Genome organisation in the murine sperm nucleus

Zygote ◽  
1995 ◽  
Vol 3 (2) ◽  
pp. 123-131 ◽  
Author(s):  
Carol Jennings ◽  
Don Powell
Keyword(s):  
Repetitive Dna ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sperm Nucleus ◽  
Genome Organisation ◽  
Telomeric Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Restricted Domains

SummaryThe organisation of DNA sequences in the murine sperm nucleus was studied using in situ hybridisation of biotinylated DNA probes. The efficiency of this reaction was assessed using a dispersed repetitive DNA probe. Telomeric DNA was distributed around the nucleus. Centromeric and ribosomal DNA sequences occupied restricted domains in the sperm nucleus. DNA sequences for a transgene and a cluster of homeogenes occupied different, and rather less defined, domains. Together these results imply that both repetitive and protein-coding sequences are arranged in the nucleus in an ordered fashion.

Physical localisation of repetitive DNA sequences in Alstroemeria: karyotyping of two species with species-specific and ribosomal DNA

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 652-658 ◽  
Author(s):  
Silvan A. Kamstra ◽  
Anja G. J. Kuipers ◽  
Marjo J. De Jeu ◽  
M. S. Ramanna ◽  
Evert Jacobsen
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Repetitive Dna Sequences ◽  
Metaphase Chromosomes ◽  
Rdna Sites ◽  
Species Specific

Fluorescence in situ hybridization (FISH) was used to localise two species-specific repetitive DNA sequences, A001-I and D32-13, and two highly conserved 25S and 5S rDNA sequences on the metaphase chromosomes of two species of Alstroemeria. The Chilean species, Alstroemeria aurea (2n = 16), has abundant constitutive heterochromatin, whereas the Brazilian species, Alstroemeria inodora, has hardly any heterochromatin. The A. aurea specific A001-I probe hybridized specifically to the C-band regions on all chromosomes. The FISH patterns on A. inodora chromosomes using species-specific probe D32–13 resembled the C-banding pattern and the A001-I pattern on A. aurea chromosomes. There were notable differences in number and distribution of rDNA sites between the two species. The 25S rDNA probe revealed 16 sites in A. aurea that closely colocalised with A001-I sites and 12 in A. inodora that were predominantly detected in the centromeric regions. FISH karyotypes of the two Alstroemeria species were constructed accordingly, enabling full identification of all individual chromosomes. These FISH karyotypes will be useful for monitoring the chromosomes of both Alstroemeria species in hybrids and backcross derivatives.Key words: Alstroemeria, fluorescence in situ hybridization, FISH, repetitive DNA, ribosomal DNA, karyotype.

scholarly journals CHROMOSOMAL LOCALIZATION OF REPETITIVE DNA IN THE NEWT, TRITURUS

1972 ◽  
Vol 54 (3) ◽  
pp. 580-591 ◽  
Author(s):  
Giuseppina Barsacchi ◽  
Joseph G. Gall
Keyword(s):  
In Situ Hybridization ◽  
Nucleic Acid ◽  
Repetitive Dna ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Chromosomal Localization ◽  
Nucleic Acid Hybridization ◽  
Repetitive Dna Sequences ◽  
Lampbrush Chromosomes

The repetitive DNA sequences of the newt, Triturus viridescens, have been studied by nucleic acid hybridization procedures. Complementary RNA was synthesized enzymatically from unfractionated newt DNA. This RNA hybridized strongly to the centromeric regions of both somatic and lampbrush chromosomes It also bound to other loci scattered along the lengths of the chromosomes The amplified ribosomal DNA in the multiple oocyte nucleoli was demonstrated by in situ hybridization

Fluorescence in situ hybridization on plant extended chromatin DNA fibers for single-copy and repetitive DNA sequences

2011 ◽  
Vol 30 (9) ◽  
pp. 1779-1786 ◽  
Author(s):  
Kun Yang ◽  
Hecui Zhang ◽  
Richard Converse ◽  
Yong Wang ◽  
Xiaoying Rong ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Single Copy ◽  
Repetitive Dna Sequences

scholarly journals You're one in a googol: optimizing genes for protein expression

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Mark Welch ◽  
Alan Villalobos ◽  
Claes Gustafsson ◽  
Jeremy Minshull
Keyword(s):  
Protein Expression ◽  
Dna Sequences ◽  
Ad Hoc ◽  
Protein Coding ◽  
Vast Number ◽  
Coding Sequences ◽  
Affect Expression ◽  
Continue Work ◽  
Existing Data ◽  
Rational Sequence

A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.

scholarly journals Cellular thermal shift analysis for interrogation of CRISPR-assisted proteomic changes

BioTechniques ◽  
2020 ◽  
Vol 68 (4) ◽  
pp. 180-184 ◽  
Author(s):  
Nam-Gu Her ◽  
Ivan Babic ◽  
Venkata M Yenugonda ◽  
Santosh Kesari ◽  
Elmar Nurmemmedov
Keyword(s):  
Protein Complexes ◽  
Physiological State ◽  
Protein Coding ◽  
Coding Sequences ◽  
Missing Link ◽  
Disease States ◽  
Shift Analysis ◽  
Versatile Tool ◽  
Thermal Shift

CRISPR–Cas9 has proven to be a versatile tool for the discovery of essential genetic elements involved in various disease states. CRISPR-assisted dense mutagenesis focused on therapeutically challenging protein complexes allows us to systematically perturb protein-coding sequences in situ and correlate them with functional readouts. Such perturbations can mimic targeting by therapeutics and serve as a foundation for the discovery of highly specific modulators. However, translation of such genomics data has been challenging due to the missing link for proteomics under the physiological state of the cell. We present a method based on cellular thermal shift assays to easily interrogate proteomic shifts generated by CRISPR-assisted dense mutagenesis, as well as a case focused on NuRD epigenetic complex.

Conserved repetitive DNA sequences (Bkm) in normal equine males and sex-reversed females detected by in situ hybridization

1988 ◽  
Vol 48 (2) ◽  
pp. 99-102 ◽  
Author(s):  
M.G. Kent ◽  
K.O. Elliston ◽  
W. Shroeder ◽  
K.S. Guise ◽  
S.S. Wachtel
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Dna Sequences

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1061-1069 ◽  
Author(s):  
A. Cuadrado ◽  
N. Jouve ◽  
C. Ceoloni
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Individual Identification ◽  
Highly Repetitive Dna ◽  
The Individual

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S–5.8S–18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.Key words: fluorescence in situ hybridization, repetitive DNA, rye, Secale cereale, polymorphism.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 710-717 ◽  
Author(s):  
B. Kolano ◽  
B.W. Gardunia ◽  
M. Michalska ◽  
A. Bonifacio ◽  
D. Fairbanks ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chenopodium Quinoa ◽  
5S Rdna ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

scholarly journals Transcribed germline-limited coding sequences in Oxytricha trifallax

2020 ◽  
Author(s):  
Richard V. Miller ◽  
Rafik Neme ◽  
Derek M. Clay ◽  
Jananan S. Pathmanathan ◽  
Michael W. Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Rearrangement ◽  
Life Cycles ◽  
Open Reading Frames ◽  
Developmentally Regulated ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Dna Elimination ◽  
Nuclear Development

AbstractThe germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

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