scholarly journals Inter-species conservation of organisation and function between non-homologous regional centromeres

2018 ◽  
Author(s):  
Pin Tong ◽  
Alison L. Pidoux ◽  
Nicholas R.T. Toda ◽  
Ryan Ard ◽  
Harald Berger ◽  
...  
Keyword(s):  
Species Conservation ◽  
Rrna Genes ◽  
Epigenetic Mark ◽  
Trna Genes ◽  
Histone H3 Variant ◽  
Species Establishment ◽  
5S Rrna Genes ◽  
Essential Function ◽  
And Function ◽  
Genomic Locations

Despite the conserved essential function of centromeres, centromeric DNA itself is not conserved1–4. The histone-H3 variant, CENP-A, is the epigenetic mark that specifies centromere identity5–8. Paradoxically, CENP-A normally assembles on particular sequences at specific genomic locations. To gain insight into the specification of complex centromeres we took an evolutionary approach, fully assembling genomes and centromeres of related fission yeasts. Centromere domain organization, but not sequence, is conserved between Schizosaccharomyces pombe, S. octosporus and S. cryophilus with a central CENP-ACnp1 domain flanked by heterochromatic outer-repeat regions. Conserved syntenic clusters of tRNA genes and 5S rRNA genes occur across the centromeres of S. octosporus and S. cryophilus, suggesting conserved function. Remarkably, non-homologous centromere central-core sequences from S. octosporus are recognized in S. pombe, resulting in cross-species establishment of CENP-ACnp1 chromatin and functional kinetochores. Therefore, despite the lack of sequence conservation, Schizosaccharomyces centromere DNA possesses intrinsic conserved properties that promote assembly of CENP-A chromatin. Thus, centromere DNA can be recognized and function over unprecedented evolutionary timescales.

Use of mutant RNAs in studies on yeast 5S rRNA structure and function

1991 ◽  
Vol 69 (4) ◽  
pp. 217-222 ◽  
Author(s):  
Ross N. Nazar ◽  
Don I. Van Ryk ◽  
Yoon Lee ◽  
C. David Guyer
Keyword(s):  
Structural Changes ◽  
Growth Conditions ◽  
5S Rrna ◽  
Rrna Genes ◽  
Shuttle Vectors ◽  
5S Rrna Genes ◽  
And Function ◽  
Optimized Conditions ◽  
Rna Concentration

The expression of mutant yeast 5S rRNA genes in vivo is reviewed as a basis for further studies on the structure, function, and regulation of the ribosomal 5S rRNA. Specific base substitutions, insertions, or deletions can result in substantial structural changes which can be detected readily by gel electrophoresis, permitting the assay of mutant RNA synthesis and utilization. Furthermore, the use of high and low copy shuttle vectors, as well as alternate growth conditions, permits a wide adjustment of the mutant RNA concentration. Under optimized conditions more than 80% of the cell's RNA can be replaced with mutant molecules. The application of this strategy to studies on the biosynthesis and structure of the 5S rRNA are demonstrated through recently isolated mutations.Key words: site-specific mitogenesis, 5S RNA, ribosomes, yeast transformation.

scholarly journals The only essential function of TFIIIA in yeast is the transcription of 5S rRNA genes.

1995 ◽  
Vol 92 (20) ◽  
pp. 9338-9342 ◽  
Author(s):  
S. Camier ◽  
A. M. Dechampesme ◽  
A. Sentenac
Keyword(s):  
5S Rrna ◽  
Rrna Genes ◽  
5S Rrna Genes ◽  
Essential Function

Divergent Evolution of 5 S rRNA Genes in Methanococcus

1987 ◽  
Vol 42 (4) ◽  
pp. 373-380 ◽  
Author(s):  
Günter Wich ◽  
Lionel Sibold ◽  
August Böck
Keyword(s):  
Sequence Divergence ◽  
The Other ◽  
5S Rrna ◽  
Rrna Genes ◽  
Transcriptional Unit ◽  
Divergent Evolution ◽  
Trna Genes ◽  
Rrna Gene ◽  
Gene Comparison ◽  
5S Rrna Genes

Abstract The organization of genes for 5S rRNA in the methanogenic archaebacterium Methanococcus (M .) voltae and their nucleotide sequences have been determined. M. voltae possesses three 5S rRNA genes, one of them is organized in an rRNA transcriptional unit coding for 16S-23S-5S rRNA. The other two are associated with seven tRNA genes in a putative transcriptional unit composed of 5′-tRNAThr-tRNAPro-tRNATyr-tRNALys - 5S rRNA-tRNAAsp-tRNALys - 5S rRNA-tRNAAsp-3′. Coding regions plus spacers of the tRNALys-5S rRNA-tRNAAsp block of this gene cluster occur twice with identical sequence. The 5S rRNA from this cluster displays considerable sequence divergence to the rRNA operon-linked 5S rRNA gene. Comparison of the M. voltae 5S rRNA sequences with those from M. vannielii revealed that the operon-linked genes on one hand and the tRNA-linked 5S genes on the other share a greater sequence homology than the two types of genes within each of the two organisms. This indicates an independent evolution of the two sets of 5S rRNA genes without selective pressure from other ribosomal components or, alternatively, lateral gene transfer.

