scholarly journals Transfer RNA Genes Affect Chromosome Structure and Function via Local Effects

2018 ◽  
Author(s):  
Omar Hamdani ◽  
Namrita Dhillon ◽  
Tsung-Han S. Hsieh ◽  
Takahiro Fujita ◽  
Josefina Ocampo ◽  
...  
Keyword(s):  
Long Range ◽  
Binding Sites ◽  
Transfer Rna ◽  
Chromosome Architecture ◽  
Architectural Proteins ◽  
Random Manner ◽  
And Function ◽  
Chromosome Tethering ◽  
Rna Genes

AbstractThe genome is packaged and organized in an ordered, non-random manner and specific chromatin segments contact nuclear substructures to mediate this organization. While transfer RNA genes (tDNAs) are essential for the generation of tRNAs, these loci are also binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. In this study, we investigate the role of tDNAs in genomic organization and chromosome function by editing a chromosome so that it lacks any tDNAs. Surprisingly our analyses of this tDNA-less chromosome show that loss of tDNAs does not grossly affect chromosome folding or chromosome tethering. However, loss of tDNAs affects local nucleosome positioning and the binding of SMC proteins at these loci. The absence of tDNAs also leads to changes in centromere clustering and a reduction in the frequency of long range HML-HMR heterochromatin clustering. We propose that the tDNAs primarily affect local chromatin structure that result in effects on long-range chromosome architecture.

scholarly journals tRNA Genes Affect Chromosome Structure and Function via Local Effects

2019 ◽  
Vol 39 (8) ◽  
Author(s):  
Omar Hamdani ◽  
Namrita Dhillon ◽  
Tsung-Han S. Hsieh ◽  
Takahiro Fujita ◽  
Josefina Ocampo ◽  
...  
Keyword(s):  
Long Range ◽  
Binding Sites ◽  
Genomic Organization ◽  
Chromosome Structure ◽  
Trna Genes ◽  
Local Effects ◽  
Chromosome Architecture ◽  
Architectural Proteins ◽  
And Function ◽  
Chromosome Tethering

ABSTRACT The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. In this study, we investigate the roles of tDNAs in genomic organization and chromosome function by editing a chromosome so that it lacked any tDNAs. Surprisingly our analyses of this tDNA-less chromosome show that loss of tDNAs does not grossly affect chromatin architecture or chromosome tethering and mobility. However, loss of tDNAs affects local nucleosome positioning and the binding of SMC proteins at these loci. The absence of tDNAs also leads to changes in centromere clustering and a reduction in the frequency of long-range HML-HMR heterochromatin clustering with concomitant effects on gene silencing. We propose that the tDNAs primarily affect local chromatin structure, which results in effects on long-range chromosome architecture.

scholarly journals XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture

2017 ◽  
Vol 372 (1733) ◽  
pp. 20160360 ◽  
Author(s):  
K. M. Creamer ◽  
J. B. Lawrence
Keyword(s):  
X Chromosome ◽  
Chromatin Condensation ◽  
Higher Order ◽  
Chromosome Architecture ◽  
Genome Wide ◽  
Xist Rna ◽  
Architectural Proteins ◽  
Mary Lyon ◽  
Attachment Factor

XIST RNA triggers the transformation of an active X chromosome into a condensed, inactive Barr body and therefore provides a unique window into transitions of higher-order chromosome architecture. Despite recent progress, how XIST RNA localizes and interacts with the X chromosome remains poorly understood. Genetic engineering of XIST into a trisomic autosome demonstrates remarkable capacity of XIST RNA to localize and comprehensively silence that autosome. Thus, XIST does not require X chromosome-specific sequences but operates on mechanisms available genome-wide. Prior results suggested XIST localization is controlled by attachment to the insoluble nuclear scaffold. Our recent work affirms that scaffold attachment factor A (SAF-A) is involved in anchoring XIST , but argues against the view that SAF-A provides a unimolecular bridge between RNA and the chromosome. Rather, we suggest that a complex meshwork of architectural proteins interact with XIST RNA. Parallel work studying the territory of actively transcribed chromosomes suggests that repeat-rich RNA ‘coats’ euchromatin and may impact chromosome architecture in a manner opposite of XIST . A model is discussed whereby RNA may not just recruit histone modifications, but more directly impact higher-order chromatin condensation via interaction with architectural proteins of the nucleus. This article is part of the themed issue ‘X-chromosome inactivation: a tribute to Mary Lyon’.

scholarly journals Histone H1 is essential for mitotic chromosome architecture and segregation in Xenopus laevis egg extracts

