 ◽  
Author(s):  
Joel M. Gottesfeld
Keyword(s):  
Chromatin Structure ◽  
Molecular Level ◽  
Regulation Of Gene Expression ◽  
Large Body ◽  
Regulation Of Transcription ◽  
Research Papers ◽  
Post Translational Modifications ◽  
Essential Components ◽  
Initial Discovery

During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and post-translational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression.

scholarly journals Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains

2020 ◽  
Author(s):  
Shuai Jiang ◽  
Hao Li ◽  
Hao Hong ◽  
Guifang Du ◽  
Xin Huang ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Functional Characterization ◽  
Regulation Of Gene Expression ◽  
Joint Effect ◽  
Spatial Density ◽  
Open Chromatin ◽  
Temporal Regulation ◽  
Topologically Associated Domains ◽  
Regulatory Landscape

Abstract Topologically associated domains (TADs) are spatial and functional units of metazoan chromatin structure. Interpretation of the interplay between regulatory factors and chromatin structure within TADs is crucial to understand the spatial and temporal regulation of gene expression. However, a computational metric for the sensitive characterization of TAD regulatory landscape is lacking. Here, we present the spatial density of open chromatin (SDOC) metric as a quantitative measurement of intra-TAD chromatin state and structure. SDOC sensitively reflects epigenetic properties and gene transcriptional activity in TADs. During mouse T-cell development, we found that TADs with decreased SDOC are enriched in repressed developmental genes, and the joint effect of SDOC-decreasing and TAD clustering corresponds to the highest level of gene repression. In addition, we revealed a pervasive preference for TADs with similar SDOC to interact with each other, which may reflect the principle of chromatin organization.

Plant long non-coding RNAs in the regulation of transcription

2021 ◽  
Author(s):  
Julia A. Chekanova
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Environmental Changes ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Time Control ◽  
Large Numbers ◽  
Root Organogenesis ◽  
Non Coding Rnas ◽  
Flowering Time Control

Abstract Eukaryotic genomes are pervasively transcribed, producing large numbers of non-coding RNAs (ncRNAs), including tens of thousands of long ncRNAs (lncRNAs), defined as ncRNAs longer than 200 nucleotides. Recent studies have revealed the important roles lncRNAs play in the regulation of gene expression at various levels in all eukaryotes; moreover, emerging research in plants has identified roles for lncRNAs in key processes such as flowering time control, root organogenesis, reproduction, and adaptation to environmental changes. LncRNAs participate in regulating most steps of gene expression, including reshaping nuclear organization and chromatin structure; governing multiple steps of transcription, splicing, mRNA stability, and translation; and affecting post-translational protein modifications. In this review, I present the latest progress on the lncRNA-mediated regulatory mechanisms modulating transcription in Arabidopsis thaliana, focusing on their functions in regulation of gene expression via chromatin structure and interactions with the transcriptional machinery.

scholarly journals How Do Post-Translational Modifications Influence the Pathomechanistic Landscape of Huntington’s Disease? A Comprehensive Review

2020 ◽  
Vol 21 (12) ◽  
pp. 4282 ◽  
Author(s):  
Beata Lontay ◽  
Andrea Kiss ◽  
László Virág ◽  
Krisztina Tar
Keyword(s):  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Neurodegenerative Disorder ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Post Translational Modifications ◽  
Cell Functions ◽  
Cellular Events ◽  
Mutant Huntingtin Protein

Huntington’s disease (HD) is an autosomal dominant inherited neurodegenerative disorder characterized by the loss of motor control and cognitive ability, which eventually leads to death. The mutant huntingtin protein (HTT) exhibits an expansion of a polyglutamine repeat. The mechanism of pathogenesis is still not fully characterized; however, evidence suggests that post-translational modifications (PTMs) of HTT and upstream and downstream proteins of neuronal signaling pathways are involved. The determination and characterization of PTMs are essential to understand the mechanisms at work in HD, to define possible therapeutic targets better, and to challenge the scientific community to develop new approaches and methods. The discovery and characterization of a panoply of PTMs in HTT aggregation and cellular events in HD will bring us closer to understanding how the expression of mutant polyglutamine-containing HTT affects cellular homeostasis that leads to the perturbation of cell functions, neurotoxicity, and finally, cell death. Hence, here we review the current knowledge on recently identified PTMs of HD-related proteins and their pathophysiological relevance in the formation of abnormal protein aggregates, proteolytic dysfunction, and alterations of mitochondrial and metabolic pathways, neuroinflammatory regulation, excitotoxicity, and abnormal regulation of gene expression.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