scholarly journals A Methylated Neurospora 5S rRNA Pseudogene Contains a Transposable Element Inactivated by Repeat-Induced Point Mutation

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 1787-1797
Author(s):  
Brian S Margolin ◽  
Phillip W Garrett-Engele ◽  
Judith N Stevens ◽  
Deborah Y Fritz ◽  
Carrie Garrett-Engele ◽  
...  
Keyword(s):  
Transposable Element ◽  
Point Mutation ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Related Sequence ◽  
5S Rrna Genes ◽  
And Function ◽  
Type Strains ◽  
Repeat Induced Point Mutation

Abstract In an analysis of 22 of the roughly 100 dispersed 5S rRNA genes in Neurospora crassa, a methylated 5S rRNA pseudogene, Ψ63, was identified. We characterized the Ψ63 region to better understand the control and function of DNA methylation. The 120-bp 5S rRNA-like region of Ψ63 is interrupted by a 1.9-kb insertion that has characteristics of sequences that have been modified by repeat-induced point mutation (RIP). We found sequences related to this insertion in wild-type strains of N. crassa and other Neurospora species. Most showed evidence of RIP; but one, isolated from the N. crassa host of Ψ63, showed no evidence of RIP. A deletion from near the center of this sequence apparently rendered it incapable of participating in RIP with the related full-length copies. The Ψ63 insertion and the related sequences have features of transposons and are related to the Fot1 class of fungal transposable elements. Apparently Ψ63 was generated by insertion of a previously unrecognized Neurospora transposable element into a 5S rRNA gene, followed by RIP. We name the resulting inactivated Neurospora transposon PuntRIP1 and the related sequence showing no evidence of RIP, but harboring a deletion that presumably rendered it defective for transposition, dPunt.

scholarly journals Pat1 protects centromere-specific histone H3 variant Cse4 from Psh1-mediated ubiquitination

2015 ◽  
Vol 26 (11) ◽  
pp. 2067-2079 ◽  
Author(s):  
Prashant K. Mishra ◽  
Jiasheng Guo ◽  
Lauren E. Dittman ◽  
Julian Haase ◽  
Elaine Yeh ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Chromosome Segregation ◽  
Histone H3 ◽  
Structure And Function ◽  
Epigenetic Mark ◽  
Critical Determinant ◽  
Essential Components ◽  
Histone H3 Variant ◽  
And Function

Evolutionarily conserved histone H3 variant Cse4 and its homologues are essential components of specialized centromere ( CEN)-specific nucleosomes and serve as an epigenetic mark for CEN identity and propagation. Cse4 is a critical determinant for the structure and function of the kinetochore and is required to ensure faithful chromosome segregation. The kinetochore protein Pat1 regulates the levels and spatial distribution of Cse4 at centromeres. Deletion of PAT1 results in altered structure of CEN chromatin and chromosome segregation errors. In this study, we show that Pat1 protects CEN-associated Cse4 from ubiquitination in order to maintain proper structure and function of the kinetochore in budding yeast. PAT1-deletion strains exhibit increased ubiquitination of Cse4 and faster turnover of Cse4 at kinetochores. Psh1, a Cse4-specific E3-ubiquitin ligase, interacts with Pat1 in vivo and contributes to the increased ubiquitination of Cse4 in pat1∆ strains. Consistent with a role of Psh1 in ubiquitination of Cse4, transient induction of PSH1 in a wild-type strain resulted in phenotypes similar to a pat1∆ strain, including a reduction in CEN-associated Cse4, increased Cse4 ubiquitination, defects in spatial distribution of Cse4 at kinetochores, and altered structure of CEN chromatin. Pat1 interacts with Scm3 and is required for its maintenance at kinetochores. In conclusion, our studies provide novel insights into mechanisms by which Pat1 affects the structure of CEN chromatin and protects Cse4 from Psh1-mediated ubiquitination for faithful chromosome segregation.

scholarly journals The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1517
Author(s):  
Se-Hwan Cheon ◽  
Min-Ah Woo ◽  
Sangjin Jo ◽  
Young-Kee Kim ◽  
Ki-Joong Kim
Keyword(s):  
Northeast Asia ◽  
Single Copy ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Protein Coding ◽  
Tropical Regions ◽  
Relationship Of ◽  
The Relationship ◽  
Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

scholarly journals CENP-A overexpression promotes distinct fates in human cells, depending on p53 status

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Daniel Jeffery ◽  
Alberto Gatto ◽  
Katrina Podsypanina ◽  
Charlène Renaud-Pageot ◽  
Rebeca Ponce Landete ◽  
...  
Keyword(s):  
Cell Fate ◽  
Epithelial Mesenchymal Transition ◽  
Clonogenic Survival ◽  
Response To Therapy ◽  
Epigenetic Mark ◽  
Mammalian Development ◽  
Mesenchymal Transition ◽  
Histone H3 Variant ◽  
Tumour Cell Invasion ◽  
P53 Status