2005 ◽  
Vol 169 (6) ◽  
pp. 859-869 ◽  
Author(s):  
Thomas J. Maresca ◽  
Benjamin S. Freedman ◽  
Rebecca Heald
Keyword(s):  
Xenopus Laevis ◽  
Metaphase Plate ◽  
Histone H1 ◽  
Linker Histone ◽  
Chromosome Architecture ◽  
Linker Histone H1 ◽  
Egg Extracts ◽  
Chromatin Proteins ◽  
And Function

During cell division, condensation and resolution of chromosome arms and the assembly of a functional kinetochore at the centromere of each sister chromatid are essential steps for accurate segregation of the genome by the mitotic spindle, yet the contribution of individual chromatin proteins to these processes is poorly understood. We have investigated the role of embryonic linker histone H1 during mitosis in Xenopus laevis egg extracts. Immunodepletion of histone H1 caused the assembly of aberrant elongated chromosomes that extended off the metaphase plate and outside the perimeter of the spindle. Although functional kinetochores assembled, aligned, and exhibited poleward movement, long and tangled chromosome arms could not be segregated in anaphase. Histone H1 depletion did not significantly affect the recruitment of known structural or functional chromosomal components such as condensins or chromokinesins, suggesting that the loss of H1 affects chromosome architecture directly. Thus, our results indicate that linker histone H1 plays an important role in the structure and function of vertebrate chromosomes in mitosis.

HMGN dynamics and chromatin function

2003 ◽  
Vol 81 (3) ◽  
pp. 113-122 ◽  
Author(s):  
Frédéric Catez ◽  
Jae-Hwan Lim ◽  
Robert Hock ◽  
Yuri V Postnikov ◽  
Michael Bustin
Keyword(s):  
Binding Sites ◽  
Protein Composition ◽  
Nuclear Proteins ◽  
Chromatin Interactions ◽  
Binding Partners ◽  
Nucleosomal Dna ◽  
Transient Interactions ◽  
And Function ◽  
Nucleosome Binding

Recent studies indicate that most nuclear proteins, including histone H1 and HMG are highly mobile and their interaction with chromatin is transient. These findings suggest that the structure of chromatin is dynamic and the protein composition at any particular chromatin site is not fixed. Here we discuss how the dynamic behavior of the nucleosome binding HMGN proteins affects the structure and function of chromatin. The high intranuclear mobility of HMGN insures adequate supply of protein throughout the nucleus and serves to target these proteins to their binding sites. Transient interactions of the proteins with nucleosomes destabilize the higher order chromatin, enhance the access to nucleosomal DNA, and impart flexibility to the chromatin fiber. While roaming the nucleus, the HMGN proteins encounter binding partners and form metastable multiprotein complexes, which modulate their chromatin interactions. Studies with HMGN proteins underscore the important role of protein dynamics in chromatin function.Key words: HMG, nuclear proteins, chromatin, HMGN.

scholarly journals Three tRNAs on the ribosome slow translation elongation

2017 ◽  
Vol 114 (52) ◽  
pp. 13691-13696 ◽  
Author(s):  
Junhong Choi ◽  
Joseph D. Puglisi
Keyword(s):  
Protein Synthesis ◽  
Ionic Strength ◽  
Binding Sites ◽  
Elongation Factor ◽  
Transfer Rna ◽  
Dissociation Kinetics ◽  
Translation Elongation ◽  
Trna Species ◽  
Trna Binding

During protein synthesis, the ribosome simultaneously binds up to three different transfer RNA (tRNA) molecules. Among the three tRNA binding sites, the regulatory role of the exit (E) site, where deacylated tRNA spontaneously dissociates from the translational complex, has remained elusive. Here we use two donor–quencher pairs to observe and correlate both the conformation of ribosomes and tRNAs as well as tRNA occupancy. Our results reveal a partially rotated state of the ribosome wherein all three tRNA sites are occupied during translation elongation. The appearance and lifetime of this state depend on the E-site tRNA dissociation kinetics, which may vary among tRNA species and depends on temperature and ionic strength. The 3-tRNA partially rotated state is not a proper substrate for elongation factor G (EF-G), thus inhibiting translocation until the E-site tRNA dissociates. Our result presents two parallel kinetic pathways during translation elongation, underscoring the ability of E-site codons to modulate the dynamics of protein synthesis.

scholarly journals The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo.

