Nuclear Proteome: Isolation of Intact Nuclei, Extraction of Nuclear Proteins, and 2-DE Analysis

2017 ◽  
pp. 41-55 ◽  
Author(s):  
Aarti Pandey ◽  
Subhra Chakraborty ◽  
Niranjan Chakraborty
Keyword(s):  
Nuclear Proteins ◽  
Nuclear Proteome

scholarly journals Differential nuclear import sets the timing of protein access to the embryonic genome

2021 ◽  
Author(s):  
Thao Nguyen ◽  
Eli Costa ◽  
Tim Deibert ◽  
Jose Reyes ◽  
Felix Keber ◽  
...  
Keyword(s):  
Gene Expression ◽  
Early Development ◽  
Control Cell ◽  
Gene Activation ◽  
Nuclear Proteins ◽  
Control Of Gene Expression ◽  
Embryonic Genome ◽  
Regulatory Cascades ◽  
Protein Entry ◽  
Nuclear Proteome

The development of a fertilized egg to an embryo requires the proper temporal control of gene expression. During cell differentiation, timing is often controlled via cascades of transcription factors (TFs). However, in early development, transcription is often inactive, and many TF levels are constant, suggesting that unknown mechanisms govern the observed rapid and ordered onset of gene expression. Here, we find that in early embryonic development, access of maternally deposited nuclear proteins to the genome is temporally ordered via importin affinities, thereby timing the expression of downstream targets. We quantify changes in the nuclear proteome during early development and find that nuclear proteins, such as TFs and RNA polymerases, enter nuclei sequentially. Moreover, we find that the timing of the access of nuclear proteins to the genome corresponds to the timing of downstream gene activation. We show that the affinity of proteins to importin is a major determinant in the timing of protein entry into embryonic nuclei. Thus, we propose a mechanism by which embryos encode the timing of gene expression in early development via biochemical affinities. This process could be critical for embryos to organize themselves before deploying the regulatory cascades that control cell identities.

scholarly journals Analysis of rice nuclear-localized seed-expressed proteins and their database (RSNP-DB)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Priyanka Deveshwar ◽  
Shivam Sharma ◽  
Ankita Prusty ◽  
Neha Sinha ◽  
Sajad Majeed Zargar ◽  
...  
Keyword(s):  
Nuclear Export ◽  
Nuclear Proteins ◽  
Composition Analysis ◽  
Rice Seed ◽  
Protein Database ◽  
Nuclear Localization Signals ◽  
Prediction Tools ◽  
Go Enrichment ◽  
Nuclear Proteome ◽  
Combine Information

Abstract Nuclear proteins are primarily regulatory factors governing gene expression. Multiple factors determine the localization of a protein in the nucleus. An upright identification of nuclear proteins is way far from accuracy. We have attempted to combine information from subcellular prediction tools, experimental evidence, and nuclear proteome data to identify a reliable list of seed-expressed nuclear proteins in rice. Depending upon the number of prediction tools calling a protein nuclear, we could sort 19,441 seed expressed proteins into five categories. Of which, half of the seed-expressed proteins were called nuclear by at least one out of four prediction tools. Further, gene ontology (GO) enrichment and transcription factor composition analysis showed that 6116 seed-expressed proteins could be called nuclear with a greater assertion. Localization evidence from experimental data was available for 1360 proteins. Their analysis showed that a 92.04% accuracy of a nuclear call is valid for proteins predicted nuclear by at least three tools. Distribution of nuclear localization signals and nuclear export signals showed that the majority of category four members were nuclear resident proteins, whereas other categories have a low fraction of nuclear resident proteins and significantly higher constitution of shuttling proteins. We compiled all the above information for the seed-expressed genes in the form of a searchable database named Rice Seed Nuclear Protein DataBase (RSNP-DB) https://pmb.du.ac.in/rsnpdb. This information will be useful for comprehending the role of seed nuclear proteome in rice.

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

Nuclear proteins in primary biliary cirrhosis as guardians against HCC development

2013 ◽  
Vol 51 (01) ◽  
Author(s):  
C Hintemann ◽  
K Straub ◽  
S Biesterfeld ◽  
PR Galle ◽  
J Erthle ◽  
...  
Keyword(s):  
Primary Biliary Cirrhosis ◽  
Nuclear Proteins ◽  
Biliary Cirrhosis

GENE ACTIVATION IN MAMMARY CELLS

1972 ◽  
Vol 71 (2_Suppla) ◽  
pp. S346-S368 ◽  
Author(s):  
Roger W. Turkington ◽  
Nobuyuki Kadohama
Keyword(s):  
Cell Differentiation ◽  
Gene Transcription ◽  
Hormonal Regulation ◽  
Gene Activation ◽  
Milk Proteins ◽  
Mouse Mammary Gland ◽  
Nuclear Proteins ◽  
Mammary Cells ◽  
Alveolar Cells ◽  
Mammary Cell

ABSTRACT Hormonal activation of gene transcription has been studied in a model system, the mouse mammary gland in organ culture. Transcriptive activity is stimulated in mammary stem cells by insulin, and in mammary alveolar cells by prolactin and insulin. Studies on the template requirement for expression of the genes for milk proteins demonstrate that DNA methylation has an obligatory dependence upon DNA synthesis, but is otherwise independent from hormonal regulation of mammary cell differentiation. Incorporation of 5-bromo-2′deoxyuridine into DNA selectively inhibits expression of the genes for specific milk proteins. Undifferentiated mammary cells activate the synthesis of specific acidic nuclear proteins when stimulated by insulin. Several of these induced acidic nuclear proteins are undetectable in unstimulated undifferentiated cells, but appear to be characteristic components of the nuclei of differentiated cells. These results indicate that mammary cell differentiation is associated with a change in acidic nuclear proteins, and they provide evidence to support the concept that acidic nuclear proteins may be involved in the regulation of gene transcription and of mammary cell differentiation.

Identification of Nuclear Proteins in Soybean Under Flooding Stress using Proteomic Technique

2014 ◽  
Vol 21 (5) ◽  
pp. 458-467 ◽  
Author(s):  
Myeong Oh ◽  
Yohei Nanjo ◽  
Setsuko Komatsu
Keyword(s):  
Nuclear Proteins ◽  
Flooding Stress

Outfielders Playing in the Infield: Functions of Aging-Associated "Nuclear" Proteins in the Mitochondria

2014 ◽  
Vol 14 (10) ◽  
pp. 1247-1251 ◽  
Author(s):  
P. Czypiorski ◽  
J. Altschmied ◽  
L.L. Rabanter ◽  
C. Goy ◽  
S. Jakob. ◽  
...  
Keyword(s):  
Nuclear Proteins
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