AbstractTumour evolution is driven by both genetic and epigenetic changes. CENP-A, the centromeric histone H3 variant, is an epigenetic mark that directly perturbs genetic stability and chromatin when overexpressed. Although CENP-A overexpression is a common feature of many cancers, how this impacts cell fate and response to therapy remains unclear. Here, we established a tunable system of inducible and reversible CENP-A overexpression combined with a switch in p53 status in human cell lines. Through clonogenic survival assays, single-cell RNA-sequencing and cell trajectory analysis, we uncover the tumour suppressor p53 as a key determinant of how CENP-A impacts cell state, cell identity and therapeutic response. If p53 is functional, CENP-A overexpression promotes senescence and radiosensitivity. Surprisingly, when we inactivate p53, CENP-A overexpression instead promotes epithelial-mesenchymal transition, an essential process in mammalian development but also a precursor for tumour cell invasion and metastasis. Thus, we uncover an unanticipated function of CENP-A overexpression to promote cell fate reprogramming, with important implications for development and tumour evolution.

scholarly journals Ribosomal DNA localization on Lathyrus species chromosomes by FISH

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Hoda B. M. Ali ◽  
Samira A. Osman
Keyword(s):  
Genome Mapping ◽  
Chromosome Complement ◽  
5S Rdna ◽  
Rdna Locus ◽  
5S Rrna ◽  
Rrna Genes ◽  
45S Rdna ◽  
Metaphase Chromosomes ◽  
Lathyrus Odoratus ◽  
5S Rrna Genes

Abstract Background Fluorescence In Situ Hybridization (FISH) played an essential role to locate the ribosomal RNA genes on the chromosomes that offered a new tool to study the chromosome structure and evolution in plant. The 45S and 5S rRNA genes are independent and localized at one or more loci per the chromosome complement, their positions along chromosomes offer useful markers for chromosome discriminations. In the current study FISH has been performed to locate 45S and 5S rRNA genes on the chromosomes of nine Lathyrus species belong to five different sections, all have chromosome number 2n=14, Lathyrus gorgoni Parl, Lathyrus hirsutus L., Lathyrus amphicarpos L., Lathyrus odoratus L., Lathyrus sphaericus Retz, Lathyrus incospicuus L, Lathyrus paranensis Burkart, Lathyrus nissolia L., and Lathyrus articulates L. Results The revealed loci of 45S and 5S rDNA by FISH on metaphase chromosomes of the examined species were as follow: all of the studied species have one 45S rDNA locus and one 5S rDNA locus except L. odoratus L., L. amphicarpos L. and L. sphaericus Retz L. have two loci of 5S rDNA. Three out of the nine examined species have the loci of 45S and 5S rRNA genes on the opposite arms of the same chromosome (L. nissolia L., L. amphicarpos L., and L. incospicuus L.), while L. hirsutus L. has both loci on the same chromosome arm. The other five species showed the loci of the two types of rDNA on different chromosomes. Conclusion The detected 5S and 45S rDNA loci in Lathyrus could be used as chromosomal markers to discriminate the chromosome pairs of the examined species. FISH could discriminate only one chromosome pair out of the seven pairs in three species, in L. hirsutus L., L. nissolia L. and L. incospicuus L., and two chromosome pairs in five species, in L. paranensis Burkart, L. odoratus L., L. amphicarpos L., L. gorgoni Parl. and L. articulatus L., while it could discriminate three chromosome pairs in L. sphaericus Retz. these results could contribute into the physical genome mapping of Lathyrus species and the evolution of rDNA patterns by FISH in the coming studies in future.

scholarly journals riboCIRC: a comprehensive database of translatable circRNAs

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huihui Li ◽  
Mingzhe Xie ◽  
Yan Wang ◽  
Ludong Yang ◽  
Zhi Xie ◽  
...  
Keyword(s):  
De Novo ◽  
Species Conservation ◽  
Structure And Function ◽  
Research Community ◽  
Genome Browser ◽  
Valuable Resource ◽  
Sequence Structure ◽  
A Genome ◽  
Context Specific ◽  
And Function

AbstractriboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www.ribocirc.com.

scholarly journals Complete Genome Sequence of Cupriavidus necator H16 (DSM 428)

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Gareth T. Little ◽  
Muhammad Ehsaan ◽  
Christian Arenas-López ◽  
Kamran Jawed ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cupriavidus Necator ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Cupriavidus Necator H16

The hydrogen-utilizing strain Cupriavidus necator H16 (DSM 428) was sequenced using a combination of PacBio and Illumina sequencing. Annotation of this strain reveals 6,543 protein-coding genes, 263 pseudogenes, 64 tRNA genes, and 15 rRNA genes.

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