1997 ◽  
Vol 17 (8) ◽  
pp. 4811-4819 ◽  
Author(s):  
L G Burns ◽  
C L Peterson
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Protein Assembly ◽  
Transcriptional Activators ◽  
Regulate Gene Expression ◽  
Activation Of Transcription ◽  
Free Region ◽  
And Function

The Saccharomyces cerevisiae SWI-SNF complex is a 2-MDa protein assembly that is required for the function of many transcriptional activators. Here we describe experiments on the role of the SWI-SNF complex in activation of transcription by the yeast activator GAL4. We find that while SWI-SNF activity is not required for the GAL4 activator to bind to and activate transcription from nucleosome-free binding sites, the complex is required for GAL4 to bind to and function at low-affinity, nucleosomal binding sites in vivo. This SWI-SNF dependence can be overcome by (i) replacing the low-affinity sites with higher-affinity, consensus GAL4 binding sequences or (ii) placing the low-affinity sites into a nucleosome-free region. These results define the criteria for the SWI-SNF dependence of gene expression and provide the first in vivo evidence that the SWI-SNF complex can regulate gene expression by modulating the DNA binding of an upstream activator protein.

scholarly journals Mucosal glycan degradation of the host by the gut microbiota

Glycobiology ◽  
2020 ◽  
Author(s):  
Andrew Bell ◽  
Nathalie Juge
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Binding Sites ◽  
Short Review ◽  
Commensal Bacteria ◽  
Glycoside Hydrolases ◽  
Safe Distance ◽  
Human Gut ◽  
And Function

Abstract The gut microbiota plays a major role in human health and an alteration in gut microbiota structure and function has been implicated in several diseases. In the colon, mucus covering the epithelium is critical to maintain a homeostatic relationship with the gut microbiota by harboring a microbial community at safe distance from the epithelium surface. The mucin glycans composing the mucus layer provide binding sites and a sustainable source of nutrients to the bacteria inhabiting the mucus niche. Access to these glycan chains requires a complement of glycoside hydrolases (GHs) produced by bacteria across the phyla constituting the human gut microbiota. Due to the increased recognition of the role of mucus-associated microbes in human health, how commensal bacteria breakdown and utilize host mucin glycans has become of increased interest and is reviewed here. This short review provides an overview of the strategies evolved by gut commensal bacteria to access this rich source of the nutrient with a focus on the GHs involved in mucin degradation.

scholarly journals Cell type-specific role of lamin-B1 and its inflammation-driven reduction in organ building and aging

2018 ◽  
Author(s):  
Sibiao Yue ◽  
Xiaobin Zheng ◽  
Yixian Zheng
Keyword(s):  
Structural Proteins ◽  
Thymic Epithelial Cells ◽  
Cell Type ◽  
Organ Building ◽  
Lamin B1 ◽  
Architectural Proteins ◽  
Cell Type Specific ◽  
Developmental Role ◽  
And Function

SummaryCellular architectural proteins often participate in organ development and maintenance. Although functional decay of some of these proteins during aging is known, the cell-type specific developmental role and the cause and consequence of their subsequent decay remain to be established especially in mammals. By studying lamins, the nuclear structural proteins, we demonstrate that lamin-B1 functions specifically in the thymic epithelial cells (TECs) for proper thymus organogenesis. An upregulation of proinflammatory cytokines in the intra-thymic myeloid immune cells during aging accompanies a gradual reduction of adult TEC lamins-B1. These cytokines cause adult TEC senescence and lamin-B1 reduction. We identify 17 adult TEC subsets and show that TEC lamin-B1 maintains the composition of these TECs. Lamin-B1 supports the expression of TEC genes needed for maintaining adult thymic architecture and function. Thus, structural proteins involved in organ building and maintenance can undergo inflammation-driven decay which can in turn contribute to age-associated organ degeneration.

scholarly journals G-quadruplexes offer a conserved structural motif for NONO recruitment to NEAT1 architectural lncRNA

2020 ◽  
Author(s):  
Eric A J Simko ◽  
Honghe Liu ◽  
Tao Zhang ◽  
Adan Velasquez ◽  
Shraddha Teli ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Structural Features ◽  
Structural Motif ◽  
Non Coding Rna ◽  
G Quadruplex ◽  
And Function ◽  
Long Non Coding Rna

Abstract The long non-coding RNA NEAT1 serves as a scaffold for the assembly of paraspeckles, membraneless nuclear organelles involved in gene regulation. Paraspeckle assembly requires NEAT1 recruitment of the RNA-binding protein NONO, however the NEAT1 elements responsible for recruitment are unknown. Herein we present evidence that previously unrecognized structural features of NEAT1 serve an important role in these interactions. Led by the initial observation that NONO preferentially binds the G-quadruplex conformation of G-rich C9orf72 repeat RNA, we find that G-quadruplex motifs are abundant and conserved features of NEAT1. Furthermore, we determine that NONO binds NEAT1 G-quadruplexes with structural specificity and provide evidence that G-quadruplex motifs mediate NONO-NEAT1 association, with NONO binding sites on NEAT1 corresponding largely to G-quadruplex motifs, and treatment with a G-quadruplex-disrupting small molecule causing dissociation of native NONO-NEAT1 complexes. Together, these findings position G-quadruplexes as a primary candidate for the NONO-recruiting elements of NEAT1 and provide a framework for further investigation into the role of G-quadruplexes in paraspeckle formation and function.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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