Management of Vatarakta w.s.r. to Gout through Panchakarma

2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Dr. Chandramohan Arya ◽  
Dr.Sanjay Gupta
Keyword(s):  
Metabolic Disorders ◽  
Molecular Level ◽  
Modern Science ◽  
Monosodium Urate ◽  
Monosodium Urate Crystals ◽  
Predominant Symptom ◽  
Essential Components ◽  
Unique Approach ◽  
Ayurvedic Treatment ◽  
Urate Crystals

Vatarakta is more distressing and common metabolic disorder prevalent in present era. It is Vatapradhana Tridoshaja Vatavyadhi where Rakta is main Dushya. Vata is a predominant Dosha in Vatarakta, when it is excessively aggravated with vitiated Rakta is called Vatarakta. Vatarakta is correlated with gout in modern science. Gout is an abnormality of purine metabolism causes hyperuricemia and deposition of monosodium urate crystals in joints. Pain is predominant symptom of gout, which disturbs day-today life of the patients. The Panchakarma is not only a important component of Ayurvedic treatment but it is also forms the fundamental basis of Ayurveda therapy. The different procedures like Swedana, Vamana, Virechana, Basti, Sirovirechana, Raktamokshana focus on the purification which detoxifies the human body, i.e. the correction of the metabolism at molecular level. These detoxification procedures are essential components of the management in various metabolic disorders. So Panchakarma is an unique approach in the management of Vatarakta.

scholarly journals Identification and in Silico Characterization of Novel and Conserved MicroRNAs in Methyl Jasmonate-Stimulated Scots Pine (Pinus sylvestris L.) Needles

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 384
Author(s):  
Baiba Krivmane ◽  
Ilze Šņepste ◽  
Vilnis Šķipars ◽  
Igor Yakovlev ◽  
Carl Gunnar Fossdal ◽  
...  
Keyword(s):  
Methyl Jasmonate ◽  
Scots Pine ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Stem Loop ◽  
Protein Coding ◽  
Stem Loop Structure ◽  
In Silico Characterization ◽  
Potential Precursor

MicroRNAs (miRNAs) are non-protein coding RNAs of ~20–24 nucleotides in length that play an important role in many biological and metabolic processes, including the regulation of gene expression, plant growth and developmental processes, as well as responses to stress and pathogens. The aim of this study was to identify and characterize novel and conserved microRNAs expressed in methyl jasmonate-treated Scots pine needles. In addition, potential precursor sequences and target genes of the identified miRNAs were determined by alignment to the Pinus unigene set. Potential precursor sequences were identified using the miRAtool, conserved miRNA precursors were also tested for the ability to form the required stem-loop structure, and the minimal folding free energy indexes were calculated. By comparison with miRBase, 4975 annotated sequences were identified and assigned to 173 miRNA groups, belonging to a total of 60 conserved miRNA families. A total of 1029 potential novel miRNAs, grouped into 34 families were found, and 46 predicted precursor sequences were identified. A total of 136 potential target genes targeted by 28 families were identified. The majority of previously reported highly conserved plant miRNAs were identified in this study, as well as some conserved miRNAs previously reported to be monocot specific. No conserved dicot-specific miRNAs were identified. A number of potential gymnosperm or conifer specific miRNAs were found, shared among a range of conifer species.

scholarly journals Proteomic Advances in Milk and Dairy Products

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3832
Author(s):  
Rubén Agregán ◽  
Noemí Echegaray ◽  
María López-Pedrouso ◽  
Radwan Kharabsheh ◽  
Daniel Franco ◽  
...  
Keyword(s):  
Dairy Products ◽  
Two Dimensional Gel Electrophoresis ◽  
Vast Number ◽  
Post Translational Modifications ◽  
Fundamental Parameters ◽  
Complex Fluid ◽  
Proteins And Peptides ◽  
Milk And Dairy Products

Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes makes it also applicable to other areas of science. Milk is a highly heterogeneous and complex fluid, where there are numerous genetic variants and isoforms with post-translational modifications (PTMs). Due to the vast number of proteins and peptides existing in its matrix, proteomics is presented as a powerful tool for the characterization of milk samples and their products. The technology developed to date for the separation and characterization of the milk proteome, such as two-dimensional gel electrophoresis (2DE) technology and especially mass spectrometry (MS) have allowed an exhaustive characterization of the proteins and peptides present in milk and dairy products with enormous applications in the industry for the control of fundamental parameters, such as microbiological safety, the guarantee of authenticity, or the control of the transformations carried out, aimed to increase the quality of the final product.

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